Document [original]

New Motifs in DNA Nanotechnology and

their Applications

vorgelegt von

Diplom-Ingenieur

Jens Kopatsch

Von der Fakult¨at III (Prozesswissenschaften)

der Technischen Universit¨at Berlin

zur Erlangung des akademischen Grades

Doktor der Ingenieurwissenschaften

- Dr.-Ing -

genehmigte Dissertation

Promotionsausschuss:

Vorsitzender: Prof. Dr. Roland Lauster

Berichter: Prof. Dr. Ulf Stahl

Berichter: Prof. Dr. Nadrian C. Seeman

Tag der wissenschaftlichen Aussprache: 1. September 2004

Berlin 2004

D 83

Vorver¨offentlichungen

Publications:

3D Fractal DNA Assembly from Coding, Geometry and Protec-

tion,A.Carbone, C.Mao, P.E.Constantinou, B.Ding, J.Kopatsch,

W.B.Sherman, N.C.Seeman. Natural Computing 2004

The Design of Self-Assembled 3D DNA Networks. C. Mao, P.E.

Constantinou, F. Liu, J. Kopatsch, T. Wang, B. Ding, R. Sha,

H. Yan, J.J. Birktoft, R. Sha, H.Zhong, P.S. Lukeman, Y. Pinto,

L. Foley, L.A. Wenzler, R. Sweet, M. Becker and N.C. Seeman,

Proceedings of the Electrochemical Society in press 2004

DX Cohesion in Structural DNA Nanotechnology. P.E. Con-

stantinou, T. Wong, J. Kopatsch, L.B. Israel, C. Mao, B. Ding,

R. Sha, X. Zhang, N.C. Seeman. In preparation

Abstracts

Albany 2003 Meeting, The 13th Conversation Structural DNA

Nanotechnology, Nadrian Seeman, Hao Yan, Chengde Mao, Ruo-

jie Sha et. al. Journal of Biomolecular Structure and Dynamics

Vol. 20 Issue 6, June 2003 Page 925

American Crystallographic Association, Annual Meeting 2004,

Abstract: The Design of Self-Assembled 3D DNA Crystals. Nadrian

C. Seeman,Pamela E. Constantinou, Baoquan Ding, Tong Wang,

Jens Kopatsch, Ruojie Sha,Jens J. Birktoft, Furong Liu, Robert

Sweet & Chengde Mao

Patents:

Polygonal nanostructures of polynucleic acid multi-crossover molecules

and assembly of lattices based on double crossover cohesion Pro-

visional US patent application, Nadrian C. Seeman et al.

Acknowledgments

I would like to thank Prof. Dr. Nadrian Seeman for the opportunity to

perform my research project at the Chemistry Department of New York

University and Prof. Dr. Ulf Stahl for the support of my thesis.

Further I would like to thank all my lab members and former lab members

for the good collaboration and time we had together in New York: Banani

Chakraborty, Baoquan Ding, Gang Wu, Hong Zhong, Xiaoping Zhang, Xing

Wang, Yoel P Ohayon, Jiwen Zheng, Liang Ding, Lisa Israel, Alejandra Vic-

toria Garibotti, Pamela E Constantinou, Ruojie Sha, Shiping Liao, Tong

Wang and Wanqiu Shen, Phiset Sa-Ardyen, Loraine Foley and Andrea Giro.

A special thanks to Philip Lukeman, Jens Birktoft, Yariv Pinto and William

Sherman for scientific discussions, Philip Lukeman, William Sherman and

Hans Martin Sieg for proof reading and Jeff Birac for providing the com-

puter aided modelling program GIDEON.

In addition I want to thank Prof. Kathleen Kinnally for the friendly

collaboration with the ion-channel project and the people in her laboratory

Sonia Martinez-Caballero, Laurent Marc Dejean and Serguei Grigoriev for

the friendly work climate.

iii

Zusammenfassung (German Abstract)

Es wurden Versuche mit dem DX-Motiv durchgef¨

uhrt, um die Mindestl¨

ange

von Sticky Ends f¨

ur das Self-Assembly zu ermitteln. Weiterhin wurden Kri-

stallisationsversuche mit dem TX-Motiv, ausgestattet mit Sticky-Ends, un-

ternommen. Kristallisationsversuche einer TX-Version mit glatten Enden

wurden unternommen, um Aussagen ¨

uber einen eventuell vorhandenen Torsi-

onsstress zu treffen. Von einem Dreiecksmotiv (Chengde-Mao-Dreieck) wur-

den Gelmobilit¨

atsuntersuchungen von verschiedenen Versionen vorgenom-

men. Diese Untersuchungen offenbarten m¨

oglichen Torsionsstress in einigen

der Versionen. Mit drei Helizit¨

at-Variationen (Version mit 14nt per inne-

rer Dreiecks-Seitenkante) des Dreiecks wurden Kristallisationsversuche un-

ternommen. Zwei Variationen des Motivs bildeten reproduzierbare Kristalle,

die unter R¨

ontgenstrahlen Diffraktion bis zu zehn ˚

Angstr¨

om zeigten. Ein

weiteres Dreiecksmotiv, genannt TXDX, bestehend aus einem Dreieck, auf-

gebaut aus drei versatzverschr¨

ankten TX-Motiven, wurde als vielverspre-

chendes Motiv entwickelt. Die Verbindungen zu anderen TXDX-Dreiecken

ist ¨

uber das DX-Motiv realisiert. Ein- und zweidimensionale Felder konnten

nach einer Modifikation, die das Self-Assembly auf ein bzw. zwei Dimensionen

beschr¨

ankt, erzeugt werden. Es sind jeweils drei Variationen f¨

ur die ein- und

zweidimensionalen Felder m¨

oglich. Alle wurden erfolgreich erzeugt und mit

dem Rasterkraftmikroskop nachgewiesen. Ein rohrartiges Motiv, bestehend

aus sechs ca. 30 nm langen DNS-Helices, verbunden durch ¨

Uberkreuzungen,

wurde entwickelt. Dieses Motiv sollte in eine k¨

unstliche Membran inkorpo-

rieren und als Ionenkanal fungieren. Typisches Ionenkanalverhalten konnte

beobachtet werden.

Abstract

Experiments with the well characterized DX motif were undertaken to see

which number of nucleotides is necessary for sticky ended assembly. A sticky

ended crystallization attempt was made with the TX motif. In addition a

crystallization attempt with a blunt ended TX motif was made to disclose a

possible torsion stress within the motif. Nondenaturating gel mobility stud-

ies of a triangle motif (Chengde Mao triangle) were performed and showed

torsion stress in some versions of these molecules. Three molecules that

contained 14nt per inner triangle edge, yet have a structure designed to as-

semble with a different overall helical repeat in the crystal were constructed

and crystallization was attempted. Reproducible crystals were obtained from

two helicity variations and showed diffraction down to ten ˚

Angstr¨om. An-

other triangle motif, named TXDX triangle, consisting of a triangle based

on three TX motifs, connected with a skew, was developed. TXDX triangles

were connected with each other using a variation of the DX motif. One and

two-dimensional arrays were created after the motif was modified to limit

self-assembly to one and two dimensions. Due to the design there are three

possible versions of the one and two dimensional arrays. All possible array

variations were observed with an atomic force microscope. A tube like mo-

tif was designed, consisting of six 30 nm long DNA helices, connected by

cross-overs. This motif was supposed to incorporate itself into an artificial

membrane and function as an ion channel. Typical ion channel behavior was

observed with this motif.

Where nature finishes producing its shapes, there man begins,

with natural things and with the help of nature itself, to create

infinite varieties of shapes.

Leonardo Da Vinci

Contents

1 Introduction 1

1.1 Nanotechnology.......................... 1

1.1.1 Introduction to Nanotechnology . . . . . . . . . . . . . 1

1.1.2 Self-Assembly . . . . . . . . . . . . . . . . . . . . . . . 2

1.2 DNA Nanotechnology . . . . . . . . . . . . . . . . . . . . . . . 3

1.2.1 DNA Structure and Function . . . . . . . . . . . . . . 3

1.2.2 Holiday Junction and Branch Migration . . . . . . . . 11

1.2.3 De novo Designed Junctions and Avoidance of Branch

Migration ......................... 12

1.2.4 2 Dimensional DNA Arrays . . . . . . . . . . . . . . . 14

1.2.5 Other Molecules for DNA Nanotechnology . . . . . . . 22

1.3 Nanomechanical Devices based on DNA . . . . . . . . . . . . 26

1.3.1 A Nanomechanical Device Predicated on the B-Z Tran-

sitionofDNA....................... 26

1.3.2 DNA Nanomechanical Devices Based on Hybridization

Topology.......................... 27

1.4 DNA Based Computing . . . . . . . . . . . . . . . . . . . . . 29

1.4.1 Introduction to DNA Based Computing . . . . . . . . 29

1.4.2 DNA Computations with Rectangular Tiles . . . . . . 32

vii

1.4.3 Cumulative XOR Computation with DNA . . . . . . . 35

1.5 Crystallography . . . . . . . . . . . . . . . . . . . . . . . . . . 37

1.5.1 Traditional DNA Crystallography . . . . . . . . . . . . 37

1.5.2 3-Dimensional DNA assembly . . . . . . . . . . . . . . 37

1.5.3 DNA Cages for Trapping and Characterization of Biomolecules 39

1.6 IonChannels ........................... 40

1.6.1 Ion Channels in Organisms . . . . . . . . . . . . . . . . 40

1.6.2 Artificial Ion Channels . . . . . . . . . . . . . . . . . . 41

1.7 Presentation of a Problem . . . . . . . . . . . . . . . . . . . . 42

1.7.1 DNA Crystallization . . . . . . . . . . . . . . . . . . . 42

1.7.2 6 Helix Bundle as an Artificial Ion Channel . . . . . . 42

2 Materials and Methods 43

2.1 Design of New Molecules . . . . . . . . . . . . . . . . . . . . . 43

2.1.1 De novo Design of Sticky Ends . . . . . . . . . . . . . 43

2.1.2 De novo Design of DNA Sequences . . . . . . . . . . . 44

2.1.3 DNA Junctions . . . . . . . . . . . . . . . . . . . . . . 44

2.1.4 Computer Aided molecular modeling . . . . . . . . . . 44

2.2 From DNA Synthesis to Annealing of Motifs . . . . . . . . . . 45

2.2.1 DNA Synthesis . . . . . . . . . . . . . . . . . . . . . . 45

2.2.2 Denaturating Gels and DNA Purification . . . . . . . . 45

2.2.3 Native Gels (Non-Denaturating Gels) . . . . . . . . . . 46

2.2.4 Stochiometry of DNA Strands . . . . . . . . . . . . . . 47

2.2.5 Fast Annealing of Oligonucleotides for Native Gel Based

Studies........................... 48

2.2.6 Slow Annealing of Oligonucleotides . . . . . . . . . . . 48

2.3 Atomic Force Microscopy . . . . . . . . . . . . . . . . . . . . . 48

2.3.1 Preparation of sample . . . . . . . . . . . . . . . . . . 48

viii

2.3.2 AFM Imaging . . . . . . . . . . . . . . . . . . . . . . . 49

2.3.3 Post Processing of AFM Pictures . . . . . . . . . . . . 49

2.4 3D Assembly - DNA Crystallization . . . . . . . . . . . . . . . 49

2.4.1 Hanging Drop Crystallization . . . . . . . . . . . . . . 49

2.4.2 Crystallization with Temperature Control . . . . . . . 50

2.4.3 General Crystallization and Crystal Mounting Tech-

niques ........................... 51

2.4.4 X-Ray Examination of DNA Crystals . . . . . . . . . . 52

2.5 Crystallization Experiments . . . . . . . . . . . . . . . . . . . 52

2.5.1 3D Assembly with TXA Tiles Under High Magnesium

Ion Concentration . . . . . . . . . . . . . . . . . . . . . 52

2.5.2 2D-Assembly of DX Molecules with Short Sticky Ends 53

2.5.3 Crystallization Attempt of Blunt Ended DX Tiles . . . 53

2.5.4 3D Assembly and Gel Studies of Chengde Mao Triangles 54

2.5.5 3D Assembly with a TXDX Triangle Motif and 0D, 1D

and 2D examination of the motif . . . . . . . . . . . . 57

2.6 DNA Nanotube as an Artificial Ion Channel . . . . . . . . . . 60

2.6.1 Design of a DNA Nanotube for Use as an Artificial Ion

Channel .......................... 60

2.6.2 DNA Minor Groove Binder . . . . . . . . . . . . . . . 63

2.6.3 Tip Dip and Patch Clamp Experiments . . . . . . . . . 65

3 Results 68

3.1 3D Assembly - DNA Crystallization . . . . . . . . . . . . . . . 68

3.1.1 3D Assembly with TX Tiles Under High Magnesium

Ion Concentration . . . . . . . . . . . . . . . . . . . . . 68

3.1.2 2D-Assembly of DX Molecules with Short Sticky Ends 70

3.1.3 Crystallization Attempt of Blunt Ended DX Tiles . . . 72

3.1.4 3D Assembly and Gel Studies of ChengdeMao Triangles 74

3.1.5 3D Assembly with a TXDX triangle motif and 0D, 1D

and 2D examination of the motif . . . . . . . . . . . . 82

3.2 DNANanotubes ......................... 87

3.2.1 DNA Nanotube for Use as an Artificial Ion Channel . . 87

4 Discussion 90

4.1 Crystallization Experiments . . . . . . . . . . . . . . . . . . . 90

4.1.1 3D Assembly with TX Tiles Under High Magnesium

Ion Concentration . . . . . . . . . . . . . . . . . . . . . 90

4.1.2 2D-Assembly of DX Molecules with Short Sticky Ends 90

4.1.3 Crystallization Attempt of Blunt Ended DX Tiles . . . 91

4.1.4 3D Assembly and Gel Studies of ChengdeMao Triangles 91

4.1.5 3D Assembly with a TXDX Triangle Motif and 0D, 1D

and 2D examination of the motif . . . . . . . . . . . . 95

4.2 DNA Nanotube as an Artificial Ion Channel . . . . . . . . . . 96

4.3 Conclusion and Outlook . . . . . . . . . . . . . . . . . . . . . 98

4.3.1 3D Assembly . . . . . . . . . . . . . . . . . . . . . . . 98

4.3.2 6 Helix Bundle . . . . . . . . . . . . . . . . . . . . . . 99

5 Bibliography 101

6 Appendix 119

6.1 Gel for XOR Operation . . . . . . . . . . . . . . . . . . . . . . 120

6.2 Length Marker for Gel Based Studies . . . . . . . . . . . . . . 121

6.3 Natrix Formulation from Hampton Research . . . . . . . . . . 122

6.4 Crystall Mounting in Capillaries . . . . . . . . . . . . . . . . . 130

6.5 Netropsin Binding Thermodynamics . . . . . . . . . . . . . . 132

6.6 Properties and Sequences of Used Sticky Ends . . . . . . . . . 133

6.7 TXDX Triangle Motif with Attached DNA Sequence . . . . . 136

6.8 Pipetting Strand Combinations for the TXDX Triangle . . . . 137

6.9 Calculation of Unique 7mers for the AT-rich sequence . . . . . 139

6.10 DNA Crystallization Conditions from Literature . . . . . . . . 144

6.11 Calculation of CDM Triangle Properties . . . . . . . . . . . . 147

6.12 All DNA Strand Sequences used in 5’to 3’ Direction . . . . . . 154

6.12.1 Strands for DX 2D Array with Short Sticky Ends . . . 154

6.12.2 Strands used for 3D project with TX Motif . . . . . . . 155

6.12.3 Strands for Crystallization of Blunt ended DX Motif . 156

6.12.4 DNA Triangle Strands Designed by Prof. ChengDe Mao157

6.12.5 DNA Strands for Gel-based studies of Triangles . . . . 158

6.12.6 DNA Stands for 3D Triangle with 14nt per Edge . . . . 160

6.12.7 DNA Strands for 6 Helix Bundle with Netropsin Bind-

ingSites..........................163

6.12.8 DNA Strands for the TXDX Triangle Motif . . . . . . 166

6.13 Lebenslauf - Curriculum Vitae . . . . . . . . . . . . . . . . . . 171

List of Figures

1.1 Watson-Crick base pairing∗. Adenine pairs with thymine (up-

per part of the figure) and guanine pairs with cytosine (lower

part)................................ 4

1.2 Adenine self pairing∗....................... 4

1.3 Adenine can pair with uracil in Hoogsteen base paring∗.... 5

1.4 Adenine can pari with uracil in reversed Hoogsteen base paring∗5

1.5 Adenine can pair with thymine in reversed Watson-Crick base

pairing∗.............................. 6

1.6 Guanine can pair with uracil in sheared Watson-Crick base

pairing∗. The cytosine position in regular Watson-Crick pair-

ingisdrawninred......................... 6

1.7 B-DNA double helix∗.B-DNA is the most stable helical form

of DNA formed by a random sequence. The right side of the

figure shows a view down the helical axis. . . . . . . . . . . . . 7

1.8 A-DNA helix∗can form under dehydrating conditions. The

right side of the figure is a view down the helical axis. . . . . . 8

∗Picture obtained from public sources

xii

1.9 D-DNA is shown∗in the left side of the picture and can occur

with alternating A and T sequences . Z-DNA (right side∗) is

formd by GC rich sequences under high salt conditions. The

Z-DNA back bone is left handed. . . . . . . . . . . . . . . . . 9

1.10 DNA triplex∗formed by three DNA strands. Hoogsteen base

pairing is involved in this structure. . . . . . . . . . . . . . . . 10

1.11 Quadruplex DNA∗are found in the end of eukaryontic chro-

mosomes and contain G-rich repetitive sequences. . . . . . . . 11

1.12 Branch migration†. Crossing-over of homologous areas (II) of

two double helices (I), followed by branch migration (II-III) of

the Holliday junction and resolvation (IV) lead to two possible

products (V). VI shows a possible ligation step. . . . . . . . . 11

1.13 Four arm junction with symmetry minimization†. It does not

possess the symmetry necessary to perfom branch point mi-

gration. .............................. 13

1.14 Three arm junctions with sticky ends. Ligation studies show

that regular three arm junctions (left side) equipped with

sticky ends tend to cyclize. Bulged three arm junctions (right

side) show less tendency to cylize. . . . . . . . . . . . . . . . . 13

1.15 Sticky ended cohesion†. Two DNA helices with complemen-

tary sticky ends can associate due to Watson-Crick base pair-

ing and can optionally be ligated together. . . . . . . . . . . . 15

1.16 Basic concept of self assembly†. A motif can associate to form

a lager predicted complex due to specific sticky ends. . . . . . 16

†Picture kindly provided by Prof. Dr. Seeman

xiii

1.17 Different types and nomenclature of DNA double crossover

molecules†The first character ’D’ stands for double crossing

over, the second character refers to the to the relative orienta-

tions of their two double helical domains, ’A’ for antiparallel

and ’P’ for parallel. The third character refers to the number

(modulus 2) of helical half-turns between crossovers, ’E’ for an

even number and ’O’ for an odd number. A fourth character

is needed to describe parallel double crossover molecules with

an odd number of helical half-turns between crossovers. The

extra half-turn can correspond to a major (wide) groove sepa-

ration, designated by ’W,’ or an extra minor (narrow) groove

separation, designated by ’N.’ . . . . . . . . . . . . . . . . . . 17

1.18 Assembly principle of a 2D-DNA array consisting of two dif-

ferent DX tiles†. A hairpin, serving as a topograhic label, is

incorporated into the blue tile. . . . . . . . . . . . . . . . . . . 18

1.19 AFM picture of a 2D DX array†. The hairpin on every second

tile can be clearly seen and shows the predicted spacing. . . . 18

1.20 TX motif consisting of three helices connected by 4 cross-overs,

shown in a blunt ended version. . . . . . . . . . . . . . . . . . 19

1.21 Assembly principle of a 2D array consisting of two different TX

tiles†. A hairpin, serving as a topograhic label, is incorporated

intotheredtile........................... 20

1.22 AFM picture a 2D DNA array consisting of TX tiles. The

hairpin on every second tile can be clearly seen and shows the

predicted spacing. . . . . . . . . . . . . . . . . . . . . . . . . . 20

1.23 Schematic picture of parallelogram assembly†. Four junctions

can be combined into a rhombus like motif. . . . . . . . . . . 21

xiv

1.24 AFM picture of parallelogram array†. The rhombus like struc-

ture can be distinguished. . . . . . . . . . . . . . . . . . . . . 21

1.25 The DNA strands in this molecule†have the connectivity of

a cube. It consists of six cyclic strands. The cube is created

by ligating two ends of two quadrilaterals to from a belt-like

molecule. The nucleotides are represented by white dots (nu-

cleic base) in this drawing, the colored dots represent the sugar

phosphate backbone of the DNA strands with one color per

strand................................ 22

1.26 The DNA strands in this molecule†have the connectivity of

a truncated octahedron. The truncated octahedron is viewed

down the four fold axis of one of the squares. The edges of the

truncated octahedron consist of two full turns of dsDNA. The

complete truncated octahedron contains 14 cyclic strands of

DNA and each cyclic strand corresponds to a face of the trun-

cated octahedron. The nucleotides are represented by white

dots (nucleic base) in this drawing, the colored dots represent

the sugar phosphate backbone of the DNA strands. . . . . . . 23

1.27 Borromean rings made of DNA†. Borromean rings are special

because if one of the three rings is destroyed it will free the

other two rings while leaving them intact and not connected

to each other. The conventional nodes in Borromean rings (a)

have been replaced by three nodes, derived from 1.5 turns of

DNA double helix (b). The stereoscopic representation (c) is

shown in the middle part of the picture. A stereoscopic view

of the synthesized DNA molecule with hairpins is shown in the

lower part of the picture (d). The hairpins contain sequences

for restriction enzymes that can be used for digestion and,

depending on the restriction site used, release of the other two

DNArings. ............................ 25

1.28 A nanomechanical device predicated on the B-Z transition of

DNA†. Twenty nucleotide pairs of this helix can be converted

into Z-DNA and induce a nanomechanical movement of the

rigid DX tiles. The part acting as a bridge between the tiles

is shown in yellow. The relative movement of the DX tiles is

caused by the transition of right handed B-DNA to left handed

Z-DNA (induced with Hexaamminecobalt(III) chloride) and

can be measured with FRET (Fluorescence resonance energy

transfer of donor and aceptor molecules attached to the DX

molecules in the appropiate place marked by green and purple

dots). The upper part of the figure shows the bridge DNA in

B From (right handed) and the lower part shows it in Z-Form

(lefthanded). ........................... 26

xvi

1.29 Nanomechanical device based on hybridization topology†. Left

side (a): The letters A, B, C and D, along with the color cod-

ing, show that the bottom of the JX2motif (C and D) are

rotated 180

relative to the PX motif. The set strands are

shown in green, they can be removed by the addition of bi-

otinylated green fuel strands (biotin indicated by black circles,

process step I). The addition of the purple set strands (process

step II) converts the unstructured intermediate into the JX2

motif. In process step III the JX2molecule is converted to

the unstructured intermediate by the addition of biotinylated

yellow fuel strands. The PX device is restored and the cycle

completed by the addition of green set strands (IV). Right

side (b): AFM observation of the cycle with DNA trapezoids

attached as a marker. . . . . . . . . . . . . . . . . . . . . . . . 28

1.30 Graph with 7 nodes. Arrows indicate possible connections

between two nodes. . . . . . . . . . . . . . . . . . . . . . . . . 29

1.31 Algorithmic assembly by Wang tiles†, each edge pairs with

another edge of the same color. If this rule is strictly employed

the assembly mimics the operation of a Turing machine. The

mosaic on the bottom shows the principle of an addition. The

5th, 9th and 14th columns of the mosaic in the first row show

a special tile, which corresponds to the sum of 5 + 9. Based

on a perfect assembly concerning the edge color pairing rule,

the 3rd special tile in the first row marks the result of the

addition:14. ........................... 33

xvii

1.32 XOR calculation with DNA†. (a) shows a triple crossover

molecule that contains a reporter strand. (b) shows the sev-

eral TX molecules used in the operation. The final result is

found by ligating the reporter strand, amplifying it with PCR,

treating it with restriction enzymes and examining it on a gel. 35

1.33 3D Assembly with TX molecules†. Assembly in the 3rd di-

mension can be achieved by connecting the middle helix with

sticky ends which enable another 90

rotated TX tile do connect. 38

1.34 DX tiles can be arranged to fill 3D space when each DX is

rotated 135

relative to the next DX†............... 38

1.35 DNA cages containing oriented guests†. If DNA crystals can

be created they might be able to capture biomolecules and

serve as crystallization scaffolding. . . . . . . . . . . . . . . . . 39

2.1 Example of a CDM triangle with 17nt per inner triangle edge.

The basic design of this molecule was thought up by Prof.

Chengde Mao. If equipped with sticky ends then this motif

can assemble along each helical DNA axis and fill space. . . . 56

2.2 DNA triangle handedness by Dr. William Sherman. The

CDM triangle can occur in two different conformations (left

or right handed), depending on the number of nt per inner

triangleedge. ........................... 56

2.3 Computer generated model of a TXDX triangle tile. The motif

is shown in a blunt ended version. . . . . . . . . . . . . . . . . 58

2.4 Top view of a computer generated model of a TXDX triangle

tile.................................. 59

xviii

2.5 Computer generated model of one side of the TXDX triangle

tile. The TXDX triangle consists of three of such “sub-motifs,”

connected with a skew. This “sub-model” lacks some strand

nicks of the actual TXDX triangle. . . . . . . . . . . . . . . . 59

2.6 End view of a computer generated model of the 6 helix bundle.

Six DNA helices are connected via cross-overs. Each helix has

9 full turns of DNA, the motif consits of 19 strands. . . . . . 60

2.7 Angled view of a computer generated model of the 6 helix

bundle. Six DNA helices are connected via cross-overs. Each

helix has 9 full turns of DNA, the motif consits of 19 strands. 61

2.8 Molecular structure of Netropsin∗................. 64

2.9 Stereoscopic picture of a dsDNA Crystal structure with Netropsin

attached in the minor groove∗................... 64

2.10 The tip dip method. Ion channels can be reconstituted into bi-

layers formed at the tip of a microelectrode in a method called

tip-dip. A microelectrode is submerged in a bath. Lipids (typ-

ically in an organic solvent like decane) are layered on top of

the bath and allowed to form a monolayer on the bath surface

(A). The microelectrode is raised out of the bath (B). A bi-

layer is formed like a sandwich as the microelectrode is again

returned to the bath (C). Channels are added to the bath and

insert spontaneously (not shown).∗∗ ............... 66

3.1 Light microscope picture of annealed TX crystals under po-

larizedlight ............................ 69

∗∗Picture Kindly Provided by Prof. Dr. Kinnaly

xix

3.2 Light microscopy picture of TX crystals grown with a combi-

nation of slow temperature decrease and hanging drop vapor

diffusion............................... 69

3.3 AFM picture of a DX array with short sticky ends. Picture

scale 1.1 µm x 1.1 µm ...................... 70

3.4 AFM picture of a DX array with short sticky ends. Picture

scale 595 nm X 595 nm . . . . . . . . . . . . . . . . . . . . . . 71

3.5 Light microscope picture of a crystallization attempt via hang-

ing drop vapor diffusion of a blunt ended DX tile (upper part

of the drop). Crystals were grown in Natrix kit buffer 26. . . . 72

3.6 Light microscope picture of a crystallization attempt via hang-

ing drop vapor diffusion of a blunt ended DX tile (lower part

of the drop). Crystals were grown in Natrix kit buffer 26. . . . 73

3.7 Light microscope picture of a crystallization attempt via hang-

ing drop vapor diffusion of a blunt ended DX tile. Crystals

were grown in Natrix kit buffer 44. . . . . . . . . . . . . . . . 73

3.8 Picture of a gel (5% polyacylamide) study of CDM triangles

with 13 nt and 14 nt per inner edge. Lane 1 contains HaeIII

digested pBR marker, lanes 2-5 show the 13 nt triangle with

a logarithmically decreasing concentration from 12 µM to 1.5

µM, lanes 6-9 show the same for the 14 nt triangle. 10 µl were

loaded................................ 74

3.9 Picture of a gel (5% polyacylamide) study of CDM triangles

with 15 nt per inner edge. Lane 1 contains HaeIII digested

pBR marker, lanes 2-5 CDM triangle, 12 µM to 1.5 µM loga-

rithmic concentration series). 10 µl were loaded.. . . . . . . . 75

3.10 Picture of a gel (5% polyacylamide) study of CDM triangles

with 17 nt and 18 nt per inner edge. Lane 1 contains HaeIII

digested pBR marker, lanes 2-5 show the 17 nt triangle, lanes

6-9 show the 18 nt, both with logarithmically decreasing con-

centration from 12 µM to 1.5 µM. 10 µl were loaded. . . . . . 76

3.11 Light microscope picture of crystals from system CDM-A (po-

larized light). Crystals were grown in Natrix kit buffer 5. . . . 77

3.12 Light microscope picture of crystals from system CDM-B (po-

larized light). Crystals were grown in Natrix kit buffer 45. . . 77

3.13 Light microscope picture of crystals from system CDM-C (po-

larized light). Crystals were grown in Natrix kit buffer 19. . . 78

3.14 X-ray diffraction pattern form a CDM-A triangle system . . . 78

3.15 X-ray diffraction pattern form a CDM-B triangle system. . . . 79

3.16 Light microscope picture of crystals from system CDM-B1BE

(polarized light). Crystals were grown in Natrix kit buffer 19. 80

3.17 Composite of 10 X-ray diffraction patterns collected from sys-

tem CDM-B1BE .......................... 81

3.18 Picture of a gel (5% acrylamided) study of the TXDX trian-

gle motif. The motif is blunted “around the clock.” Lane 1

shows HaeIII digested pBR marker, lane 2 the 10 bp ladder

marker, lanes 3-8 contain a logarithmic concentration series of

the blunted TXDX triangle 0.1 µM - 2 µM. 10 µl were loaded. 82

3.19 Atomic force microscopy picture of 2D arrays consisting of

TXDX triangles (flavor A). . . . . . . . . . . . . . . . . . . . . 83

3.20 Atomic force microscopy picture of 2D arrays consisting of

TXDX triangles (flavor B) . . . . . . . . . . . . . . . . . . . . 84

xxi

3.21 Atomic force microscopy picture of 2D arrays consisting of

TXDX triangles (flavor C) . . . . . . . . . . . . . . . . . . . . 85

3.22 Atomic force microscopy picture of 2D arrays consisting of

TXDX triangles flavor B . . . . . . . . . . . . . . . . . . . . . 86

3.23 Current trace at 50 mV showing ion channel behaviour (800

pS transitions). Sample contained 5 µl 6HB (0.1 µM) and 1 x

Netropsin bundle saturation. . . . . . . . . . . . . . . . . . . . 87

3.24 Current trace at 50 mV showing ion channel behaviour (800

pS and 2 nS transitions). Sample contained 5 µl 6HB (0.1

µM) and 1 x Netropsin saturation. . . . . . . . . . . . . . . . 88

3.25 Current trace at 50 mV showing ion channel behaviour (200

pS, 600 pS and 1 nS transitions). Sample contained 5 µl 6HB

(0.1 µM) and 1 x Netropsin saturation. . . . . . . . . . . . . . 88

4.1 Sierpinsky carpet. A 2D fractal derived from a square by

cutting it into 9 equal squares with a 3-by-3 grid, removing

the central piece and then applying the same procedure ad

infinitum to the remaining 8 squares. . . . . . . . . . . . . . . 93

4.2 The Menger sponge or the Sierpinsky cube fractal‡is the 3D

version of the Sierpinsky carpet . It may be possible to assem-

ble a version of the sponge out of DNA. . . . . . . . . . . . . . 94

4.3 A paralellogram consisting of four 6 helix bundles. This might

be a promising motif because it may offer the possibility to

cross conductor paths on a nanometer scale. . . . . . . . . . . 99

6.1 XOR calculation with DNA†. ..................120

6.2 Capillary crystal mounting step 1∗................130

‡Rendered Cube Picture Kindly provided by Prof. Dr. Alessandra Carbone

xxii

6.3 Capillary crystal mounting step 2∗................131

6.4 Sequence and strand structure of TXDX triangle. . . . . . . . 136

xxiii

List of Tables

2.1 Buffer compositions . . . . . . . . . . . . . . . . . . . . . . . . 46

2.2 Buffer compositions . . . . . . . . . . . . . . . . . . . . . . . . 47

2.3 Triangles designed and synthesized based on a basic design by

ProfChengdeMao ........................ 55

3.1 TXDX Triangle distances . . . . . . . . . . . . . . . . . . . . . 86

6.1 pBR HaeIII digested marker fragment sizes . . . . . . . . . . . 121

6.2 Natrix Buffer Compositions . . . . . . . . . . . . . . . . . . . 122

6.3 Sequence dependent Netropsin binding energies. . . . . . . . . 132

6.4 Sticky ends for the DX Motif for 2D Arrays . . . . . . . . . . 133

6.5 Sticky ends for the CDM Triangle Motif for 3D Assembly . . . 134

6.6 Sticky ends for the TxDx Triangle Motif . . . . . . . . . . . . 134

6.7 Sticky Ends for the TXA Motif for 3D Assembly . . . . . . . . 135

6.8 Strand combinations for the 3D TXDX Triangle . . . . . . . . 137

6.9 Calculation of unique 7 mers . . . . . . . . . . . . . . . . . . . 139

6.10 DNA Crystalls and Crystallization Conditions . . . . . . . . . 144

6.11 CDM Triangle Properties with Minimal Turns. . . . . . . . . . 147

6.12 CDM Triangle Properties with 1 Turn. . . . . . . . . . . . . . 149

6.13 CDM Triangle Properties with 1 Turn. . . . . . . . . . . . . . 151

6.14 CDM Triangle Properties with 1 Turn. . . . . . . . . . . . . . 152

xxiv

Nomenclature

πThe mathematical constant π3.14, the ratio of a circle’s circumference

to its diameter

σConductivity if used within a equation

0D 0-dimensional, molecule without sticky ends

1D 1-dimensional, molecule designed to form linear structure

2D 2-dimensional, m Designed to form an array

3D 3-dimensional, molecule designed to fill space

6HB 6 helix bundle

A Adenin

A Area if used in ion channel equations

AFM Atomic force microscope

arrang. arrangement

ATP Adenosinetriphosphate

C Cytosin

xxv

c small c, Brominated Cytosin if used within a DNA Sequence

CDM Prof. Chengde Mao

Compl. Complementary

conc. Concentration

DNA Deoxyribonucleic acid

ds Double stranded

DX DNA Tile consisting of two helices connected by two cross-overs

FRET Fluorescence resonance energy transfer

G Conductance in Siemens [S], inverse of resistance

G Guanin

helicity Number of nucleotides per DNA full turn

HPLC High pressure liquid chromatography

IV Current - voltage curve

junc. Junction

l Length if used in equations

M Molarity g x mol−1

min. Minute[s]

mRNA messenger ribonucleic acid

xxvi

n.a. Not available

NMR Nuclear magnetic resonance

No. Number

nt Nucleotides

NYU New York University

PAGE Polyacrylamid gel electrophoresis

PCR Polymerase chain reaction

PEG Polyethylene glycol

RNA Ribonucleic acid

S Siemens - unit of measurement for electric conductance, being the

inverse of ohm

SEQUIN A program designed by Prof. Seeman to assign nucleic acids SE-

Quences INteractively

ss Single stranded

T Thymin

t small t, Brominated Thymin if used within a DNA Sequence

TX DNA Tile consisting of three helices connected by four cross-overs

U Uracil

x x direction in TXDX Triangle arrays

y y direction in TXDX Triangle arrays

xxvii

Chapter 1

Introduction

1.1 Nanotechnology

1.1.1 Introduction to Nanotechnology

Nanotechnology is described as the art and science of building complex de-

vices and structures with atomic precision [17]. The prefix nano itself stands

for one billionth ( 1

1000000000 ). In general the term nanoscience and nanotech-

nology are used for structures in the 1-100 nm size range which are artifi-

cially synthesized by a variety of physical, chemical and mechanical meth-

ods [14] [23].

Two approaches to create structures on a nanoscale are possible:



Bottom Up



Top Down

The so called top down approach to nanostructures employs manufactur-

ing methods such as lithography to create smaller and smaller structures,

down to nanostructures. The bottom up approach is the manufacturing of

1. Introduction 2

nanomaterials directly on a molecular scale. The synthesis of nanoscale struc-

tures uses a variety of methods: molecular precursors as chemical or physical

vapor deposition, gas condensation, chemical precipitation, aerosol reactions,

biological templating, processing of bulk precursors (mechanical attrition,

crystallization from the amphorphous state, phase separation), and from na-

ture (biologically mimicked systems) [68]. Siegel [68] gives three properties

by which nanoscale materials are determined:



The ability to control the size and the size distribution of the desired

nanoscale structures



The compositions of the constituent phases in a nanostructure material



The control of the nature of the interfaces created between constituent

phases and the interactions across the interfaces

Microtechnologists are trying to build miniature mechanical devices, store

information in less space and develop computers that offer more operations

x time−1x space−1. This kind of engineering requires control of matter

on a molecular level. The IBM



logo has been made of single atoms, posi-

tioned by an AFM (Atomic force microscope) tip [21]. A single, propeller-like

molecule’s rotation at high speeds within a supramolecular lattice has been

observed with scanning tunneling microscopy (STM) [25]. Such molecular

propellers may lead to the development of nanomechanical devices. These

achievements show the possibilities of nanotechnology and the need for con-

trol on a molecular level.

1.1.2 Self-Assembly

One approach to nanoscale structures is the assembly of simple and complex

structures via molecular self-assembly. Molecular self assembly uses non co-

1. Introduction 3

valent interactions in both solid and liquid states to form larger aggregates

of atomic or molecular units with specific geometries [14]. This “bottom

up” approach to the assembly of nanostructures uses molecular recognition

to build a wide variety of structures. The process of self-assembly is widely

used in biological systems. The self-assembly of viruses may be given as an

example. The nanometer scale is used by the living cell to construct its com-

ponents, which often cohere by non bonded interactions, such as microtubes,

filaments built from protein subunits and formation of the double helix [86].

1.2 DNA Nanotechnology

1.2.1 DNA Structure and Function

Nucleotide Base Pairing

DNA (Deoxyribonucleic acid), in its double-stranded form is the genetic ma-

terial of most organisms and organelles, although phage and viral genomes

may use single-stranded DNA, single stranded RNA (ribonucleic acid) or

double stranded RNA [103]. The backbone of the DNA is formed by sugar-

phosphate molecules. At the C1-position of the ribose a nucleic base is

attached. The most common nucleic bases are shown in fig. 1.1 in Watson-

Crick base pairing. The Watson-Crick DNA structure model was founded on

the idea that adenine (A) pairs to thymine (T) by hydrogen bonding, and

guanine (G) to cytosine (C) and hence the content of G always equals the

content of C as T equals A (Chargaff’s rule). Currently, DNA Nanotech-

nology is mainly based on Watson-Crick base paring (see fig. 1.1) but this

pairings are not the only pairs that form nor is the A-T pair even among

the most stable. Just about any base can hydrogen bond to any other base

1. Introduction 4

Figure 1.1: Watson-Crick base pairing∗. Adenine pairs with thymine (upper

part of the figure) and guanine pairs with cytosine (lower part)

Figure 1.2: Adenine self pairing∗

including self-pairs. Fig. 1.2 shows an Adenine base pairing with another

Adenine base, fig. 1.3 shows Hoogsteen base pairing and fig. 1.4 shows re-

1. Introduction 5

Figure 1.3: Adenine can pair with uracil in Hoogsteen base paring∗

Figure 1.4: Adenine can pari with uracil in reversed Hoogsteen base paring∗

versed Hoogsteen base pairing. Reversed Watson-Crick base pairing is shown

in fig. 1.5, sheared Watson-Crick base pairing can be seen in fig. 1.6. The

Watson-Crick base pairing G-C and A-T shares a unique geometry, both C-1’

Atoms are 10.8 ˚

Aapart from each other. This allows complementary (con-

cerning the Watson-Crick base pairing) sequences to form a double DNA

helix with the least amount of helix backbone disturbance. With the ex-

1. Introduction 6

Figure 1.5: Adenine can pair with thymine in reversed Watson-Crick base

pairing∗

Figure 1.6: Guanine can pair with uracil in sheared Watson-Crick base

pairing∗. The cytosine position in regular Watson-Crick pairing

is drawn in red.

ception of unusual motifs such as quadruplexes or triplexes, Watson-Crick

paired helices are usually at a thermodynamical minimum relative to other

structures due to base stacking, hydrogen bonding and minimal helix dis-

tortion. If paired DNA strands are heated complementary sequences can

maintain a double helix form at the highest temperature before dissociation.

In contrast, if a solution containing DNA strands is allowed to cool from high

temperature, complementary DNA sequences will be the first to form double

1. Introduction 7

stranded DNA helices corresponding to the most thermodynamically stable

product. In aqueous solution the H-Bond formation alone does not provide

sufficient energy to form a stable double helix. Base stacking provides an-

other -16.0 to -61.6 kJ

mol per 4 complementary bases (two 2mers), depending

on the base sequence.

B-DNA

Figure 1.7: B-DNA double helix∗.B-DNA is the most stable helical form of

DNA formed by a random sequence. The right side of the figure

shows a view down the helical axis.

B-DNA is shown in fig. 1.7. Under physiological conditions B-DNA is the

most stable helical form of DNA formed by a random sequence. The two

strands run in opposite directions and the bases project towards each other

like the rungs of a ladder due to Watson-Crick complementary base pairing.

In its B molecular form the helix is 2.0 nm in diameter with a pitch of 3.6

nm [100]. One full turn in the double helical structure corresponds to 10.5

nucleotides in solution and 10.0 nucleotides in crystal form [100].

1. Introduction 8

A-DNA

Figure 1.8: A-DNA helix∗can form under dehydrating conditions. The right

side of the figure is a view down the helical axis.

Under dehydrating conditions DNA can form A-DNA, as seen in fig. 1.8.

A-DNA corresponds also to the conformation of dsRNA due to avoidance

of steric interference of 2’O. DNA/RNA hybrids form a structure similar to

A-DNA. In A-DNA the helix has 11 nt per DNA full turn.

C-DNA

C-DNA can occur under low relative humidity and in the absence of excess

salt and in the presence of Li-ions [61]. The C-DNA helix has 91

3nucleotides

per full turn. A structural model of C-DNA displays the displacement of the

bases to the outside of the helix in the major groove and the development of

a very deep minor groove.

D-DNA and Z-DNA

Alternating T and A sequences can form D-DNA. Promoter sites are AT rich

and AT rich regions are less stable compared to GC containing sequences.

1. Introduction 9

Figure 1.9: D-DNA is shown∗in the left side of the picture and can occur

with alternating A and T sequences . Z-DNA (right side∗) is

formd by GC rich sequences under high salt conditions. The

Z-DNA back bone is left handed.

These sequences can switch from normal B-DNA to D-DNA in high ionic

concentrations or under the influence of binding proteins. In D-DNA a full

turn corresponds to 8 bp. At high salt concentrations Z-DNA is formed

from GC rich sequences with strictly alternating purine pyrimidine sequences.

Z-DNA has 12 bp per DNA full turn [77]. In contrast to standard DNA

backbone conformations Z-DNA has a left-handed sense. Z-DNA has a zigzag

backbone due to C sugar conformation compensating for G glycosidic bond

conformation and a narrow minor groove [77].

PNA

Peptide nucleic acid (PNA) can be synthesized and possesses polyaminoethyl-

glycine, a polymer of amide bonds [22] and is given as an example of a nucleic

acid with a backbone not found in nature. PNA is not degraded by any known

enzyme and offers unique features for antisense expression blockers. Many

1. Introduction 10

other derivatives have been synthesized and might be applied to DNA nan-

otechnology due to the advantage of the non-ionic backbone, resistance to

enzyme degration and hydrophobic properties. PNA-DNA hybrids are more

stable than RNA-DNA and hence PNA can used to displace a hybridisized

strand.

DNA Triplex

Figure 1.10: DNA triplex∗formed by three DNA strands. Hoogsteen base

pairing is involved in this structure.

Base triplets can form due to the accessible wide major groove of B-DNA

and exposed access to the Hoogsteen face of the base pair purines 1.10. The

third (yellow) strand runs parallel to the red purine strand in fig. 1.10. The

CCG triplex has protonated C in the Hoogsteen position.

DNA quadruplex and G quartets

Quadruplexes consisting of guanine are found as terminating sequences at the

end of eukaryotic chromosomes [106]. Telomeres contain G-rich repetitive

sequences and are synthesized by telomerases using RNA templates. The

four strands of the quadruplex are associated through guanine quartets. Each

1. Introduction 11

Figure 1.11: Quadruplex DNA∗are found in the end of eukaryontic chromo-

somes and contain G-rich repetitive sequences.

guanine pairs with its Watson-Crick face to H-bond to the Hoogsteen face of

its neighbor.

1.2.2 Holiday Junction and Branch Migration

Figure 1.12: Branch migration†. Crossing-over of homologous areas (II) of

two double helices (I), followed by branch migration (II-III) of

the Holliday junction and resolvation (IV) lead to two possible

products (V). VI shows a possible ligation step.

1. Introduction 12

One of the main properties of the DNA in organisms is that it is a long

(E. coli 1.3 mm [100]), unbranched and linear molecule. Branched DNA

occurs in replication and in the process of genetic recombination when the

homologous areas of two double helices cross over (fig. 1.12). Both replica-

tive and recombinational intermediates are normally unstable due to internal

sequence symmetries, which allow their resolution to double helices, via the

process of branch point migration [96]. Fig. 1.12 shows the process of cross-

ing over and branch migration as it occurs during genetic recombination.

Both helices consisting of homologous regions carry flanking markers, A and

B in the strands on the left, and a and b on the right. Fig. 1.12 I shows two

double helices, II shows the crossing over of the homologues sequences, III

shows a state formed by branch migration and IV a state reached by cross-

over isomerization. V shows two possible end products formed from state III

and IV and finally VI as the two possible final ligated products.

1.2.3 De novo Designed Junctions and Avoidance of

Branch Migration

Fig 1.13 shows a four-arm junction that is the equivalent to the Holliday

structure [38] found in the process of genetic recombination. The Holliday

structure, as found in the process of recombination, has two-fold sequence

symmetry. In contrast, the sequence shown in fig. 1.13 prevents branch mi-

gration through sequence symmetry minimization [84] and does not contain

the two-fold symmetry necessary to perform branch migration. Arrowheads

indicate 3’-ends. Each strand is paired with two other strands and labeled

with Arabic numerals, the four arms are numbered with roman numerals.

The base pairing is symbolized by a dot between complementary bases. This

junction can not perform branch migration because there is no homologous

1. Introduction 13

Figure 1.13: Four arm junction with symmetry minimization†. It does not

possess the symmetry necessary to perfom branch point migra-

tion.

Figure 1.14: Three arm junctions with sticky ends. Ligation studies show

that regular three arm junctions (left side) equipped with sticky

ends tend to cyclize. Bulged three arm junctions (right side)

show less tendency to cylize.

1. Introduction 14

two-fold sequence symmetry flanking the central branch point. Furthermore

all tetramer (4mer) segments are unique.

It is possible to design oligonucleotides that preferentially form a three arm

junction via Watson-Crick base pairing [84, 57]. Fig. 1.14 A shows a three

arm junction with sticky ends and fig. 1.14 B shows a bulged 3 arm junction.

Three arm junctions are not able to perform branch migration. The three

arm junctions equipped with sticky ends are able to form linear complexes

and also several cyclic products because they are flexible about a bending

axis and maybe twist-wise as well [57]. Bulged three arm junctions are less

likely to cyclize [54]. Further, junctions with five [105], six [105], eight, ten

and twelve arms (unpublished) have been designed and constructed in Prof

Seeman’s laboratory.

1.2.4 2 Dimensional DNA Arrays

Requirements and Basic Concept

Three key elements necessary for the control of three dimensional structure

in molecular construction are given by Li et al. [51]:



The predictable specificity of intermolecular interactions between com-

ponents



The local structural predictability of intermolecular compounds



The structural rigidity of the components

The first two requirements make DNA excellent building blocks because

sticky ended association directed by Watson-Crick base pairing between sticky

ended molecules has been used successfully to direct intermolecular speci-

ficity [15] and the ligated or unligated product is double helical B-DNA,

1. Introduction 15

whose geometric properties are well known [4].

Figure 1.15: Sticky ended cohesion†. Two DNA helices with complementary

sticky ends can associate due to Watson-Crick base pairing and

can optionally be ligated together.

Fig. 1.15 shows sticky ended cohesion moderated by Watson-Crick base

pairing and optional final ligation step. The basic concept of assembly of

complex structures from individual tiles can be seen in fig. 1.16. It has

been reported that one of the key problems when using branched DNA as a

construction medium is that branched junctions seem to be extremely flexible

molecules [57, 71]. Ligated three and four arm junctions (using conventional

sticky end methods) show a series of macro cyclic products [56]. Thus, a key

goal is to find DNA structures that lack the ability to cyclize.

1. Introduction 16

Figure 1.16: Basic concept of self assembly†. A motif can associate to form

a lager predicted complex due to specific sticky ends.

Double Crossover molecules

Different types of double crossover (DX) molecules are shown in fig. 1.17. DX

molecules consits of two helices connected by four arm junctions. The first

character ’D’ stands for double crossing over, the second character refers to

the relative orientations of their two double helical domains, ’A’ for antipar-

allel and ’P’ for parallel. The third character refers to the number of helical

half-turns between crossovers, ’E’ for an even number and ’O’ for an odd num-

ber. The two double crossover molecules on the right side in fig. 1.17 show

parallel double crossover molecules with an odd number between cross-overs,

’W’ indicates the extra half turn corresponds to a major groove separation,

’N’ indicates a minor groove separation. Arrowheads indicate 3’ ends of DNA

strands in fig. 1.17. It has been shown that DAE molecules can be ligated

extensively without showing a large propensity to cyclize [51]. Parallel dou-

ble crossover molecules are not well behaved on non-denaturating gels, unless

their ends have been closed off in hairpin loops. Antiparallel double crossover

1. Introduction 17

Figure 1.17: Different types and nomenclature of DNA double crossover

molecules†The first character ’D’ stands for double crossing

over, the second character refers to the to the relative orienta-

tions of their two double helical domains, ’A’ for antiparallel

and ’P’ for parallel. The third character refers to the number

(modulus 2) of helical half-turns between crossovers, ’E’ for an

even number and ’O’ for an odd number. A fourth character

is needed to describe parallel double crossover molecules with

an odd number of helical half-turns between crossovers. The

extra half-turn can correspond to a major (wide) groove sepa-

ration, designated by ’W,’ or an extra minor (narrow) groove

separation, designated by ’N.’

molecules appear to be stable molecules[51].

2 Dimensional DNA Arrays with DX Molecules

A DNA hairpin can be incorporated into a DX molecule. The hairpin is per-

pendicular to the DX tile and is inserted between cross-overs, using a bulged

3-arm junction [84, 57]. Double cross-over molecules have been successfully

1. Introduction 18

Figure 1.18: Assembly principle of a 2D-DNA array consisting of two dif-

ferent DX tiles†. A hairpin, serving as a topograhic label, is

incorporated into the blue tile.

Figure 1.19: AFM picture of a 2D DX array†. The hairpin on every second

tile can be clearly seen and shows the predicted spacing.

used to build 2D DNA lattices. By using a DX molecule with a hairpin in

every 2nd tile, serving as a topographic label, stripes above the surface at

1. Introduction 19

intervals have been produced [108]. Fig. 1.18 shows how the DX molecules

assemble in a chessboard like structure, fig. 1.19 shows an AFM picture of

the produced array. Further, arrays with four tiles and a topographic label

on every 4th tile have been produced with the predicted spacing [108].

2 Dimensional DNA Arrays with TX Molecules

Figure 1.20: TX motif consisting of three helices connected by 4 cross-overs,

shown in a blunt ended version.

Three DNA helices can be connected by four cross-overs to from a TX

molecule as shown in fig. 1.20. Like DX molecules the TX molecules can

assemble into 2 dimensional arrays. The principle of the array assembly

is shown in fig. 1.21. An AFM picture of a produced array is shown in

fig. 1.22 [45].

1. Introduction 20

Figure 1.21: Assembly principle of a 2D array consisting of two different TX

tiles†. A hairpin, serving as a topograhic label, is incorporated

into the red tile.

Figure 1.22: AFM picture a 2D DNA array consisting of TX tiles. The hair-

pin on every second tile can be clearly seen and shows the pre-

dicted spacing.

1. Introduction 21

2 Dimensional DNA Arrays with Parallelograms

Figure 1.23: Schematic picture of parallelogram assembly†. Four junctions

can be combined into a rhombus like motif.

Figure 1.24: AFM picture of parallelogram array†. The rhombus like struc-

ture can be distinguished.

The Holliday junction forms a stacked structure in the presence of mag-

1. Introduction 22

nesium ions, see fig. 1.23 (a). Four junctions can be combined into a rhombus

like motif (b) and can form a linear (1d) array (c)or a crystal (2d array) (d),

depending on the provided sticky ends. An AFM picture of a 2d array is

shown in fig. 1.24.

1.2.5 Other Molecules for DNA Nanotechnology

DNA Cube

Figure 1.25: The DNA strands in this molecule†have the connectivity of a

cube. It consists of six cyclic strands. The cube is created by lig-

ating two ends of two quadrilaterals to from a belt-like molecule.

The nucleotides are represented by white dots (nucleic base) in

this drawing, the colored dots represent the sugar phosphate

backbone of the DNA strands with one color per strand.

The helices of the molecule shown in fig. 1.25 have the connectivity of

a cube. It consists of six cyclic strands. The cube is created by ligating

two ends of two quadrilaterals to from a belt-like molecule that has to be

1. Introduction 23

purified to remove side products [83]. The nucleotides are represented by

white dots (nucleic base) in this drawing, the colored dots represent the

sugar phosphate backbone of the DNA strands with one color per strand.

The successful synthesis has been reported in Nature [83].

DNA Truncated Octahedron

Figure 1.26: The DNA strands in this molecule†have the connectivity of

a truncated octahedron. The truncated octahedron is viewed

down the four fold axis of one of the squares. The edges of

the truncated octahedron consist of two full turns of dsDNA.

The complete truncated octahedron contains 14 cyclic strands

of DNA and each cyclic strand corresponds to a face of the

truncated octahedron. The nucleotides are represented by white

dots (nucleic base) in this drawing, the colored dots represent

the sugar phosphate backbone of the DNA strands.

The molecule shown in fig. 1.26 consits of DNA helices with the connec-

tivity of a truncated octahedron. The structure, containing six squares and

1. Introduction 24

eight hexagons, has been successfully synthesized with DNA (fig. 1.26) [116].

The truncated octahedron shown in fig. 1.26 is viewed down the four fold

axis of one of the squares. The edges of the truncated octahedron consist

of two full turns of dsDNA. The complete truncated octahedron contains 14

cyclic strands of DNA and each cyclic strand corresponds to a face of the

truncated octahedron. The nucleotides are represented by white dots (nu-

cleic base) in this drawing, the colored dots represent the sugar phosphate

backbone of the DNA strands. The truncated octahedron has 36 edges and

each vertex contains a DNA hairpin of DNA extending from it, drawn in

red. Those strands correspond to the squares that form the squares. The

backbones of the strands that form the hexagons are drawn in different colors

(yellow (upper right), cyan (upper left), magenta (lower left) and green(lower

right). The molecular weight of the truncated octahedron has been reported

at 790,000 Daltons [116].

Borromean Rings Made out of DNA

Fig. 1.27 shows Borromean rings made of DNA. Borromean rings are special

because if one of the three rings is destroyed it will free the other two rings

while leaving them intact and not connected to each other. The conventional

nodes in Borromean rings have been replaced by three nodes, derived from

1.5 turns of DNA double helix. Fig. 1.27 c is the stereoscopic representa-

tion of fig. 1.27 b. Fig. 1.27 d is the stereoscopic view of the synthesized

DNA molecule with hairpins. The hairpins contain sequences for restriction

enzymes that can be used for digestion and, depending on the restriction

site used, release of the other two DNA rings. This work is published in

Nature [58].

1. Introduction 25

Figure 1.27: Borromean rings made of DNA†. Borromean rings are special

because if one of the three rings is destroyed it will free the

other two rings while leaving them intact and not connected to

each other. The conventional nodes in Borromean rings (a) have

been replaced by three nodes, derived from 1.5 turns of DNA

double helix (b). The stereoscopic representation (c) is shown

in the middle part of the picture. A stereoscopic view of the

synthesized DNA molecule with hairpins is shown in the lower

part of the picture (d). The hairpins contain sequences for re-

striction enzymes that can be used for digestion and, depending

on the restriction site used, release of the other two DNA rings.

1. Introduction 26

1.3 Nanomechanical Devices based on DNA

1.3.1 A Nanomechanical Device Predicated on the B-Z

Transition of DNA

Figure 1.28: A nanomechanical device predicated on the B-Z transition of

DNA†. Twenty nucleotide pairs of this helix can be converted

into Z-DNA and induce a nanomechanical movement of the rigid

DX tiles. The part acting as a bridge between the tiles is shown

in yellow. The relative movement of the DX tiles is caused by

the transition of right handed B-DNA to left handed Z-DNA (in-

duced with Hexaamminecobalt(III) chloride) and can be mea-

sured with FRET (Fluorescence resonance energy transfer of

donor and aceptor molecules attached to the DX molecules in

the appropiate place marked by green and purple dots). The up-

per part of the figure shows the bridge DNA in B From (right

handed) and the lower part shows it in Z-Form (left handed).

1. Introduction 27

DNA has been shown to be a material useful for the assembly of arrays

on the nanometer scale. It is desirable to assemble nanomechanical devices

from the same material. The simplest device is a rigid object that can re-

spond to an external signal. A device based on DNA has been constructed

that consists of two DX molecules connected by a DNA double helix with 4.5

full turns (fig. 1.28) [59]. Twenty nucleotide pairs of this helix can be con-

verted into Z-DNA [77] and induce a nanomechanical movement of the rigid

DX tiles. The part acting as a bridge between the tiles is shown in yellow in

fig. 1.28. The relative movement of the DX tiles is caused by the transition of

right handed B-DNA to left handed Z-DNA and can be measured with FRET

(Fluorescence resonance energy transfer of donor and aceptor molecules at-

tached to the DX molecules in the appropiate place marked by green and

purple dots). The upper part of fig. 1.28 shows the bridge DNA in B From

(right handed) and the lower part shows it in Z-Form (left handed). The

transition was induced with the addition of Hexaamminecobalt(III) chloride

to the solution and reversed by dialyzing Hexaamminecobalt(III) chloride

away [59].

1.3.2 DNA Nanomechanical Devices Based on Hybridiza-

tion Topology

A new form of nanomolecular, sequence-dependent device based on DNA was

introduced as “Molecular DNA tweezers” [115]. Based on this basic concept

of set and unset strands further sequence dependent devices using a motif

called PX with the advantage of rigidity have been designed. The PX motif,

postulated to be involved in genetic recombination, consists of two helical

domains formed by four strands that flank a central dyad. See molecule

and sequence-depended device cycle in fig. 1.29 (left side (a)). Every possi-

1. Introduction 28

Figure 1.29: Nanomechanical device based on hybridization topology†. Left

side (a): The letters A, B, C and D, along with the color coding,

show that the bottom of the JX2motif (C and D) are rotated

180

relative to the PX motif. The set strands are shown in

green, they can be removed by the addition of biotinylated green

fuel strands (biotin indicated by black circles, process step I).

The addition of the purple set strands (process step II) converts

the unstructured intermediate into the JX2motif. In process

step III the JX2molecule is converted to the unstructured in-

termediate by the addition of biotinylated yellow fuel strands.

The PX device is restored and the cycle completed by the addi-

tion of green set strands (IV). Right side (b): AFM observation

of the cycle with DNA trapezoids attached as a marker.

ble crossover occurs between the two helical domains of the PX motif. The

JX2motif is similar to the PX motif but lacks two crossovers in the middle

(see fig. 1.29 (right side of (a)). The letters A, B, C and D, along with the

color coding, show that the bottom of the JX2motif (C and D) are rotated

1. Introduction 29

180

relative to the PX motif. Fig. 1.29 (a) illustrates the principles of device

operation. The set strands are shown in green (fig. 1.29). They can be re-

moved by the addition of biotinylated green fuel strands (biotin indicated by

black circles, process step I). The addition of the purple set strands (process

step II) converts the unstructured intermediate into the JX2motif. In process

step III the JX2molecule is converted to the unstructured intermediate by

the addition of biotinylated yellow fuel strands. The intermediates between

step I to II and step III to IV are identical. The PX device is restored and

the cycle completed by the addition of green set strands (process step IV,

fig. 1.29). Fig. 1.29 (b): shows an AFM observation of the cycle with DNA

trapezoids attached as a marker.

1.4 DNA Based Computing

1.4.1 Introduction to DNA Based Computing

Figure 1.30: Graph with 7 nodes. Arrows indicate possible connections be-

tween two nodes.

DNA based computing exploits DNA molecules to solve mathematical

problems. DNA based computing was first demonstrated by Adleman in

1. Introduction 30

“Molecular computation of solutions to combinatorial problems” [3] to solve

the Hamiltonian path problem1. Hamilton’s problem is NP-complete2and

hence also NP-hard3. In the Hamiltonian path problem, a path in a given

graph has to be found from node 1 to node N that passes every node only

once. Every node has to be visited but is not allowed to be visited more

than once. The Hamiltonian path problem does not include the problem

of finding the shortest path through a given graph what would correspond

to the traveling sales man problem4Fig. 1.30 shows a graph with 7 nodes.

1Hamiltonian problem (Or “Hamilton’s problem”) A problem in graph theory posed

by William Hamilton: given a graph, is there a path through the graph, which visits each

vertex precisely once (a “Hamiltonian path”)? Is there a Hamiltonian path which ends up

where it started (a “Hamiltonian cycle” or “Hamiltonian tour”) Entry from Free Online

Dictionary of computing [39]

2NP-complete - (NPC, Nondeterministic Polynomial time complete) A set or property

of computational decision problems, which is a subset of NP (i.e. can be solved by a

nondeterministic Turing Machine in polynomial time), with the additional property that

it is also NP-hard. Thus a solution for one NP-complete problem would solve all problems

in NP. Many (but not all) naturally arising problems in class NP are in fact NP-complete.

There is always a polynomial-time algorithm for transforming an instance of any NP-

complete problem into an instance of any other NP-complete problem. So if you could

solve one you could solve any other by transforming it to the solved one. Entry from Free

Online Dictionary of computing [39]

3NP-hard - A set or property of computational search problems. A problem is NP-

hard if solving it in polynomial time would make it possible to solve all problems in class

NP in polynomial time. Some NP-hard problems are also in NP (these are called “NP-

complete”), some are not. If you could reduce an NP problem to an NP-hard problem

and then solve it in polynomial time, you could solve all NP problems. Entry from Free

Online Dictionary of computing [39]

4traveling salesman problem: Given a set of towns and the distances between them,

determine the shortest path starting from a given town, passing through all the other towns

and returning to the first town. This is a famous problem with a variety of solutions

of varying complexity and efficiency. The simplest solution (the brute force approach)

1. Introduction 31

Adleman suggested [3] the following algorithm to solve the problem:

1. Generate random path though the graph

2. Keep only those paths that begins with vin and end with vout

3. If the graph has nvertices, then keep only those paths that enter exactly

nvertices

4. Keep only those paths that enter all of the vertices at least once.

5. If any path remains, say ’yes’, otherwise say ’no’.

Adleman solved this problem by representing each vertex iin the graph

with a random 20mer sequence of DNA Oi. He created an oligonucleotide

for each edge in the graph i→jthat was the 3’ 10 mer of Oi (for i >0,

otherwise it was all of Oi) followed by the 5’ 10 mer of Oj (j < 6, otherwise it

was all of Oj). The 20mer oligonucleotide with the sequence complementary

to Oi was denoted Oi. All Oi and Oi →jsequences were ligated together

(step 1), followed by a PCR with primers O0and O6(step 2). Thus, only

those molecules encoding paths that begin with vertex 0 and end with vertex

6 were amplified. By separation on an agarose gel (only the 140 bp bands,

representing exactly 7 vertices, were kept) step 3 was realized. By affinity

purification with a biotin-avidin magnetic beads system all the encoded paths

generates all possible routes and takes the shortest. This becomes impractical as the

number of towns, N, increases since the number of possible routes is !(N-1). A more

intelligent algorithm (similar to iterative deepening) considers the shortest path to each

town, which can be reached in one hop, then two hops, and so on until all towns have

been visited. At each stage the algorithm maintains a “frontier” of reachable towns along

with the shortest route to each. It then expands this frontier by one hop each time. Entry

from Free Online Dictionary of computing [39]

1. Introduction 32

that miss a vertex of the path were eliminated (step 4). The remaining

product was PCR amplified and run on a gel. A band would indicate that

a path exists (step 5). DNA computing might be superior in some tasks

comparing to traditional von Neumann computers 5because it is massively

parallel. In particular some optimization and code breaking algorithms [2, 78]

can take full advantage of parallel computing.

1.4.2 DNA Computations with Rectangular Tiles

Rectangular tiles, known as Wang tiles, with programmable interactions can

mimic the operation of a given Turing machine6[109, 107]. Fig. 1.31 shows

5von Neumann architecture - A computer architecture conceived by mathematician

John von Neumann, which forms the core of nearly every computer system in use today

(regardless of size). In contrast to a Turing machine, a von Neumann machine has a

random-access memory (RAM) which means that each successive operation can read or

write any memory location, independent of the location accessed by the previous operation.

A von Neumann machine also has a central processing unit (CPU) with one or more

registers that hold data that are being operated on. The CPU has a set of built-in

operations (its instruction set) that is far richer than with the Turing machine, e.g. adding

two binary integers, or branching to another part of a program if the binary integer in

some register is equal to zero (conditional branch). The CPU can interpret the contents

of memory either as instructions or as data according to the fetch-execute cycle. Von

Neumann considered parallel computers but recognized the problems of construction and

hence settled for a sequential system. For this reason, parallel computers are sometimes

referred to as non-von Neumann architectures. A von Neumann machine can compute the

same class of functions as a universal Turing machine. Entry from Free Online Dictionary

of computing [39]

6Turing Machine - A hypothetical machine defined in 1935-6 by Alan Turing and used

for computability theory proofs. It consists of an infinitely long “tape” with symbols

(chosen from some finite set) written at regular intervals. A pointer marks the current

position and the machine is in one of a finite set of “internal states”. At each step the

1. Introduction 33

Figure 1.31: Algorithmic assembly by Wang tiles†, each edge pairs with an-

other edge of the same color. If this rule is strictly employed

the assembly mimics the operation of a Turing machine. The

mosaic on the bottom shows the principle of an addition. The

5th, 9th and 14th columns of the mosaic in the first row show a

special tile, which corresponds to the sum of 5 + 9. Based on a

perfect assembly concerning the edge color pairing rule, the 3rd

special tile in the first row marks the result of the addition: 14.

machine reads the symbol at the current position on the tape. For each combination of

current state and symbol read, a program specifies the new state and either a symbol

to write to the tape or a direction to move the pointer (left or right) or to halt. In an

alternative scheme, the machine writes a symbol to the tape *and* moves at each step.

This can be encoded as a write state followed by a move state for the write-or-move

machine. If the write-and-move machine is also given a distance to move then it can

emulate an write-or-move program by using states with a distance of zero. A further

variation is whether halting is an action like writing or moving or whether it is a special

state. Without loss of generality, the symbol set can be limited to just “0” and “1” and

the machine can be restricted to start on the leftmost 1 of the leftmost string of 1s with

1. Introduction 34

Wang tiles in the left upper section, as designed in ’Tilings and Patterns’ [31].

The edges of the tiles are colored. Some contain up to four different colors,

some consist of only one color. The assembly principle of Wang Tile assembly

is based on the idea that each edge pairs with another edge of the same color.

If this rule is strictly employed the assembly mimics the operation of a Turing

machine. The mosaic on the bottom in fig. 1.31 shows the principle of an

addition. The 5th, 9th and 14th columns of the mosaic in the first row

show a special tile, which corresponds to the sum of 5 + 9. Based on a

perfect assembly concerning the edge color pairing rule, the 3rd special tile

in the first row marks the result of the addition: 14. The tiles 2 to 8 in the

top row have to be unique to assure that the right result is presented. It

was pointed out by Prof. Winfree that such operations might be performed

with DNA structures, equipped with sticky ends representing the colored

tile edges. Fig. 1.31 shows in the upper right the J1 junction, a symmetry

minimized equivalent of the Holliday structure, equipped with sticky ends.

Such structures might put the theory in practice. The J1 structures tend

to cyclize [51] and hence might not be the preferred structures. Structures

created by Prof. Yan, that form a cross like structure like the Holliday

junction with the DX motif [114] might be more suitable to act as Wang

tiles.

1. Introduction 35

Figure 1.32: XOR calculation with DNA†. (a) shows a triple crossover

molecule that contains a reporter strand. (b) shows the sev-

eral TX molecules used in the operation. The final result is

found by ligating the reporter strand, amplifying it with PCR,

treating it with restriction enzymes and examining it on a gel.

1.4.3 Cumulative XOR Computation with DNA

A cumulative XOR computation with DNA has been reported [85]. A cumu-

lative XOR operation is defined as:

strings of 1s being separated by a single 0. The tape may be infinite in one direction only,

with the understanding that the machine will halt if it tries to move off the other end.

All computer instruction sets, high level languages and computer architectures, including

parallel processors, can be shown to be equivalent to a Turing Machine and thus equivalent

to each other in the sense that any problem that one can solve, any other can solve given

sufficient time and memory. Entry from Free Online Dictionary of computing [39]

1. Introduction 36

Y(i) = XOR[Y(i−1), X(i)] (1.1)

The result is 1 if the two inputs are different ((0 and 1) or (1 and 0)),

the result is 0 if they are the same ((1 and 1) or (0 and 0)). The calculation

was performed with the components shown in fig. 1.32, the actual gel can

be seen in appendix fig. 6.1. Fig. 1.32 (a) shows a triple crossover molecule

that contains a reporter strand [45]. The reporter strand is drawn in red

color. Fig. 1.32 (b) shows the several TX molecules used in the operation.

Input X(i) tiles are drawn in light blue, their value is shown at the center

of each tile. The value ’1’ is presented by a restriction site for EcoRV and

a ’0’ is presented by a restriction site for PvuII in the tile. All x tiles were

equipped with unique sticky ends. The X(i) tiles were allowed to associate

randomly, giving, for a four-bit problem, 16 different final answer strands.

The X-tiles connect to the Y tiles by the two green connector tiles. The

four red Y TX answering tiles, corresponding to the two different inputs, are

shown under b in fig. 1.32. The X and C (input) tiles assemble first in the

annealing protocol due to longer sticky ends. Fig. 1.32 shows two calculations

performed in section (c) and (d). In (c), the inputs are X(1) = 1; X(2) =

1; X(3) =1; X(4) = 0. This should lead to Y(1) = 1; Y(2) = 0; Y(3) = 1;

Y(4) = 1. In (d), the input values are X(1) = 1; X(2) = 0; X(3) = 1; X(4)

= 0, leading to Y(1) = 1; Y(2) = 1, Y(3) = 0; Y(4) = 0. The final result

is found by ligating the reporter strand, amplifying it with PCR, treating

it with restriction enzymes and examining it on a gel (for gel see appendix

fig. 6.1).

1. Introduction 37

1.5 Crystallography

1.5.1 Traditional DNA Crystallography

Relatively large quantities of material are required for X-ray crystallography.

5-10 mg of high purity material are considered typical for a crystallization

screening [64]. These quantities can today be easily obtained with auto-

mated DNA synthesis [64]. At least 95% purity is considered necessary to

obtain high quality crystals [64]. Most DNA strands for crystallization are

purified via HPLC to remove unwanted blocking agents, precursors and trun-

cated sequences [64]. HPLC purification archives reasonable purity for DNA

strands up to 20nt, for longer sequences PAGE purification becomes neces-

sary [64]. Nearly all the DNA crystals reported to public crystals databases

are of duplex DNA [64]. Probably less than 20% of all tried sequences can

be successfully crystallized and even small changes in the sequence may re-

sult in a failure to crystallize [64]. Successful oligonucleotide crystallization

has been performed in a quite narrow range of crystallization conditions. A

crystallization buffer kit can be commercially obtained from Hampton Re-

search that includes a matrix of 48 of the most common DNA crystallization

buffers based on a double screening procedure suggested by Scott et al. [81].

An overview of common crystallization conditions and concentrations based

on the protein data bank from the institute of molecular biotechnology (Jena,

Germany) is given in the appendix (s. tbl 6.10 and tbl. 6.10).

1.5.2 3-Dimensional DNA assembly

One of the questions arising with 3-dimensional DNA assembly is how to

fill space. In contrast to traditional crystallization, a sticky ended approach

is taken to assemble rigid, predicted periodic structures to fill space. The

1. Introduction 38

Figure 1.33: 3D Assembly with TX molecules†. Assembly in the 3rd dimen-

sion can be achieved by connecting the middle helix with sticky

ends which enable another 90

rotated TX tile do connect.

Figure 1.34: DX tiles can be arranged to fill 3D space when each DX is

rotated 135

relative to the next DX†.

TX motif (s. fig. 1.20) can be used to fill space. The assembly in the first

two directions is the same as for 2 dimensional arrays (s. fig. 1.22), the 3rd

dimension can be achieved by exchanging the closed loops of the middle helix

with sticky ends which enable another 90

rotated TX tile to connect with

it (s. fig. 1.33). Crystals have been grown from this motif but showed poor

1. Introduction 39

diffraction (data not published). Another motif able to fill space is the DX

motif (s. fig. 1.17), where each DX tile is rotated 135

, relative to the next

DX tile, which corresponds to 4 nt (assembly principle see fig. 1.34). Once

poor diffraction for this system was observed by Prof. Mao but could never

be repeated (data not published, data not shown).

1.5.3 DNA Cages for Trapping and Characterization

of Biomolecules

Figure 1.35: DNA cages containing oriented guests†. If DNA crystals can be

created they might be able to capture biomolecules and serve

as crystallization scaffolding.

Crystallization as applied to proteins has been described as a “black art”

or alchemy [64]. Things have improved since then, but crystallization of

proteins is still a very work intensive process that requires a high investment

of work power and protein substance and still, diffracting crystals might

not be achieved. One use of space filling DNA tiles assembled via sticky

ends might be the capturing of trapped, oriented guest molecules within the

DNA framework. Fig. 1.35 shows two connected networks that function as

a scaffold and contain trapped, oriented guest molecules. Proteins or other

biological macromolecules that are hard to crystallize might be forced this

1. Introduction 40

way into crystallization and could be examined with x-rays. The left cage

in fig. 1.35 consists of octahedra and a truncated cube, the right network

consists only of a cube. Each network is meant to represent an infinite

network to be constructed from DNA. The kidney-shaped objects represent

the guest molecules, their structure could be resolved via x-rays as long as

they are parallel within the crystals. The octahedra cage and the cube cage in

fig. 1.35 are given as examples but other motifs may be used for the trapping

of biomolecules as long as they fill space and diffract down to a reasonable

resolution.

1.6 Ion Channels

1.6.1 Ion Channels in Organisms

Ion channels are macromolecular pores in cell membranes [36]. The model of

embedded proteins in membranes was suggested by Singer and Nicolson [90].

Membrane proteins are either an integral membrane protein or an assembly

of several proteins, consisting of sub-units. The arrangement is typically

circular with a water filled pore, perpendicular to the lipid bilayer membrane.

Ion channels bear the same relation to electric signaling as enzymes bear to

metabolism [36]. There are three major types of gated ion channels:



Ligand gated - open or close in respose to signalling molecules



Stretch/Mechanically gated - react to mecanical signals



Voltage gated - act in response to changes in the charge

Channel behaviour can be examined the via patch clamp technique which

allows examination of single ion channels and recording of macroscopic cur-

rents in the pA-scale. In this technique, a fine pipette with a tip diameter of

1. Introduction 41

only of few µm is pressed against a cell membrane and a part of the mem-

brane is sucked into the pipette. In this way Neher and Sakmann [66] were

able to trap ion channels in the membrane and make single channel record-

ings. They were awarded the Nobel price for their efforts in 1993. A single

ion channel conducts about 10 million ions per second which corresponds to

a few pA. Ion channels are implicated in many diseases and are a major drug

target [36].

1.6.2 Artificial Ion Channels

Artificial ion channels might be used to build artificial molecular machines

and nanometer devices [13]. A few artificial ion channels were already cre-

ated [13, 6, 101, 102]. Flomenbom and Klafter [24] discuss single stranded

DNA movement through a nanopore and a possible application as a new

fast sequencing method. Further, artificial ion channels might be suitable

for monitoring mRNA (messanger ribonucleic acid) in vivo by recording a

current spectrum when the mRNA passes through an artificial nanopore.

1. Introduction 42

1.7 Presentation of a Problem

1.7.1 DNA Crystallization

Preliminary steps to 3D assembly have been performed in Prof. Seeman’s

laboratory. Crystallization attempts with the TX and DX motifs were under-

taken. Further crystallization attempts to be undertaken can be categorized

into the following categories:



Further crystallization attempts of known and already examined motifs



Development and application of new crystallization techniques



Development of new motifs for sticky ended DNA crystallization

The overall goal is to achieve a system that assembles via sticky ends

reproducible and in a designed fashion into a 3 dimensional crystal lattice

that shows diffraction, when exposed to x-rays, down to a high resolution (≤

3˚

A).

1.7.2 6 Helix Bundle as an Artificial Ion Channel

Preliminary experiments with six DNA dublexes, connected by crossovers,

that can self assemble into a hollow bundle have been performed and a tube

like structure could be observed, consisting of the annealed 6 helix bundle

and connected by sticky ends [62], see section Materials and Methods for

further description of the motif and pictures (section 2.6). This motif was to

be redesigned to explore it’s possible application as an artificial ion channel.

Chapter 2

Materials and Methods

2.1 Design of New Molecules

2.1.1 De novo Design of Sticky Ends

Sticky ends are normally obtained through DNA digestion by restriction

enzymes, a basic process used in genetic cloning [100]. Sticky ends obtained

from digestion with restriction enzymes have the disadvantage that they

are self-complementary because most restriction enzymes cut palindromic

sequences. For building defined structures with DNA molecules the sticky

ends were designed de novo applying the following rules:



All sticky ends should be the same length (number of nucleotides)



same GC

AT content



reaction energy ∆G for different sticky ends differs by less than 30%



never more than two guanosines in a stretch



not self-complementary

2. Materials and Methods 44

The free reaction energy of all sticky ends designed in this thesis were

calculated with the HyTher



webpage, described by Santa Lucia [72, 79].

2.1.2 De novo Design of DNA Sequences

New sequences were engineered using the SEQUIN program. The SEQUIN

(assign nucleic acids SEQuences INteractively) program is based on the so

called CRITON-SEEMAN algorithm [82] which uses CRTION elements for

the new assignment of nucleotides. The program is written in FORTRAN77

by Prof. Seeman and was run on a SGI ORIGIN 200 workstation with 4 x

180 MHz IP27 RISC processors and 256 MB RAM.

2.1.3 DNA Junctions

For the branch points in new motifs the well known and characterized junc-

tion J1 (see fig. 1.13) was used if possible or symmetry minimized junction

to prevent branch migration.

2.1.4 Computer Aided molecular modeling

The computer program GIDEON, written by Jeffrey Birac, was used for

computer aided design of new motifs (to be published). It was run on dual

processor G4 Mac computers.

2. Materials and Methods 45

2.2 From DNA Synthesis to Annealing of Mo-

tifs

2.2.1 DNA Synthesis

All strands were synthesized on an Applied Biosystems 380 B, an Applied

Biosystems 394 DNA/RNA, a PerSeptive Biosystems Expedite automatic

DNA synthesizer or obtained from IDT Integrated DNA Technologies and

deprotected for at least 24 hours in 10 ml ammonium hydroxide solution at



2.2.2 Denaturating Gels and DNA Purification

All used DNA strands were PAGE purified. The denaturating gels contained

8.3mol

lurea, were run at 55



and contained between 10% and 20% acrylamide

(19:1 acrylamide:bisacrylamide), depending on the length of the sequences.

Gels were run on at 28.6 V

cm with constant voltage (for running and sample

buffer see tbl. 2.1). The bands were visualized with ethidium bromide and

UV light, the target band was cut out and eluted over night in a 1.5 ml

reaction tube in elution buffer (see tbl. 2.1). The elution buffer with the

eluted DNA was butanol extracted 6 times to remove ethidium bromide

traces. The aqueous solution was added to a new tube and ethanol was

added (3:1). The DNA was finally precipitated by incubation of the tubes in

dry ice for one hour, spun at 14,000 g for 30 minutes, the supernatant was

discarded, the DNA dried and resuspended in double distilled water, filtered

though a 0.22 µm filter and dialyzed in a mini dialysis unit from PIERCE

(Slide-A-Lyzer



3500 MWCO) over night.

2. Materials and Methods 46

Table 2.1: Buffer compositions

Buffer Ingredients

Running buffer pH 8.0 89 mM TrisHCl

89 mM boric acid

2 mM EDTA

Sample buffer 10 mM NaOH

1 mM EDTA

0.1 % xylene cyanol as a tracking dye

Elution buffer pH 8.0 500 mM Ammonium acetate

10 mM [CH3COO]2Mg*4 H2O

2 mM EDTA

2.2.3 Native Gels (Non-Denaturating Gels)

Native gels contained between 4 % and 10 % acrylamide (19:1, acrylamide:

bisacrylamide) and were run with 10-14 V

cm (constant voltage) at room tem-

perature (21



), for sample and running buffer see tbl.2.2. The bands were

visualized with stainsall dye obtained from Sigma. pBR322 HaeIII digested

length marker from SIGMA (see Appendix tbl. 6.1) and/or 10 base pair lad-

der from Invitrogen



was used for native gel studies as a reference (10bp

ladder contains DNA fragments from 330 bp to 10 bp in 10 pb steps, the

fragments 100 bp and 330 bp appear three times brighter on a gel).

2. Materials and Methods 47

Table 2.2: Buffer compositions

Buffer Ingredients

Sample buffer pH 8.0 40 mM TrisHCl

20 mM acetic acid

2 mM EDTA

12.5 mM magnesium acetate

Running buffer pH 8.0 40 mM Tris-acetate

2 mM EDTA

12.5 mM magnesium acetate

2.2.4 Stochiometry of DNA Strands

The optical density of each strand was measured after purification (2.2.2)

with a Spectronic Genesys 5 spectrophotometer at 260 nm wavelength. The

concentration of each strand was estimated with Lambert Beer’s law (1 OD

= 35 µl x g−1x cm−1) and an average molecular weight of 330 g x mol−1x

nucleic base−1. If necessary, the stochiometry was corrected by titrating pairs

of strands that should bind to each other by Watson-Crick base pairing. The

amount used of one of the strands was varied by using different volumes of

one of the strands (e.g. volumestrand1

volumestrand2:1

0.8,1

0.9... 1

1.4). The mixed strands were

annealed by the annealing protocol given in 2.5 and visualized by native

gel electrophoresis and Stains All



solution from SIGMA. The absence of a

monomer band was taken to indicate the titration end point.

2. Materials and Methods 48

2.2.5 Fast Annealing of Oligonucleotides for Native Gel

Based Studies

The strands that were to form a complex or an array were pipetted stoichio-

metrically (s. 2.2.4) into a reaction tube, buffer was added and the volume

finalized with double distilled, 0.22 µm filtered water. The reaction tubes

were then exposed to the following temperatures:





for 5 min.





for 15 min.





for 20 min.





(room temperature) for 20 min.

2.2.6 Slow Annealing of Oligonucleotides

The strands were stoichiometrically (see 2.2.4) mixed, buffer was added and

the volume finalized with double distilled, 0.22 µm filtered water. The tube

was closed with a clip, placed in a 2 liter vessel of boiling water for 2 minutes.

Then the vessel with the tube was transferred to a Styrofoam box (3.5 cm

wall thickness) and left there for 2-4 days. This slow cool down process was

intended to enable the strands to find their complements that correspond to

the lowest energy level and therefore form the desired motif or array.

2.3 Atomic Force Microscopy

2.3.1 Preparation of sample

5µl were carefully pipetetted onto the surface of a freshly cleaved piece of

mica (Ruby Red Mica Sheets from Electron Microscopy Sciences). After

2. Materials and Methods 49

adsorption times between 1 - 20 min., 5-6 drops of double distilled and 0.22

µm filtered water were carefully placed on the mica surface, forming a big

drop on the mica, stabilized by the surface tension. The mica was picked up

and the drop shaken off. A filter paper was moved to the edge of the mica,

removing the remaining liquid by capillary forces. The prepared sample was

examined under the AFM within the next ten minutes.

2.3.2 AFM Imaging

AFM imaging was done under isopropanol in a fluid cell on a NanoScope

IV model from Digital Instruments Inc.. Si3N4cantilevers with integral tips

coated from NanoProbes



Digital Instruments Inc. were used as scanning

tips.

2.3.3 Post Processing of AFM Pictures

All images were processed with the WSxM



computer software obtained from

Nanotec Electronica (http://www.nanotec.es). All AFM pictures were flat-

tened and the contrast was adjusted. All shown AFM pictures are comput-

erized close ups from AFM acquired data.

2.4 3D Assembly - DNA Crystallization

2.4.1 Hanging Drop Crystallization

Hanging drop crystallization was performed with 12 well crystallization plates

obtained from Hampton Research. The motif was pre-annealed (2.2.6) with

0.1 x Cacodylate buffer and 10 mM Mg2+. The crystallization buffer in

the well was 300 µl. 2 µl of the sample was pipetted on a siliconized glass

2. Materials and Methods 50

cover slide from Hampton research and 2 µl of the same buffer as in the

well was added to the sample and mixed on the cover slide. Silicon Grease

from DOW Corning was put between the side of the well and the cover

slide was pressed on the grease with the sample on the bottom of the cover

slide, the grease prevents any exchange with the outer atmosphere. The

DNA concentration in the sample (hanging drop) will increase due to vapor

diffusion until the concentration of salts, buffers and precipitant is the same

as in the well. The increase of DNA concentration will often force the DNA

to crystallize or precipitate. Hampton recommends a DNA concentration of

12 mg x ml−1, leading to a final concentration of 6 mg x ml−1. Dilution

series were done with each motif and concentrations between 24 mg x ml−1

and 1 mg x ml−1. The hanging drop crystallization technique was done

with TAE, HEPES and Cacodylate buffers in the presence of magnesium

ions. Further the Natrix Kit, a matrix of common crystallization conditions

was used [81]. The Natrix Kit, offered by Hampton Research, was used for

crystallization attempts of several motifs. It consists of 48 unique buffer,

salt and precipitant combinations, covering a broad range of solutions that

have already been successfully used to crystallize nucleic acids [81]. For the

composition of all 48 buffer solutions see Appendix 6.3.

2.4.2 Crystallization with Temperature Control

Crystal Annealing in Reaction Tubes

Crystals were annealed in buffer (either HEPES, TAE or Cacodylate with

Mg2+ concentrations from 10 mM to 100 mM) with the same protocol used

for 2D arrays (see 2.2.6). The DNA concentrations were between 1 µM and

4µM.

2. Materials and Methods 51

Crystallization with Hanging Drop and Temperature Control

In addition, a hybrid technique using parts of hanging drop crystallization

and crystallization with temperature control was used. The tile was pre-

annealed (2.2.6) with 0.1 x Caccdylate buffer and 10 mM Mg2+. A 12

well crystallization plate from Hampton was prepared the same way as de-

scribed in 2.4.1. A Petri dish with 45



water was put on the top over the

cover slides and the plate was put in an incubator (Torrey Pines Scientific

ECHOTherm



) at 45



and cooled down to 37



with 0.1

hour controlled

temperature decrease. The preheated Petri dish prevents condensation on

the cover slide caused by the higher water volume in the Petri dish compared

to the volume in the wells.

2.4.3 General Crystallization and Crystal Mounting

Techniques

Crystal Mounting in Loops

Crystals were transferred to different buffers with increasing content of anti-

freeze (e.g. PEG, Glycerol, (NH4)2SO4) to prevent the formation of water

crystals during flash cooling. When the crystal environment reached the fi-

nal anti-freeze agent concentration, the crystal was captured under a light

microscope with a loop (CryoLoop



from Hampton Research) and put im-

mediately in liquid nitrogen for 30 seconds. Finally the loop was put into a

cap (CrystalCap from Hampton Research) and stored in liquid nitrogen until

exposed to x-rays.

2. Materials and Methods 52

Crystal Mounting in Capillaries

Crystals were sucked into a capillary (Quartz capillaries from Hampton Re-

search, different diameters), pretreated with SigmaCoat (SIGMA).The liquid

around the crystal was removed with a micro wick (Hampton Research). A

small reservoir of buffer was kept in the capillary to prevent the crystal from

drying. The capillaries were sealed and kept at 20



until exposed to x-rays.

The crystal mounting technique is shown in appendix fig. 6.2 and fig. 6.3.

2.4.4 X-Ray Examination of DNA Crystals

All crystals were examined by x-rays at the National Synchrotron Light

Source, department of energie (NSLS Brookhaven/Long Island). The diffrac-

tion was collected at the National Light synchrotron beamline X8C on a

MarCCD collector. The wavelength was 1.1˚

A exposure times were between

2 and 20 minutes.

2.5 Crystallization Experiments

2.5.1 3D Assembly with TXA Tiles Under High Mag-

nesium Ion Concentration

The TXA (fig. 1.20) motif for 3D assembly is a modified version of the TXA

motif that was developed in my master thesis [45]. The middle helix was

cut to allow 3D assembly by connecting to another, 90

rotated TXA via

sticky ends (see fig. 1.33). The modified design, the sequence assignment

and the design of the sticky ends were made by Pamela Constantinou. Crys-

tals were obtained but diffracted at low resolution. The same motif was to

be used for crystallization experiments with higher magnesium ion concen-

2. Materials and Methods 53

tration. The experiments performed should examine the possibility of aiding

3D assembly by increasing magnesium ion concentrations (50 mM and 100

mM Mg2+ instead of 10 mM Mg2+). The crude strands for the TX motif

were obtained from Pamela Constantinou, purified (2.2.2) and slow annealed

(2.2.6) with Caccdylate buffer and 4 µM DNA tile concentration. In addition

a crystallization attempt with a hanging drop/annealing combination (2.4.2)

was done with Cacodylate Buffer and the Natrix Kit. For sequences see Ap-

pendix 6.12.2, for sticky end sequences properties see Appendix (Tbl. 6.4).

2.5.2 2D-Assembly of DX Molecules with Short Sticky

Ends

After many unsuccessful sticky ends guided crystallization attempts with

different motifs the question arose how many nucleotides are sufficient for 3

dimensional assembly. To answer this question the well known and character-

ized DX motif was modified and equipped with sticky ends consisting of only

3 nt to see if this will be enough to form a 2-dimensional array. The sequences

were designed according to sections 2.1.1, 2.1.3 and 2.1.2, synthesized and

purified according to sections 2.2.1 and 2.2.2, slow annealed(2.2.6, HEPES,

10 mM Mg2+), AFM examined (2.3.1,2.3.2) and the pictures post processed

(2.3.2). For sequences see Appendix 6.12.1, for sticky end sequences and

properties see Appendix, Tbl. 6.7.

2.5.3 Crystallization Attempt of Blunt Ended DX Tiles

Due to difficulties obtaining x-ray diffraction via sticky ended interactions,

a blunt ended DAE tile was to be examined. A resolved crystal structure

would reveal any bending or torsion stress within the tile. It was designed

2. Materials and Methods 54

according to sections 2.1.1, 2.1.3 and 2.1.2, synthesized and purified according

to sections 2.2.1 and 2.2.2. A crystallization attempt was made with the

hanging drop crystallization technique (2.4.1), selected crystals were mounted

in loops (2.4.3) and exposed to x-rays (2.4.4). For sequences and brominated

sequences see appendix 6.12.3.

2.5.4 3D Assembly and Gel Studies of Chengde Mao

Triangles

Gel Based Studies of Blunt Ended ChengdeMao Triangles

A new motif for DNA Nanotechnology was invented by Prof. Chengde

Mao [55] from Purdue University. The motif takes into account that DNA

crystals prefer to grow in the direction of the helical axis (an example of

one CDM triangle is given in fig. 2.1). The DX and TX motifs used for 3D

assembly have the disadvantage that they have to grow in one direction per-

pendicular to the helical axis. The triangle of Prof. Mao fills 3 dimensional

space with a helical axis growing in all three dimensions. Unfortunately

the motif seemed to be unstable when examined by native PAGE. A crys-

tallization attempt based on a triangle with 2 full turns between triangles,

16 nt per triangle edge and an assumption of 10.5 nt per DNA full turn

with the Natrix kit done by Prof. Mao gave crystals with well defined faces.

When exposed to x-rays in the Brookhaven National Light Synchrotron they

showed diffraction but the wrong space group. Dr. W. Sherman performed

calculations concerning the CDM triangles and their geometrical properties

(s. appendix 6.11). Based on these assumptions 5 blunt ended triangles

(13 nt, 14 nt, 15 nt, 17 nt and 18 nt per inner triangle edge) were designed

according to sections 2.1.3 and 2.1.2, synthesized and purified according to

2. Materials and Methods 55

Table 2.3: Triangles designed and synthesized based on a basic design by

Prof Chengde Mao

Name of nt per inner assumed full turns length of triangle

triangle triangle edge helicity between triangles sticky ends handedness

CDM-C 14 10.5 1 4 left

CDM-A 14 10.5 2 5 left

CDM-B 14 10.0 2 4 left

sections 2.2.1 and 2.2.2, slow annealed(2.2.6 with TAE 10 mM Mg2+) and

examined by native PAGE (s. 2.2.3).

3D Assembly with ChengdeMao Triangles with 14 nt per inner

triangle edge

Using the assumption of 14 nt per inner triangle edge three different triangles

were designed (see tbl. 2.3). Please note that the triangle with 14 nt per inner

triangle corresponds to a left handed triangle (s. fig. 2.2) based on the cal-

culations of Dr. Sherman (s. 6.11). The triangles were designed according to

sections 2.1.3 and 2.1.2, synthesized and purified according to sections 2.2.1

and 2.2.2. The crystallization attempts were made with slow annealing (1 x

Cacodylate Buffer, 10 mM Mg2+) and with a hanging drop/annealing com-

bination (2.4.2). Crystals obtained via hanging drop/annealing combination

were examined by x-rays(2.4.4) with a synchrotron. For DNA sequences see

appendix 6.12.6, for sticky end sequences and properties see 6.5.

2. Materials and Methods 56

Figure 2.1: Example of a CDM triangle with 17nt per inner triangle edge.

The basic design of this molecule was thought up by Prof.

Chengde Mao. If equipped with sticky ends then this motif can

assemble along each helical DNA axis and fill space.

Figure 2.2: DNA triangle handedness by Dr. William Sherman. The CDM

triangle can occur in two different conformations (left or right

handed), depending on the number of nt per inner triangle edge.

2. Materials and Methods 57

3D Assembly of a ChengdeMao Triangle with One Direction Blunted

A triangle system, as thought up by Prof. Chengde Mao, grows into three

axes along the helical axes. One direction was blunted to see how such

a system that is expected to grow only in 2 dimensions react to a crys-

tallization approach. For system CDM-A either strand CDM-S4-14A was

exchanged with strand CDM-S4-14A-BE or strand CDM-S6-14A was ex-

changed with strand CDM-S6-14A-BE. For system CDM-B strand CDM-

S1-14B exchanged with strand CDM S6-14B-BE. The strands were synthe-

sized and purified according to sections 2.2.1 and 2.2.2. The crystallization

attempts were made with slow annealing (1 x Cacodylate Buffer, 10 mM

Mg2+) and with a hanging drop/annealing combination (2.4.2). Crystals

obtained via hanging drop/annealing combination for system CDM-B were

examined via x-rays (2.4.4) with a synchrotron. For DNA sequences see

appendix 6.12.6.

2.5.5 3D Assembly with a TXDX Triangle Motif and

0D, 1D and 2D examination of the motif

Stimulated by the design of Prof. Chengde Mao a new triangle was thought

up that grows into space along the helical axes but is based on more rigid

motifs (DX, s. fig. 1.17 and TX, s. fig 1.20). The triangles inner motif

consists of three TX tiles, connected by bulged three arm junctions (2 per

edge). The triangle corners extend via a rigid DX motif to the next triangle.

The triangle is shown in fig. 2.3, a top view is given in fig. 2.4. Fig. 2.5 shows

a side view of a “sub-motif” of the trianlge. The trianlge consists of three of

such “sub-motifs”, connected with a skew. The “sub-motif” is only given for

better understanding, it does not show how the actual connections between

2. Materials and Methods 58

Figure 2.3: Computer generated model of a TXDX triangle tile. The motif

is shown in a blunt ended version.

the three “sub-motifs”. A drawing with the attached DNA sequence, the

position of the bulged 3arm connections is shown in the appendix (s. fig. 6.4).

The triangle motif could be designed that the strand nicks possess perfect

three fold symmetry but the nicks were set instead on positions that surround

the nick with G and/or C bases. The triangle was designed according to

sections 2.1.3, 2.1.2, 2.1.4, synthesized and purified according to sections 2.2.1

and 2.2.2. A blunt ended tile was examined on a native gel (2.2.3), 1D and 2D

arrays were AFM examined (1 X HEPES Buffer, 10 mM Mg2+, 2.3.1, 2.3.2).

Please note that there are 3 flavors for the 1D motif as well as for the 2D

motif (see section 6.8). All three possible flavors for 1D and 2D assembly were

examined. Crystallization attempts (3D) were made with slow annealing (1

x Cacodylate Buffer, 1 x TAE Buffer or HEPES Buffer, each had 10 mM

Mg2+) and with a hanging drop/annealing combination (2.4.2). For DNA

2. Materials and Methods 59

Figure 2.4: Top view of a computer generated model of a TXDX triangle tile.

Figure 2.5: Computer generated model of one side of the TXDX triangle

tile. The TXDX triangle consists of three of such “sub-motifs,”

connected with a skew. This “sub-model” lacks some strand nicks

of the actual TXDX triangle.

2. Materials and Methods 60

sequences see appendix 6.12.8, for sticky end sequences and properties see 6.6,

for pipetting strand combinations (how to get 0D, 1D, 2D and 3D motifs)

see appendix, section 6.8.

2.6 DNA Nanotube as an Artificial Ion Chan-

nel

2.6.1 Design of a DNA Nanotube for Use as an Arti-

ficial Ion Channel

Figure 2.6: End view of a computer generated model of the 6 helix bundle.

Six DNA helices are connected via cross-overs. Each helix has 9

full turns of DNA, the motif consits of 19 strands.

A motif can be constructed that links six helices together to form a bun-

dle or a tube. A version of this motif, containing six helices with 9 full turns,

connected by cross-overs that form a bundle has been designed by Prof.

2. Materials and Methods 61

Figure 2.7: Angled view of a computer generated model of the 6 helix bundle.

Six DNA helices are connected via cross-overs. Each helix has 9

full turns of DNA, the motif consits of 19 strands.

Seeman, preliminary experiments for 1D and 2D assembly were done by for-

mer student Frederick Mathieu. A new version was designed with GIDEON

(2.1.4) with an additional 4 cross-overs to increase the rigidity of the motif.

A GIDEON model of the motif is shown in fig. 2.6 and fig. 2.7. The modified

motif does not contain any sticky ends. An AT-rich sequence is placed out-

side of the three inner middle turns which in combination with netropsin, a

minor groove binder (see section 2.6.2) should make this region hydrophobic.

In this context, an AT-rich sequence shall be defined as consisting only of A’s

and T’s. The position of the outside sequence in the 6 helix bundle molecule

was found by computer aided molecular modeling with GIDEON. Three full

turns of each helix require eighteen 8 nt long AT-rich ds sequences. Further,

the AT-rich sequences should be unique to assure that the motif will form

2. Materials and Methods 62

properly. Each unique 8mer, flanked by G/C’s, consists of two unique 7mers.

Calculation of uniqe 8mer (example):



All possible 7mers were calculated and converted to binary code:

Decimal Binary Sequence Complemantary

015 0001111 5’AAATTTT 3’TTTAAAA

021 0010101 5’AATATAT 3’TTATATA

043 0101011 5’ATATATT 3’TATATAA

106 1101010 5’TTATATA 3’AATATAT



All sequences that contain more than three A or T in a row were elim-

inated:

021 0010101 5’AATATAT 3’TTATATA

043 0101011 5’ATATATT 3’TATATAA

106 1101010 5’TTATATA 3’AATATAT



All sequences that would oocur twice if the complementary sequences

are taken into account were eleminated:

021 0010101 5’AATATAT 3’TTATATA

043 0101011 5’ATATATT 3’TATATAA



18 uniqe 8mers were calculated (appendix tbl. 6.9), each consisting of

two uniqe 7mers:

A ATATAT A

All possible unique 8mers, fulfilling all restrictions, can be described with

2. Materials and Methods 63

regular expression1(see eqn. 2.1).

/[(A|T){8} − (AAAA|TTTT)]/(2.1)

All AT-rich sequences were assigned first, based on the calculated unique

8mer and the remaining molecule sequences were designed according to sec-

tions 2.1.3 and 2.1.2, synthesized and purified according to sections 2.2.1

and 2.2.2 and slow annealed (sec. 2.2.6, HEPES, 10mM Mg2+). The an-

nealed sample was either AFM examined (2.3.1, 2.3.2, 2.3.2), native gel ex-

amined (2.2.3) or used for tip-dip bilayer experiments (2.6.3). For DNA

strands sequences see section 6.12.7.

2.6.2 DNA Minor Groove Binder

Netropsin is known to bind the minor groove of DNA, the molecular formula

is shown in fig. 2.8. Several short ds DNA helices have been crystallized with

Netropsin [5]. It binds to the minor groove and is able to distinguish between

DNA sequences (appendix, tab. 6.3) and preferably binds to AT rich se-

quences. Neptropsin displaces the spine of hydration in the minor groove and

may make the DNA slightly hydrophobic. Resolvation of crystal structures

with netropsin show one netropsin molecule in the minor groove but NMR

(nuclear magnetic resonance) studies show that two netropsin molecules bind

to the AT-rich minor groove in solution [11]. Fig. 2.9 shows a stereoscopic

1Any description of a pattern composed from combinations of symbols and the three

operators: Concatenation - pattern A concatenated with B matches a match for A followed

by a match for B. Or - pattern A-or-B matches either a match for A or a match for B.

Closure - zero or more matches for a pattern. The earliest form of regular expressions (and

the term itself) were invented by mathematician Stephen Cole Kleene in the mid-1950s, as

a notation to easily manipulate “regular sets”, formal descriptions of the behaviour of finite

state machines, in regular algebra. Entry from Free Online Dictionary of computing [39]

2. Materials and Methods 64

Figure 2.8: Molecular structure of Netropsin∗.

Figure 2.9: Stereoscopic picture of a dsDNA Crystal structure with

Netropsin attached in the minor groove∗.

image of a resolved crystal structure of dsDNA with netropsin.

Netropsin was obtained from SIGMA and used in different concentrations,

based on the assumption of two bound netropsin molecules per 4mer (con-

sisting of A’s and T’s). For Tip Dip experiments, 100 µl (0.1 µM) of the 6HB

was slow annealed. After 24, hours netropsin was added into the tube with

the annealed sample and the tube was incubated for another 24 hours at

room temperature. Netropsin concentrations were between 0.5 and 8 times

2. Materials and Methods 65

total bundle saturation. The outer side of one turn consists of a 8mer AT-

rich sequence, 4 netropsin molecules are expected to bind for total saturation.

The bundle has three 8mers binding sites per helix and consists of 6 helices.

Hence for 1 mol 6HB 72 mol of netropsin are considered total bundle satu-

ration, based on the oversimplified model that every netropsin binds to the

expected binding site. The association constant for an AT-rich sequence is

107M−1, for a sequence containing GC is is only 104M−1

2.6.3 Tip Dip and Patch Clamp Experiments

The possible behavior of the 6HB as an ion channel was examined with tip

dip, following published protocols [92, 33]. A 6 cm long silver wire was

cleaned with a scourer and AgCl coated via electrolysis in a 1 M AgCl solu-

tion. The silver wire was mounted into the tip and a pulled glass capillary

(Sutter Instrument Corporation, Model P-87 Micropipette puller, Capillar-

ies: World Precision Instruments Inc. Glass 1mm, 4in Item 1B100F-4), filled

with HEPES buffer (1 M KCl for symmetric, 150mM KCl for asymmetric

conditions) was put over the silver wire into the tip. A well of a 96 well

microtiter plate was filled with buffer(1 M KCl, HEPES pH 7.4) and 1 µl of

a n-decane/lipid (soy phosphatidylcholin from Avanti Lipids Inc.) mixture

was layered on top of the filled well. The tip was lowered and raised into the

solution with a Brinkmann micromanipulator. If raised two times into the

solution with the lipid layer, a lipid bilayer may form on the tip (s. fig. 2.10),

characterized by current insulating behavior. The whole system was insu-

lated against noise with a metal case by WARNER Instrument Corporation

and with a BenchMate 2200 vibration free platform.

The voltage-clamp recordings were made with a 3900A Integrating Patch

Clamp (Dagan, Minneapolis, MN). Signals were monitored with a Tektronix

2. Materials and Methods 66

Figure 2.10: The tip dip method. Ion channels can be reconstituted into bi-

layers formed at the tip of a microelectrode in a method called

tip-dip. A microelectrode is submerged in a bath. Lipids (typi-

cally in an organic solvent like decane) are layered on top of the

bath and allowed to form a monolayer on the bath surface (A).

The microelectrode is raised out of the bath (B). A bilayer is

formed like a sandwich as the microelectrode is again returned

to the bath (C). Channels are added to the bath and insert

spontaneously (not shown).∗∗

2. Materials and Methods 67

TDS 320 Two Channel Oscilloscope, a Tektronix 2201 Digital Storage Oscil-

loscope and filtered at 1 kHz with the four-pole Bessel low-pass filter. The

output was channeled into a DIGIDATA 1322A (Axon Instruments) and the

digital output signal was visualized and stored using Clampex 8.2 software

(Axon Instruments, run on a Dell Pentium 4 1.8 GHz 512 MB Ram and

Windows XPp). Ohmic behavior was recorded under symmetric and asym-

metric conditions with the Tektronix TDS 320, noise analysis was done with

WinEDR (public domain Strathclyde Electrophysiology Software package,

supplied free of charge to academic users by Dr. John Dempster, of the

University of Strathclyde in Glasgow, U.K.). Control experiments were done

with the same 6HB but without the presence of netropsin. Further controls

were done with netropsin alone and a 90mer dsDNA helix.

Chapter 3

Results

3.1 3D Assembly - DNA Crystallization

3.1.1 3D Assembly with TX Tiles Under High Magne-

sium Ion Concentration

Fig. 3.1 shows TX crystals, obtained by slow annealing in Cacodylate buffer

(4 µmol DNA concentration, 100 mM Mg2+). The crystals are needle shaped

and roughly 50µm in length. The crystals singly extinguished under plane

polarized light but showed no diffraction when exposed to x-rays. Fig. 3.2

shows TX crystals, obtained by a slow annealing - hanging drop combina-

tion 2.4.2 with Natrix buffer number 5 and 4 µmol DNA concentration. The

crystals look feather shaped. The size of the crystals is up to 0.5 mm in

length. The crystals singly extinguished under plane polarized light but

showed no diffraction when exposed to x-rays.

3. Results 69

Figure 3.1: Light microscope picture of annealed TX crystals under polarized

light

Figure 3.2: Light microscopy picture of TX crystals grown with a combina-

tion of slow temperature decrease and hanging drop vapor diffu-

sion.

3. Results 70

3.1.2 2D-Assembly of DX Molecules with Short Sticky

Ends

At room temperature no arrays out of a two tile TX system could be observed

with AFM. When the sample was annealed down to 4



arrays were found.

Fig. 3.3 shows an array and fig. 3.4 a computerized close up. The expected

distance between the hairpin loops was 33 nm. 34.8 nm were measured and

32.9 nm were found via a FFT analysis.

Figure 3.3: AFM picture of a DX array with short sticky ends. Picture scale

1.1 µm x 1.1 µm

3. Results 71

Figure 3.4: AFM picture of a DX array with short sticky ends. Picture scale

595 nm X 595 nm

3. Results 72

3.1.3 Crystallization Attempt of Blunt Ended DX Tiles

Figure 3.5: Light microscope picture of a crystallization attempt via hanging

drop vapor diffusion of a blunt ended DX tile (upper part of the

drop). Crystals were grown in Natrix kit buffer 26.

For the crystallization attempt with the Natrix kit (see appendix 6.3) the

following results were obtained after 5 days: needle shaped crystals in buffers

5 and 6, needle shaped crystals and a graph like structures (in the lower drop)

were found in buffers 10, 17, 25 and 26 (fig. 3.5 and 3.6). Very thin, hair like

crystals were found in Natrix buffer 44 (fig. 3.7). All other buffers showed

a clear drop or precipitate. The needle shaped crystals singly extinguished

under plane polarized light but showed no diffraction when exposed to x-rays.

3. Results 73

Figure 3.6: Light microscope picture of a crystallization attempt via hanging

drop vapor diffusion of a blunt ended DX tile (lower part of the

drop). Crystals were grown in Natrix kit buffer 26.

Figure 3.7: Light microscope picture of a crystallization attempt via hanging

drop vapor diffusion of a blunt ended DX tile. Crystals were

grown in Natrix kit buffer 44.

3. Results 74

3.1.4 3D Assembly and Gel Studies of ChengdeMao

Triangles

Gel Based Studies of Blunt Ended ChengdeMao Triangles

Figure 3.8: Picture of a gel (5% polyacylamide) study of CDM triangles with

13 nt and 14 nt per inner edge. Lane 1 contains HaeIII digested

pBR marker, lanes 2-5 show the 13 nt triangle with a logarithmi-

cally decreasing concentration from 12 µM to 1.5 µM, lanes 6-9

show the same for the 14 nt triangle. 10 µl were loaded.

Fig. 3.8 shows a native gel study of ChengdeMao triangles with 13 and

14 nt per inner triangle edge. Lane 1 shows pBR marker, lanes 2-5 show the

13 nt triangle with a logarithmically decreasing concentration from 12 µM to

1.5 µM, lanes 6-9 show the 14 nt triangle with decreasing concentration from

12 µM to 1.5 µM. Fig. 3.9 shows the native gel examination of the 15 nt per

inner edge ChengdeMao triangle (Lane 1 shows pBR marker, lane 2-5 CDM

triangle, 12 µM to 1.5 µM logarithmic concentration series). Fig. 3.10 shows

the native gel examination of the 17 nt and 18 nt per inner edge ChengdeMao

triangle (Lane 1 shows pBR marker, lane 2-5 show the 17 nt triangle, lane 6-9

3. Results 75

Figure 3.9: Picture of a gel (5% polyacylamide) study of CDM triangles with

15 nt per inner edge. Lane 1 contains HaeIII digested pBR

marker, lanes 2-5 CDM triangle, 12 µM to 1.5 µM logarithmic

concentration series). 10 µl were loaded..

show the 18 nt, both with logarithmically decreasing concentration from 12

µM to 1.5 µM). All triangles show lower bands (bands below the molecular

weights of the triangles). Significant upper bands are seen for the 13 nt and

the 15 nt triangles.

3D Assembly with ChengdeMao Triangles with 14 nt per inner

triangle edge

Fig. 3.11 shows the plate like crystals that were obtained from a ChengdeMao

Triangle system, based on the assumption of 10.5 nt per helical turn, 14 nt

per inner triangle edge, sticky ends consisting of 5 nt, and 2 full helical turns

in between triangles. The sample in Fig. 3.11 was crystallized with Natrix

Buffer 5 (see appendix 6.3) and a combination between hanging drop and

slow temperature decrease (see 2.4.2). Similar plate crystals were obtained

3. Results 76

Figure 3.10: Picture of a gel (5% polyacylamide) study of CDM triangles

with 17 nt and 18 nt per inner edge. Lane 1 contains HaeIII

digested pBR marker, lanes 2-5 show the 17 nt triangle, lanes

6-9 show the 18 nt, both with logarithmically decreasing con-

centration from 12 µM to 1.5 µM. 10 µl were loaded.

with Natrix buffer solutions 4,6,9 and 31 (see appendix 6.3). Fig. 3.12 shows

the diamond like crystals that were obtained from a ChengdeMao Triangle

system (10 nt per helix full turn, 14 nt per inner triangle edge, sticky ends

consisting of 4 nt, 2 full helical turns in between triangles). The sample in

Fig. 3.12 was crystallized with Natrix Buffer 45 (see 6.3) and a combination

between hanging drop and slow temperature decrease (see 2.4.2). Similar

plate crystals were obtained with Natrix buffer solutions 1,2,11,12,13,18,19

and 40 (see 6.3). Fig. 3.13 shows the crystals that were obtained from a

ChengdeMao Triangle system (10.5 nt per helix full turn, 14 nt per inner

triangle edge, sticky ends consisting of 4 nt, 1 full helical turn in between

triangles). The sample in Fig. 3.13 was crystallized with Natrix Buffer 19 (see

appendix 6.3) and a combination between hanging drop and slow temperature

3. Results 77

Figure 3.11: Light microscope picture of crystals from system CDM-A (po-

larized light). Crystals were grown in Natrix kit buffer 5.

Figure 3.12: Light microscope picture of crystals from system CDM-B (po-

larized light). Crystals were grown in Natrix kit buffer 45.

3. Results 78

Figure 3.13: Light microscope picture of crystals from system CDM-C (po-

larized light). Crystals were grown in Natrix kit buffer 19.

Figure 3.14: X-ray diffraction pattern form a CDM-A triangle system

3. Results 79

Figure 3.15: X-ray diffraction pattern form a CDM-B triangle system.

decrease (see 2.4.2). It was the only buffer ever showing crystals for system

CDM-C. The crystallization process of this system was repeated several times

but could never be reproduced.

Fig. 3.14 shows a diffraction pattern collected from system CDM-A. Cell

dimensions were a=132 ˚

A, b=133 ˚

A and c=135 ˚

A. α , β , γ are 108.4

that

is close to a rhombohedral/hexagonal cell. The resolution is about 12 ˚

Fig. 3.15 shows a diffraction pattern collected from system CDM-B. The cell

dimensions are around 350 ˚

A with another axis of 65 ˚

A or 130 ˚

A. Resolution

down to 13 ˚

A was achieved. Expected were 109

,a rhomohedral cell and cell

dimensions of 142.8 ˚

3. Results 80

3D Assembly of a ChengdeMao Triangle with One Direction Blunted

Figure 3.16: Light microscope picture of crystals from system CDM-B1BE

(polarized light). Crystals were grown in Natrix kit buffer 19.

Fig. 3.16 shows the diamond like crystals that were obtained from a CDM-

B1BE Triangle system (10 nt per helical full turn, 14 nt per inner triangle

edge, sticky ends consisting of 4 nt, 2 full helical turns in between triangles)

with one direction blunted (one assembly direction out of three was blunt

ended, Strand CDM-S1-14B exchanged with strand CDM S1-14). The sam-

ple in Fig. 3.16 was crystallized with Natrix Buffer 19 (see appendix 6.3)

and a combination between hanging drop and slow temperature decrease

(see 2.4.2). Similar plate crystals were obtained with Natrix buffer solutions

11,13 and 40 (see appendix 6.3).

For system CDM-A1BE (based on System CDM-A with one assembnly direc-

tion blunted), no single extinguishing crystals could be obtained. Fig. 3.17

shows a composite of 10 collected diffraction patterns (each 2

, 20

total). The

3. Results 81

Figure 3.17: Composite of 10 X-ray diffraction patterns collected from sys-

tem CDM-B1BE

periodicity is around 110 ˚

A to 115 ˚

A in two directions and around 680 ˚

A in

the 3rd dimension with a pseudo lattice with distances of approximately 340

A. The lower left part of the pictures is lost due to a detector malfunction.

3. Results 82

3.1.5 3D Assembly with a TXDX triangle motif and

0D, 1D and 2D examination of the motif

Gel Studies of a TXDX Triangle Motif Blunted “Around the Clock”

(0D)

Figure 3.18: Picture of a gel (5% acrylamided) study of the TXDX trian-

gle motif. The motif is blunted “around the clock.” Lane 1

shows HaeIII digested pBR marker, lane 2 the 10 bp ladder

marker, lanes 3-8 contain a logarithmic concentration series of

the blunted TXDX triangle 0.1 µM - 2 µM. 10 µl were loaded.

Fig. 3.18 shows the TXDX triangle, all sticky ends are blunted (“blunted

around the clock”, 0D). Lane 1 contains pBR marker, lane 2 contains 10bp

ladder, lanes 3-8 contain a logarithmic concentration series of the blunted

TXDX triangle 0.1 µM - 2 µM, 10 µl were loaded. In well 7 and 8 upper

bands (relative to the band that corresponds to the intact triangle motif)

3. Results 83

and material that remained in the wells can be seen.

AFM examination of 1D and 2D arrays of the TXDX triangle motif

Figure 3.19: Atomic force microscopy picture of 2D arrays consisting of

TXDX triangles (flavor A).

At first no 2D TXDX triangle arrays could be observed but 1D arrays

could be produced in all possible versions (data not shown). With an increase

from 2 minutes to 20 minutes adsorption time on the mica surface 2D arrays

with all three flavors could be produced. Fig. 3.19 shows a 2D array with

flavor A, fig. 3.20 flavor B and fig. 3.21 flavor C. The expected distances,

based on 3.6 nm per DNA helical full turn is approximately 28 nm. Distances

found by measurement over several (7-10) triangle lines and distances found

3. Results 84

Figure 3.20: Atomic force microscopy picture of 2D arrays consisting of

TXDX triangles (flavor B)

by FFT analysis are given in tbl. 3.1. For each triangle flavor, 2 directions

were measured (x and y). Please note that, according to the design of the

molecule, x and y should be same. The given numbers correspond to the

inner diameters of the rhombus like area that is defined by four triangles.

The actual triangles could be resolved in some pictures (see fig. 3.22, flavor

B).

3D Assembly with TXDX Triangles

All drops of the Natrix Kit were either clear or showed precipitate. Annealing

in HEPES, TAE and Cacodylate buffer with 10 mM Mg2+ did not give singly

3. Results 85

Figure 3.21: Atomic force microscopy picture of 2D arrays consisting of

TXDX triangles (flavor C)

extinguishing crystals when viewed with plane polarized light.

3. Results 86

Table 3.1: TXDX Triangle distances

Flavor Distances measured [nm] Distances found per FFT [nm]

Flavor A x 31.1 31.8

Flavor A y 31.6 31.8

Flavor B x 26.6 29.4

Flavor B y 29.4 29.6

Flavor C x 28.0 29.6

Flavor C y 27.6 32.1

Figure 3.22: Atomic force microscopy picture of 2D arrays consisting of

TXDX triangles flavor B

3. Results 87

3.2 DNA Nanotubes

3.2.1 DNA Nanotube for Use as an Artificial Ion Chan-

nel

Figure 3.23: Current trace at 50 mV showing ion channel behaviour (800

pS transitions). Sample contained 5 µl 6HB (0.1 µM) and 1 x

Netropsin bundle saturation.

Fig. 3.23,fig. 3.24 and fig. 3.25 show recorded channel behaviour. These

results were recorded with -50 mV voltage applied to the system and one time

netropsin binding site saturation (see calculation in section 2.6.2). Fig. 3.23

shows typical ion channel behaviour, the step sizes are around 40 pA that

corresponds to 800 pS. Fig. 3.24 from the same recording shows 800 pS

transitions on top of a 800 pS baseline. After approximately 14 seconds

(based on the figure, the shown recording is an exported time frame out of

a longer recording) the bilayer seems to be disturbed and something is seen

that could be interpreted as 2 nS transitions. Fig. 3.25 shows a recording

(-50mV, 1x bundle netropsin saturation) that shows a broader range of tran-

3. Results 88

Figure 3.24: Current trace at 50 mV showing ion channel behaviour (800 pS

and 2 nS transitions). Sample contained 5 µl 6HB (0.1 µM) and

1 x Netropsin saturation.

Figure 3.25: Current trace at 50 mV showing ion channel behaviour (200 pS,

600 pS and 1 nS transitions). Sample contained 5 µl 6HB (0.1

µM) and 1 x Netropsin saturation.

sitions. Transitions of 200 pS, 600 pS and 1 nS were observed. Often a

bilayer was created (seal test showed insulating behaviour) and immediately

current (corresponding to 400 pS to 2 pS) flow was observed but no transi-

tions. During this current flow IV (current-voltage) curves were collected that

3. Results 89

showed strong ohmic behaviour (data not shown) with the bundle. If the IV

curve was taken under unsymetrical ion conditions cation selective behaviour

was observed. Control experiments were done with the 6 helix bundle but

without netropsin. Current flow in similiar range but fewer transitions were

observed. In bilayer tip-dip experiments with a single 90mer dsDNA helix

very few transitions were observed. The experiments with netropsin and no

DNA suggest that netropsin can disturb lipid bilayers. 200 pS transitions

were observed under all conditions and even with a lipid bilayer membrane

without any further substance.

Chapter 4

Discussion

4.1 Crystallization Experiments

4.1.1 3D Assembly with TX Tiles Under High Magne-

sium Ion Concentration

Singly extinguishing crystals were obtained that indicate periodic organi-

zation of the samples down to 400 nm. No diffraction was observed when

exposed to x-rays. This suggests disorder on a molecular level.

A key observation from this experiment was that much bigger crystals were

obtained by a combination of hanging drop and temperature annealing than

by hanging drop or temperature decrease alone.

4.1.2 2D-Assembly of DX Molecules with Short Sticky

Ends

2D Arrays consisting of DX molecules with short sticky ends were success-

fully produced when annealed down to 4



. This proves that four 3mer sticky

ends are sufficient to hold the array, as designed, together at lower temper-

4. Discussion 91

atures. Based on this discovery it was assumed that a 3D array that self

assembles with four 4mers in 2D and two 3mers in the 3rd dimension should

hold together at room temperature, especially if cooperativity is taken into

account.

4.1.3 Crystallization Attempt of Blunt Ended DX Tiles

Blunt ended crystals out of DX tiles gave singly extinguishing crystals with

the Natrix kit. This indicates a periodic organized matter of the sample down

to 400 nm, the lack of diffraction, when exposed to x-rays, suggest disorder

on a molecular level. Pamela Constantinou obtained similar results with a

crystallization approach of a blunt ended TX motif.

4.1.4 3D Assembly and Gel Studies of ChengdeMao

Triangles

Gel Based Studies of Blunt Ended ChengdeMao Triangles

ChengdeMao Triangles with different number of nucleotides per inner tri-

angle edge were examined via nondenaturating gel electrophoresis. These

studies showed that triangles with 14, 17 and 18 nt per inner triangle edge

have little to no material above the target band (complete single triangle).

This fits surprisingly well to the optimal nucleotide number per inner triangle

edge as predicted by the calculations of Dr. William Sherman. Numbers of

nucleotides per inner triangle edge that do not correspond to these geometri-

cal requirements may put torsional stress on the motif and may yield triangle

multimers. All lower bands (below the complete single triangle motifs) are

due to incorrect triangle strand stochiometry.

A system based on ChengdeMao triangles has proved to be quite difficult for

4. Discussion 92

the creation of two dimensional arrays but 2D assembly was finally reported

by Prof. Chengde Mao with a triangle system [55].

3D Assembly with ChengdeMao Triangles with 14 nt per inner

triangle edge

Singly extinguishing crystals were obtained from system CDM-A and CDM-

B. Both showed diffraction when exposed to X-rays down, system CDM-A

down to 12 ˚

A and system CDM-B down to 20˚

A. The collected data were

not sufficient to resolve the molecular structure. Especially little conclusion

could be drawn about the 3rd dimension. No definite conclusions can be

drawn about the assembly but the ingredients of the Natrix kit moderate

DNA helix backbone to backbone interactions. Hence an assembly in two

directions (2D) via sticky ends and an assembly in the 3rd dimension by

stacking might be possible. Pamela Constantinou got diffraction down to

10˚

A with her ChengdeMao triangle version, based on 17nt per inner triangle

edge.

3D Assembly of a ChengdeMao Triangle with One Direction Blunted

System CDM-B1BE gave singly extinguishing crystals that showed diffraction

when exposed to x-rays down to 20˚

A. This is interesting because the system

is designed to assemble only in two dimensions. This might be further indica-

tion that assembly in the 3rd dimension is not guided by sticky ends. System

CDM-B1BE gave singly extinguishing and diffracting crystals in contrast to

system CDM-A1BE . In the crystallization attempt of the one-side-blunted

CDM triangle motif, the strand in system CDM-B1BE was blunted that cor-

responds to the side where the nick of the inner triangle DNA resides. It can

not be excluded that this played a major role in the successful crystal for-

4. Discussion 93

mation. On the other hand a 3D assembly approach, undertaken by Pamela

Constantinou, with a CDM triangle (sticky ends for all three directions, 18nt

per inner triangle edge) with an inner strand containing nick symmetry (the

strand is cut down to three strands, hence 3 nicks instead of one) showed

no different behavior (same diffraction) compared to her original design with

only one nick.

Fractal Assembly with ChengdeMao Triangles

Figure 4.1: Sierpinsky carpet. A 2D fractal derived from a square by cutting

it into 9 equal squares with a 3-by-3 grid, removing the central

piece and then applying the same procedure ad infinitum to the

remaining 8 squares.

DNA fractals1were discussed by Erik Winree who used DNA tiles to

1Fractals are generally irregular (not smooth) in shape, and thus are not objects de-

finable by traditional geometry. That means that fractals tend to have significant detail,

visible at any arbitrary scale; when there is self-similarity, this can occur because “zoom-

ing in” simply shows similar pictures. Such sets are usually defined instead by recursion.

Wikipedia

4. Discussion 94

Figure 4.2: The Menger sponge or the Sierpinsky cube fractal‡is the 3D

version of the Sierpinsky carpet . It may be possible to assemble

a version of the sponge out of DNA.

self-assemble the boundary for 2 dimensional Sierpinski triangle [80]. Fractal

patterns represent an important class in DNA nanotechnology and prove

the ability to assemble complex and aperiodic matter. It was suggested by

Carbone and Seeman [10] that the 3 dimensional version of the Sierpinski

carpet2(see fig. 4.1), the Menger sponge (see. fig. 4.2) can be assembled

out of DNA with the ChengdeMao triangle motif and with aid of protective

groups.

2The Sierpinski carpet, named after Waclaw Sierpinski, is a fractal derived from a

square by cutting it into 9 equal squares with a 3-by-3 grid, removing the central piece

and then applying the same procedure ad infinitum to the remaining 8 squares. From

Wikipedia, the free encyclopedia.

4. Discussion 95

4.1.5 3D Assembly with a TXDX Triangle Motif and

0D, 1D and 2D examination of the motif

Gel studies of a TXDX Triangle Motif Blunted Around the Clock

(0D)

The non-denaturating examination (0D, see fig. 3.18) of the TXDX triangle

shows a clear band for concentrations up to 0.5 µM. A faint upper band

can be seen at 1 µM and 2 µM concentrations probably corresponding to

a dimer of the motif. For a motif of the size of the TXDX triangle (1260

nt) the behavior of the triangle on the gel is amazingly distinct. The dimer

band at the higher concentrations is not unexpected, if considered that 2 µM

concentration corresponds to aproximately 8 µg (10 µl per well) and that the

gel is heavily overloaded.

AFM Examination of 1D and 2D Arrays of the TXDX Triangle

Motif

Nice 2D arrays of the TXDX triangle have been produced. Initial difficulties

in observing arrays with the AFM can be explained by the different nature

of the motif relative to others that have produced 2D arrays observed by

AFM. It is a quite huge motif, but relative to its size, very little of the

motif hits the mica surface, especially if the skew of the motif is taken into

account. The motif minimizes surface (mica) contact and this might explain

why adsorption times up to 20 minutes on the mica surface were needed to

observe the arrays.

The measured distances are within the predicted length. Some arrays do

not seem to have perfect straight lines but it has to be considered that each

triangle hits the mica surface with half a floppy DX motif (with the blunted

4. Discussion 96

sticky ends), so it can not be excluded that this might induce some slight

disorder in the 2D array. Further the 2D arrays have two possibilities to

absorb on the surface. The geometry, as long as sequence independed, should

be the same. No differences in the pictures could be observed that would

suggest two geometries.

3D Assembly with TXDX Triangles

No crystals were obtained from the TXDX triangles. No ultimate explana-

tion can be given why no crystals could be produced. If the TXDX motif is

endowed with sticky ends in a different order, the system is predicted to as-

semble into hexagonal screw axis. A 3D assembly approach with the modified

motif might be undertaken in the future.

4.2 DNA Nanotube as an Artificial Ion Chan-

nel

R=l

σA (4.1)

G=1

R(4.2)

G=σA

l=σπr2

l(4.3)

G= 100 mS

3.14 1 nm2

30 nm ∼1nS (4.4)

Typical ion channel behaviour could be observed with the 6 helix bundle and

netropsin. In a comparison between the 6 helix bundle with and without

netropsin no definite conclusions could be drawn, especially if current flow

4. Discussion 97

and less transitions were compared. A noise analysis between current flow

through the bilayer membrane (no transitions, variance pA2against median

frequency Hz) showed no difference. If both systems show similar results

concerning current flow (with no transitions) the bundle with netropsin was

expected to show less noise due the hydrophonic part of the bundle. This

prediction was not observed. The 200 pA transitions that were always ob-

served suggest a contamination of the phospholipid. The disturbance of the

bilayer by netropsin alone should not be a big problem because most of it

is assumed to bind at the 6 helix bundle in solution. Goudet et al [30] re-

port that a non-peptidal fungal toxin can form ion channel-like structures in

presence of magnesium. Fortunately no channel like behaviour was recorded

with netropsin alone.

A rough calculation of the expected transition size can be done. We as-

sume the resistance of the ion channel formed by the 6 helix bundle with

length of the bundle divided through the conductivity of the solution times

the inner area of the bundle (eqn. 4.1). The conductivity is the reciprocal

value (eqn. 4.2). Eqn. 4.4 shows the calculation of the expected value (radius

1nm, length 30nm, conductivity of 1M KCl σ= 100 mS

cm ) of 1 nS. Transitions

around this value were observed and exciting data was collected but it still

can not be excluded at this stage that the observed current flow is due to

leaks in the lipid bilayer membrane and the transitions are artifacts. On

the other hand the recorded transitions (fig. 3.23 and 3.24) have definitive

ion channel behaviour. The cationic selective behaviour that was observed

is expected due to the anionic backbone of the DNA and might be a further

indication that the observed behaviour is caused by the 6 helix bundle.

4. Discussion 98

4.3 Conclusion and Outlook

4.3.1 3D Assembly

I prefer the term 3D assembly to the term crystallization if working with

a motif that fills space via sticky end guided assembly. In standard crys-

tallization of macromolecules, molecules are forced out of solution by over

saturation and lack of water molecules to assemble into a periodic close pack-

ing structure. None of the motifs used so far for sticky ended guided DNA

crystallization assembles by design into a close packed structure. The forces

that guide conventional crystallization might even fight the forces that are

supposed to enable the sticky ended 3D assembly approach.

One of the questions that remain unsolved is the helicity of DNA in such a

system. Crystallized B-DNA shows a helicity of 10.0 nt per helical full turn

but studies of DNA digestion with enzymes in solution suggest a helicity of

10.5 nt per helical full turn [76, 104]. 3D assembly with sticky ends migth

reveal which number is more appropiate. Diffraction from cystals were ob-

tained with designs assuming 10.0 nt per helical full turn and 10.5 nt per

helical full turn. A final system, diffracting down to high resolution, might

suggest a number in between those numbers or migth even show that such a

systam can be created with slightly different helicities.

Major steps in 3D assembly with DNA have been achieved in the last two

years. Starting with no motif available that assembles into a crystal that

shows any diffraction, crystals with resolutions down to 10 ˚

A are now rou-

tinely produced in in Prof. Seeman’s laboratory. DNA crystals, diffracting

down to a few ˚

A seem to be within reach. They could be used to trap

biomolecules that are hard to crystallize and might revolutionize the field of

macromolecule crystallization. Further, applications in telecommunications

4. Discussion 99

as photonic crystals[113, 112, 43] might be possible.

4.3.2 6 Helix Bundle

Ion Channel

Promising data has been collected in the ion channel experiments that could

suggest ion channel behavior. Still, too many unknown factors forbid any

final conclusions at this stage. Further experiments are under way and might

offer more insight.

Outview to New Motifs based on the 6 Helix Bundle

Figure 4.3: A paralellogram consisting of four 6 helix bundles. This might

be a promising motif because it may offer the possibility to cross

conductor paths on a nanometer scale.

4. Discussion 100

A parallelogram, made out of 6 helix bundles could be used to assemble

2d DNA Arrays and the inner bundle could be filled with a conductor like

NanoGold



. Concerning the inner diameter of the 6HB it should also be

possible to incorporate single walled carbon nanotubes inside the bundle.

Due to the geometric properties of a possible 6 helix bundle parallelogram it

would be possible to cross conductor paths on a molecular scale.

Chapter 5

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101

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Chapter 6

Appendix

119

6. Appendix 120

6.1 Gel for XOR Operation

Figure 6.1: XOR calculation with DNA†.

6. Appendix 121

6.2 Length Marker for Gel Based Studies

DNA Length Markers

Table 6.1: pBR HaeIII digested marker fragment sizes

Upper Half Lower Half

587 123

540 104

504 89

458 80

434 64

267 57

234 51

213 21

192 18

184 11

124 8

6. Appendix 122

6.3 Natrix Formulation from Hampton Re-

Table 6.2: Natrix Buffer Compositions

Number Conc. Unit Substance

1 0.01 M magnesium chloride hexahydrate

0.05 M MES pH 5.6

2 M lithium sulfate monohydrate

2 0.01 M magnesium acetate tetrahydrate

0.05 M MES pH 5.6

2.5 M ammonium sulfate

3 0.10 M magnesium acetate tetrahydrate

0.05 M MES pH 5.6

20 %v/v MPD

4 0.2 M potassium chloride

0.01 M magnesium sulfate

0.05 M MES pH 5.6

10 %v/v polyethylene glycol 400

5 0.2 M potassium chloride

0.01 M magnesium chloride hexahydrate

0.05 M MES pH 5.6

5 %w/v polyethylene glycol 8000

6 0.1 M ammonium sulfate

0.01 M magnesium chloride hexahydrate

0.05 M MES pH 5.6

Continued on next page

6. Appendix 123

Table 6.2 – continued from previous page

Number Conc. Unit Substance

20 %w/v polyethylene glycol 8000

7 0.02 M magnesium chloride hexahydrate

0.05 M MES pH 6.0

15 %v/v iso-propanol

8 0.1 M ammonium acetate

0.005 M magnesium sulfate

0.05 M MES pH 6.0

0.6 M sodium chloride

9 0.1 M potassium chloride

0.01 M magnesium chloride hexahydrate

0.05 M MES pH 6.0

10 %v/v polyethylene glycol 400

10 0.005 M magnesium sulfate

0.05 M MES pH 6.0

5 %w/v polyethylene glycol 4000

11 0.01 M magnesium chloride hexahydrate

0.05 M sodium cacodylate pH 6.0

1 M lithium sulfate monohydrate

12 0.01 M magnesium sulfate

0.05 M sodium cacodylate pH 6.0

1.8 M lithium sulfate monohydrate

13 0.015 M magnesium acetate tetrahydrate

0.05 M sodium cacodylate pH 6.0

Continued on next page

6. Appendix 124

Table 6.2 – continued from previous page

Number Conc. Unit Substance

1.7 M ammonium sulfate

14 0.1 M potassium chloride

0.025 M magnesium chloride hexahydrate

0.05 M sodium cacodylate pH 6.0

15 %v/v iso-propanol

15 0.04 M magnesium chloride hexahydrate

0.05 M sodium cacodylate pH 6.0

5 %v/v MPD

16 0.04 M magnesium acetate tetrahydrate

0.05 M sodium cacodylate pH 6.0

30 %v/v MPD

17 0.2 M potassium chloride

0.01 M calcium chloride dihydrate

0.05 M sodium cacodylate pH 6.0

10 %w/v polyethylene glycol 4000

18 0.01 M magnesium acetate tetrahydrate

0.05 M sodium cacodylate pH 6.5

1.3 M lithium sulfate monohydrate

19 0.01 M magnesium sulfate

0.05 M sodium cacodylate pH 6.5

2 M ammonium sulfate

20 0.1 M ammonium acetate

0.015 M magnesium acetate tetrahydrate

0.05 M sodium cacodylate pH 6.5

Continued on next page

6. Appendix 125

Table 6.2 – continued from previous page

Number Conc. Unit Substance

10 %v/v iso-propanol

21 0.2 M potassium chloride

0.005 M magnesium chloride hexahydrate

0.05 M sodium cacodylate pH 6.5

10 %v/v iso-propanol

22 0.08 M magnesium acetate tetrahydrate

0.05 M sodium cacodylate pH 6.5

15 %v/v polyethylene glycol 400

23 0.2 M potassium chloride

0.01 M magnesium chloride hexahydrate

0.05 M sodium cacodylate pH 6.5

10 %w/v polyethylene glycol 4000

24 0.2 M ammonium acetate

0.01 M calcium chloride dihydrate

0.05 M sodium cacodylate pH 6.5

10 %w/v polyethylene glycol 4000

25 0.08 M magnesium acetate tetrahydrate

0.05 M sodium cacodylate pH 6.5

30 %w/v polyethylene glycol 4000

26 0.2 M potassium chloride

0.1 M magnesium acetate tetrahydrate

0.05 M sodium cacodylate pH 6.5

10 %w/v polyethylene glycol 8000

27 0.2 M ammonium acetate

Continued on next page

6. Appendix 126

Table 6.2 – continued from previous page

Number Conc. Unit Substance

0.01 M magnesium acetate tetrahydrate

0.05 M sodium cacodylate pH 6.5

30 %w/v polyethylene glycol 8000

28 0.05 M magnesium sulfate aq.

0.05 M HEPES-Na pH 7.0

1.6 M lithium sulfate monohydrate

29 0.01 M magnesium chloride hexahydrate

0.05 M HEPES-Na pH 7.0

4 M lithium chloride

30 0.01 M magnesium chloride hexahydrate

0.05 M HEPES-Na

1.6 M ammonium sulfate

31 0.005 M magnesium chloride hexahydrate

0.05 M HEPES-Na pH 7.0

25 %v/v polyethylene glycol monomethyl ether 550

32 0.2 M potassium chloride

0.01 M magnesium chloride hexahydrate

0.05 M HEPES-Na pH 7.0

20% %w/v 1,6-hexanediol

33 0.2 M ammonium chloride

0.01 M magnesium chloride hexahydrate

0.05 M HEPES-Na pH 7.0

30% %w/v 1,6-hexanediol

34 0.1 M potassium chloride

Continued on next page

6. Appendix 127

Table 6.2 – continued from previous page

Number Conc. Unit Substance

0.005 M magnesium sulfate aq.

0.05 M HEPES-Na pH 7.0

15 %v/v MPD

35 0.1 M potassium chloride

0.01 M magnesium chloride hexahydrate

0.05 M HEPES-Na pH 7.0

5 %v/v polyethylene glycol 400

36 0.1 M potassium chloride

0.01 M calcium chloride dihydrate

0.05 M HEPES-Na pH 7.0

10 %v/v polyethylene glycol 400

37 0.2 M potassium chloride

0.025 M magnesium sulfate aq.

0.05 M HEPES-Na pH 7.0

20 %v/v polyethylene glycol 200

38 0.2 M ammonium acetate

0.15 M magnesium acetate tetrahydrate

0.05 M HEPES-Na pH 7.0

5 %w/v polyethylene glycol 4000

39 0.1 M ammonium acetate

0.02 M magnesium chloride hexahydrate

0.05 M HEPES-Na pH 7.0

5 %w/v polyethylene glycol 8000

40 0.01 M magnesium chloride hexahydrate

Continued on next page

6. Appendix 128

Table 6.2 – continued from previous page

Number Conc. Unit Substance

0.05 M tris hydrochloride pH 7.5

1.6 M ammonium sulfate

41 0.1 M potassium chloride

0.015 M magnesium chloride hexahydrate

0.05 M tris hydrochloride pH 7.5

10 %v/v polyethylene glycol monomethyl ether 550

42 0.01 M magnesium acetate tetrahydrate

0.05 M tris hydrochloride pH 7.5

5 %v/v iso-propanol

43 0.05 M ammonium acetate

0.01 M magnesium chloride hexahydrate

0.05 M tris hydrochloride pH 7.5

10 %v/v MPD

44 0.2 M potassium chloride

0.05 M magnesium chloride hexahydrate

0.05 M tris hydrochloride pH 7.5

10 %w/v polyethylene glycol 4000

45 0.025 M magnesium sulfate aq.

0.05 M tris hydrochloride pH 8.5

1.8 M ammonium sulfate

46 0.005 M magnesium sulfate aq.

0.05 M tris hydrochloride pH 8.5

35 %w/v 1,6-hexanediol

Continued on next page

6. Appendix 129

Table 6.2 – continued from previous page

Number Conc. Unit Substance

47 0.1 M potassium chloride

0.01 M magnesium chloride hexahydrate

0.05 M tris hydrochloride pH 8.5

30 %v/v polyethylene glycol 400

48 0.2 M ammonium chloride

0.01 M calcium chloride dihydrate

0.05 M tris hydrochloride pH 8.5

30 %w/v polyethylene glycol 4000

6. Appendix 130

6.4 Crystall Mounting in Capillaries

Figure 6.2: Capillary crystal mounting step 1∗

6. Appendix 131

Figure 6.3: Capillary crystal mounting step 2∗

6. Appendix 132

6.5 Netropsin Binding Thermodynamics

Table 6.3: Sequence dependent Netropsin binding energies.

DNA Duplex ∆G [kcal

mol ]∆H [kcal

mol ]∆S[kcal

mol ]

polyd(AT) polyd(AT) -12.7 -11.2 5.0

polyd(A) polyd(T) -12.2 -2.2 33.0

polyd(GC) polyd(GC) -7.1 -4.3 9.3

d(GCGAATTCGC)2 -11.5 -9.3 -7.5

6. Appendix 133

6.6 Properties and Sequences of Used Sticky

Ends

Table 6.4: Sticky ends for the DX Motif for 2D Arrays

Sequence 5’-3’ ∆GO

37.0◦C[kcal

mol ]∆HO[kcal

mol ]∆SO[cal

GAT -0.17 -13.00 -41.37

GTA -0.01 -13.20 -42.53

ACG -1.60 -16.60 -48.36

ACC -1.27 -14.00 -41.05

6. Appendix 134

Table 6.5: Sticky ends for the CDM Triangle Motif for 3D Assembly

Motif Sequence 5’-3’ ∆GO

37.0◦C[kcal

mol ]∆HO[kcal

mol ]∆SO[cal

System A CATAC -2.39 -31.10 -92.57

System A GTTCT -3.01 -29.90 -86.70

System A TAGAT -1.98 -25.80 -76.80

System B CATC -1.67 -23.70 -71.03

System B ACAG -2.16 -22.30 -64.94

System B TAGC -2.09 -22.40 -65.48

System C CATC -1.67 -23.70 -71.03

System C ACAG -2.16 -22.30 -64.94

System C TAGC -2.09 -22.40 -65.48

Table 6.6: Sticky ends for the TxDx Triangle Motif

Sequence 5’-3’ ∆GO

37.0◦C[kcal

mol ]∆HO[kcal

mol ]∆SO[cal

K]TM[◦C]

GATGGC -5.75 -41.50 -115.27 37.5

GACTGC -5.75 -42.50 -118.49 37.5

GTAGCG -5.75 -43.60 -122.04 37.5

CTGACG -5.68 -43.30 -121.30 37.0

TCGTTG -5.35 -41.20 -115.59 34.6

GCTGTG -5.90 -42.80 -118.98 38.6

6. Appendix 135

Table 6.7: Sticky Ends for the TXA Motif for 3D Assembly

Sequence 5’-3’ ∆GO

37.0◦C[kcal

mol ] ∆HO[kcal

mol ] ∆SO[cal

GCT -1.51 -15.20 -44.14

CTC -0.62 -15.80 -48.94

CATG -1.39 -24.00 -72.89

6. Appendix 136

6.7 TXDX Triangle Motif with Attached DNA

Sequence

Figure 6.4: Sequence and strand structure of TXDX triangle.

6. Appendix 137

6.8 Pipetting Strand Combinations for the

TXDX Triangle

Table 6.8: Strand combinations for the 3D TXDX Trian-

gle

Strand 0D 1D-A 1D-B 1D-C 2D-A 2D-B 2D-C 3D

TXDXtri-1-22 0 0 1 1 0 1 1 1

TXDXtri-2-41 1 1 1 1 1 1 1 1

TXDXtri-3-73 1 1 1 1 1 1 1 1

TXDXtri-4-43 1 1 1 1 1 1 1 1

TXDXtri-5-48 1 1 1 1 1 1 1 1

TXDXtri-6-46 1 1 1 1 1 1 1 1

TXDXtri-7-50 1 1 1 1 1 1 1 1

TXDXtri-8-77 1 1 1 1 1 1 1 1

TXDXtri-9-20 0 0 1 1 0 1 1 1

TXDXtri-10-22 0 1 0 1 1 0 1 1

TXDXtri-11-41 1 1 1 1 1 1 1 1

TXDXtri-12-73 1 1 1 1 1 1 1 1

TXDXtri-13-43 1 1 1 1 1 1 1 1

TXDXtri-14-51 1 1 1 1 1 1 1 1

TXDXtri-15-43 1 1 1 1 1 1 1 1

TXDXtri-16-51 1 1 1 1 1 1 1 1

TXDXtri-17-76 1 1 1 1 1 1 1 1

TXDXtri-18-20 0 1 0 1 1 0 1 1

TXDXtri-19-22 0 1 1 0 1 1 0 1

Continued on next page

6. Appendix 138

Table 6.8 – continued from previous page

Strand 0D 1D-A 1D-B 1D-C 2D-A 2D-B 2D-C 3D

TXDXtri-20-41 1 1 1 1 1 1 1 1

TXDXtri-21-73 1 1 1 1 1 1 1 1

TXDXtri-22-43 1 1 1 1 1 1 1 1

TXDXtri-23-48 1 1 1 1 1 1 1 1

TXDXtri-24-44 1 1 1 1 1 1 1 1

TXDXtri-25-53 1 1 1 1 1 1 1 1

TXDXtri-26-76 1 1 1 1 1 1 1 1

TXDXtri-27-20 0 1 1 0 1 1 0 1

TXDXtri-1BE-22 1 0 1 1 1 0 0 0

TXDXtri-9BE-20 1 0 1 1 1 0 0 0

TXDXtri-10BE-22 1 1 0 1 0 1 0 0

TXDXtri-18BE-20 1 1 0 1 0 1 0 0

TXDXtri-19BE-22 1 1 1 0 0 0 1 0

TXDXtri-27BE-20 1 1 1 0 0 0 1 0

6. Appendix 139

6.9 Calculation of Unique 7mers for the AT-

rich sequence

Table 6.9: Calculation of unique 7 mers

No. Binary Eleminate Compl. Invert Replace Sort Unique

0 0000000

1 0000001

2 0000010

3 0000011

4 0000100

5 0000101

6 0000110

7 0000111

8 0001000 0001000 1110111 1110111 AAATAAA AAATAAA AAATAAAT

9 0001001 0001001 1110110 0110111 AAATAAT AAATAAT AAATAATT

10 0001010 0001010 1110101 1010111 AAATATA AAATATA AAATATAT

11 0001011 0001011 1110100 0010111 AAATATT AAATATT AAATATTA

12 0001100 0001100 1110011 1100111 AAATTAA AAATTAA AAATTAAT

13 0001101 0001101 1110010 0100111 AAATTAT AAATTAT AAATTATA

14 0001110 0001110 1110001 1000111 AAATTTA AAATTTA AAATTTAT

15 0001111 AATAAAT AATAATAT

16 0010000 AATAATA AATATAAT

17 0010001 0010001 1101110 0111011 AATAAAT AATAATT AAATAAAT

18 0010010 0010010 1101101 1011011 AATAATA AATATAA AATTAAAT

19 0010011 0010011 1101100 0011011 AATAATT AATATAT AATTTAAA

20 0010100 0010100 1101011 1101011 AATATAA AATATTA ATAAATAA

21 0010101 0010101 1101010 0101011 AATATAT AATTAAA ATAATAAA

22 0010110 0010110 1101001 1001011 AATATTA AATTAAT ATAATTAA

23 0010111 0010111 1101000 0001011 AATTATA TATATAAA

24 0011000 0011000 1100111 1110011 AATTAAA AATTTAA ATATTAAA

Continued on next page

6. Appendix 140

Table 6.9 – continued from previous page

No. Binary Eleminate Compl. Invert Replace Sort Unique

25 0011001 0011001 1100110 0110011 AATTAAT AATTTAT ATATTTAA

26 0011010 0011010 1100101 1010011 AATTATA ATAAATA ATTAATAA

27 0011011 0011011 1100100 0010011 ATAATAA ATTATTAA

28 0011100 0011100 1100011 1100011 AATTTAA ATAATAT ATTTATAT

29 0011101 0011101 1100010 0100011 AATTTAT ATAATTA

30 0011110 ATATAAA

31 0011111 ATATAAT

32 0100000 ATATATA

33 0100001 ATATTAA

34 0100010 0100010 1011101 1011101 ATAAATA ATATTTA

35 0100011 0100011 1011100 0011101 ATTAAAT

36 0100100 0100100 1011011 1101101 ATAATAA ATTAATA

37 0100101 0100101 1011010 0101101 ATAATAT ATTATAA

38 0100110 0100110 1011001 1001101 ATAATTA ATTATTA

39 0100111 0100111 1011000 0001101 ATTTAAA

40 0101000 0101000 1010111 1110101 ATATAAA ATTTATA

41 0101001 0101001 1010110 0110101 ATATAAT TAAATAA

42 0101010 0101010 1010101 1010101 ATATATA TAAATTA

43 0101011 0101011 1010100 0010101 TAATAAA

44 0101100 0101100 1010011 1100101 ATATTAA TAATATA

45 0101101 0101101 1010010 0100101 TAATTAA

46 0101110 0101110 1010001 1000101 ATATTTA TATAATA

47 0101111 TATATAA

48 0110000 TATTAAA

49 0110001 0110001 1001110 0111001 ATTAAAT TATTTAA

50 0110010 0110010 1001101 1011001 ATTAATA TTAATAA

51 0110011 0110011 1001100 0011001 TTATAAA

52 0110100 0110100 1001011 1101001 ATTATAA TTATTAA

53 0110101 0110101 1001010 0101001 TTTATAA

54 0110110 0110110 1001001 1001001 ATTATTA

Continued on next page

6. Appendix 141

Table 6.9 – continued from previous page

No. Binary Eleminate Compl. Invert Replace Sort Unique

55 0110111 0110111 1001000 0001001

56 0111000 0111000 1000111 1110001 ATTTAAA

57 0111001 0111001 1000110 0110001

58 0111010 0111010 1000101 1010001 ATTTATA

59 0111011 0111011 1000100 0010001

60 0111100

61 0111101

62 0111110

63 0111111

64 1000000

65 1000001

66 1000010

67 1000011

68 1000100 1000100 0111011 1101110 TAAATAA

69 1000101 1000101 0111010 0101110

70 1000110 1000110 0111001 1001110 TAAATTA

71 1000111 1000111 0111000 0001110

72 1001000 1001000 0110111 1110110 TAATAAA

73 1001001 1001001 0110110 0110110

74 1001010 1001010 0110101 1010110 TAATATA

75 1001011 1001011 0110100 0010110

76 1001100 1001100 0110011 1100110 TAATTAA

77 1001101 1001101 0110010 0100110

78 1001110 1001110 0110001 1000110

79 1001111

80 1010000

81 1010001 1010001 0101110 0111010

82 1010010 1010010 0101101 1011010 TATAATA

83 1010011 1010011 0101100 0011010

84 1010100 1010100 0101011 1101010 TATATAA

Continued on next page

6. Appendix 142

Table 6.9 – continued from previous page

No. Binary Eleminate Compl. Invert Replace Sort Unique

85 1010101 1010101 0101010 0101010

86 1010110 1010110 0101001 1001010

87 1010111 1010111 0101000 0001010

88 1011000 1011000 0100111 1110010 TATTAAA

89 1011001 1011001 0100110 0110010

90 1011010 1011010 0100101 1010010

91 1011011 1011011 0100100 0010010

92 1011100 1011100 0100011 1100010 TATTTAA

93 1011101 1011101 0100010 0100010

94 1011110

95 1011111

96 1100000

97 1100001

98 1100010 1100010 0011101 1011100

99 1100011 1100011 0011100 0011100

100 1100100 1100100 0011011 1101100 TTAATAA

101 1100101 1100101 0011010 0101100

102 1100110 1100110 0011001 1001100

103 1100111 1100111 0011000 0001100

104 1101000 1101000 0010111 1110100 TTATAAA

105 1101001 1101001 0010110 0110100

106 1101010 1101010 0010101 1010100

107 1101011 1101011 0010100 0010100

108 1101100 1101100 0010011 1100100 TTATTAA

109 1101101 1101101 0010010 0100100

110 1101110 1101110 0010001 1000100

111 1101111

112 1110000

113 1110001 1110001 0001110 0111000

114 1110010 1110010 0001101 1011000

Continued on next page

6. Appendix 143

Table 6.9 – continued from previous page

No. Binary Eleminate Compl. Invert Replace Sort Unique

115 1110011 1110011 0001100 0011000

116 1110100 1110100 0001011 1101000 TTTATAA

117 1110101 1110101 0001010 0101000

118 1110110 1110110 0001001 1001000

119 1110111 1110111 0001000 0001000

120 1111000

121 1111001

122 1111010

123 1111011

124 1111100

125 1111101

126 1111110

127 1111111

6. Appendix 144

6.10 DNA Crystallization Conditions from Lit-

erature

Table 6.10: DNA Crystalls and Crystallization Condi-

tions

DNA Type Length [nt] Conc.[mM ] Conc. [mg

ml ]Helicity Reference

C-DNA 1 x 10 nt 2 9 1

3[60]

B-DNA 1 x 10 nt 2 6.6 10 [34]

B-DNA 1 x 12 nt 0.8 3.2 [94]

B-DNA 2 x 12 nt 0.2 1.6 10 [67]

Holliday Junc. 1 x 10 nt 0.25 0.8 [20]

B-DNA 1 x 12 nt 3/4 2.5 10 [19]

B-DNA 1 x 10 nt n.a. 9-10 [73]

B-DNA 1 x 12 nt 0.5 2 [9]

B-DNA 1 x 12 nt 0.5 Duplex 4 [16]

B-DNA 1 x 12 nt n.a. 1.2-1.3 [111]

B-DNA 1 x 10 nt 0.2 Duplex 1.3 [1]

B-DNA 1 x 12 nt 0.5 2 [7]

Holliday Junc. 1 x 10 nt 0.5 1.7 [99]

B-DNA 1 x 12 nt 1.8 7.1 [87]

Crossed Junc. 1 x 10 nt 3 Duplex 19.8 10.1 [110]

B-DNA 1 x 12 nt 1 4 [50]

B -DNA 1 x 12 nt 1 4 [88]

B-DNA 1 x 12 nt 0.23 0.9 [46]

B-DNA 1 x 12 nt 1 4 [40]

Continued on next page

6. Appendix 145

Table 6.10 – continued from previous page

DNA Type Length [nt] Conc.[mM ] Conc. [mg

ml ] Helicity Reference

Holliday Junc. 1 x 10 nt 1 Duplex 6.6 [97]

B-DNA 1 x 12 nt 2.6 10.3 [91]

B-DNA 1 x 12 nt 1 4 [47]

Pseudo Junc. 1 x 10 nt 1.2 4 [93]

28 nt 1 x 28 nt 0.5 4.6 [42]

B-DNA 1 x 12 nt n.a. [12]

B-DNA 1 x 12 nt 0.8-1.2 3.2-4.8 [65]

B-DNA 2 x 12 nt n.a. 5 [18]

B-DNA 1 x 10 nt 0.6 2 10 [44]

B-DNA 1 x 10 nt n.a. 10 [35]

B-DNA 1 x 12 nt 0.5 Duplex 4 10 [41]

B-DNA 1 x 12 nt 1 4 [89]

Holliday Junc. [52]

B DNA 1 x 10 nt 0.37 Duplex 1.2 [32]

B-DNA 1 x 12 nt 1 4 [63]

A DNA 1 x 10 nt 2 6.6 11.1 [74]

B-DNA 1 x 12 nt 0.5 Duplex 4 [8]

B-DNA 1 x 10 nt 1.9 6.3 [53]

B-DNA 1 x 10 nt 0.54 Duplex 1.8 [29]

Holliday Junc. 1 x 10 nt 0.333 1.1 [70]

A DNA 1 x 10 nt 1 3.3 [75]

B-DNA 1 x 12 nt n.a. [5]

B-DNA 2 x 12 nt 1 Duplex 7.9 [98]

B-DNA 1 x 12 nt 0.93 3.7 [26]

Continued on next page

6. Appendix 146

Table 6.10 – continued from previous page

DNA Type Length [nt] Conc.[mM ] Conc. [mg

ml ] Helicity Reference

Holliday Junc. n.a. n.a. n.a. 9.7 [37]

B-DNA 1 x 10 nt 0.39 1.3 [28]

Cross arrang. 1 x 10 nt 1.34 4.4 [27]

B-DNA 1 x 12 nt 1 4 [49]

B-DNA 1 x 12 nt 1.2 4.8 [95]

RNA/DNA 68+20 duplex n.a. n.a. [69]

B-DNA 1 x 12 nt n.a. [48]

6. Appendix 147

6.11 Calculation of CDM Triangle Properties

Table 6.11: CDM Triangle Properties with Minimal

Turns.

INNER MINIMAL TURNS

Helicity Bases DNA Geom. Bases DNA Total Total

Angle Angle Angle DNA Geom.

10.5 13 86 116 8 274.3 0.0 30.3

10.5 13 86 116 7 240.0 -34.3 -4.0

10.5 14 120 119 7 240.0 0.0 -1.0

10.5

10.5 15 154 121 6 205.7 0.0 -33.3

10.5 15 154 121 7 240.0 34.3 1.0

10.5 16 189 236 5 171.4 0.0 47.4

10.5 16 189 236 4 137.1 -34.3 13.1

10.5 17 223 234 4 137.1 0.0 11.1

10.5 17 223 234 13 445.7 -51.4 -40.3

10.5 18 257 232 3 102.9 0.0 -25.1

10.5 18 257 232 4 137.1 34.3 9.1

10.5 19 291 230 2 68.6 0.0 -61.4

Continued on next page

6. Appendix 148

Table 6.11 – continued from previous page

INNER MINIMAL TURNS

Helicity Bases DNA Geom. Bases DNA Total Total

Angle Angle Angle DNA Geom.

10.5 19 291 230 4 137.1 68.6 7.1

10 13 108 116 7 252.0 0.0 8.0

10 14 144 118 6 216.0 0.0 -26.0

10 14 144 118 7 252.0 36.0 10.0

10 15 180 x

10 16 216 236 4 144.0 0.0 20.0

10 16 216 236 3 108.0 -36.0 -16.0

10 17 252 234 3 108.0 0.0 -18.0

10 17 252 234 4 144.0 36.0 18.0

10 18 288 232 2 72.0 0.0 -56.0

10 18 288 232 4 144.0 72.0 16.0

10 19 324 230 7 252.0 -144.0 122.0

6. Appendix 149

Table 6.12: CDM Triangle Properties with 1 Turn.

INNER ONE TURN

Helicity Bases DNA Geom. Bases DNA Total Total

Angle Angle Angle DNA Geom.

10.5 13 86 116 19 651.4 17.1 47.4

10.5 13 86 116 18 617.1 -17.1 13.1

10.5 14 120 119 18 617.1 17.1 16.1

10.5

10.5 15 154 121 17 582.9 17.1 -16.1

10.5 16 189 236 15 514.3 -17.1 30.3

10.5 16 189 236 14 480.0 -51.4 -4.0

10.5 17 223 234 14 480.0 -17.1 -6.0

10.5 17 223 234 13 445.7 -51.4 -40.3

10.5 18 257 232 14 480.0 17.1 -8.0

10.5 19 291 230 13 445.7 17.1 -44.3

10.5 19 291 230 14 480.0 51.4 -10.0

Continued on next page

6. Appendix 150

Table 6.12 – continued from previous page

INNER ONE TURN

Helicity Bases DNA Geom. Bases DNA Total Total

Angle Angle Angle DNA Geom.

10 13 108 116

10 14 144 118 18 648.0 72.0 46.0

10 14 144 118

10 15 180 x

10 16 216 236

10 17 252 234 13 468.0 0.0 -18.0

10 17 252 234 14 504.0 36.0 18.0

10 18 288 232

10 18 288 232 14 504.0 72.0 16.0

10 19 324 230

6. Appendix 151

Table 6.13: CDM Triangle Properties with 1 Turn.

INNER 11

2TURNS

Helicity Bases DNA Geom. Bases DNA Total Total

Angle Angle Angle DNA Geom.

10.5 14 120 118 23 788.6 8.6 6.6

10.5 14 120 118 22 754.3 -25.7 -27.7

10.5 14 120 118 21 720.0 -60.0 -62.0

10.5 17 223 234 20 685.7 8.6 19.7

10.5 17 223 234 19 651.4 -25.7 -14.6

10.5 18 257 232 19 651.4 8.6 -16.6

10.5 18 257 232 18 617.1 -25.7 -50.9

10.5 18 257 232 17 582.9 -60.0 -85.1

10.5 18 257 232 16 548.6 -94.3 -119.4

10 14 144 118 21 756.0 0.0 -26.0

10 14 144 118 22 792.0 36.0 10.0

10 14 144 118 23 828.0 72.0 46.0

10 17 252 234 18 648.0 0.0 -18.0

10 17 252 234 19 684.0 36.0 18.0

Continued on next page

6. Appendix 152

Table 6.13 – continued from previous page

INNER 1.5 TURNS

Helicity Bases DNA Geom. Bases DNA Total Total

Angle Angle Angle DNA Geom.

10 17 252 234 19 684.0 36.0 18.0

10 18 288 232 17 612.0 0.0 -56.0

10 18 288 232 18 648.0 36.0 -20.0

10 18 288 232 19 684.0 72.0 16.0

Table 6.14: CDM Triangle Properties with 1 Turn.

INNER TWO TURNS

Helicity Bases DNA Geom. Bases DNA Total Total

Angle Angle Angle DNA Geom.

10.5 14 120 118 28 960.0 0.0 -2.0

10.5 14 120 118 27 925.7 -34.3 -36.3

10.5 14 120 118 26 891.4 -68.6 -70.6

10.5 17 223 234 25 857.1 0.0 11.1

10.5 17 223 234 24 822.9 -34.3 -23.1

10.5 17 223 234 23 788.6 -68.6 -57.4

10.5 18 257 232 25 857.1 34.3 9.1

Continued on next page

6. Appendix 153

Table 6.14 – continued from previous page

INNER TWO TURNS

Helicity Bases DNA Geom. Bases DNA Total Total

Angle Angle Angle DNA Geom.

10.5 18 257 232 24 822.9 0.0 -25.1

10.5 18 257 232 23 788.6 -34.3 -59.4

10.5 18 257 232 22 754.3 -68.6 -93.7

10 14 144 118 26 936.0 0.0 -26.0

10 14 144 118 27 972.0 36.0 10.0

10 14 144 118 28 1008.0 72.0 46.0

10 17 252 234 23 828.0 0.0 -18.0

10 17 252 234 24 864.0 36.0 18.0

10 17 252 234 25 900.0 72.0 54.0

10 18 288 232 22 792.0 0.0 -56.0

10 18 288 232 23 828.0 36.0 -20.0

10 18 288 232 24 864.0 72.0 16.0

10 18 288 232 25 900.0 108.0 52.0

6. Appendix 154

6.12 All DNA Strand Sequences used in 5’to

3’ Direction

6.12.1 Strands for DX 2D Array with Short Sticky

Ends

STRAND NTA1-47nt G A T G G C G A C A T C C T G C C G C T A T

G A T T A C A C A G C C T G A G C A T T G A C A C

STRAND NTA2-42nt T G T A G T A T C G T G G C T G T G T A

A T C A T A G C G G C A C C A A C T G G C A

STRAND NTA3-29nt A C C G T G T C A A T G C T C A C C G A

T G C A A C C A G

STRAND NTA4-24nt G T A G C G C C G T T A G T G G A T G T C G C C

STRAND NTA5-48nt A C G C T G G T T G C A T C G G A C G A

T A C T A C A T G C C A G T T G G A C T A A C G G C G C

STRAND NTB1-25nt C G T C A G G C T G C T G T G G T C G T

G C G A C

STRAND NTB2-43nt A G T A C A A C G C C A C C G A T G C G

G T C A C T G G T T A G T G G A T T G C G T

STRAND NTB3-28nt A T C C G T C G A T A C G G C A C C A T

G A T G C A C G

6. Appendix 155

STRAND NTB4-69nt T A C C G T G C A T C A T G G A C T A A

C C A G T G C T C G C T G A T T T T T C A G C G A G T T A C C

G C A T C G G A C A G C A G C C T G

STRAND NTB5-70nt G G T G T C G C A C G A C C T G G C G T

C T G T T G A C T T T T G T C A A C A G T T T G T A C T A C G

C A A T C C T G C C G T A T C G A C G

6.12.2 Strands used for 3D project with TX Motif

STRAND TX-1-60nt G A G C A T T C A G C A A G C G T G G A G T

G G C A G A C C G C A T A G G T A T C T G A C G G A C A A C A

T C G G C A C

STRAND TX-2-65nt G T A C G A C A T A C G T T G G A C T C

C T G A T A G C T C G C C A G T G G T C A C A G T A G T C G G

A C G C T T G C T G A A T G

STRAND TX-3-62-nt C A T G A C T T G A G C C T G A G G A C

T G G C G A G C T A T C A C C G A C T A C T G T G A C C T G C

G A A C T G C T A C C

STRAND TX-4-60nt G C T G G T A G C A G T T C G C A C C T

C A C C G T C A G A T A C C T A T G C G G T C T G C C T G T A

G A C A G A A T C

6. Appendix 156

STRAND TX-5-28nt A G C G A T T C T G T C T A C A C C A A

C G T A T G T C

STRAND TX-6-25nt C T C G T G C C G A T G T T G T G G C T

C A A G T

6.12.3 Strands for Crystallization of Blunt ended DX

Motif

STRAND DX1-20nt G C G A T C T A C A C C G T T C T C C G

STRAND DX2-40nt C G G A T G A G C C T G A C G A G A C T

A T T G A T A A C C T G T A G A T C G C

STRAND DX3-40ntA G T C T C G T C A C C A C A A C T C G G

G T A C T A T G T G G T T A T C A A T

STRAND DX4-40nt C G G A G A A C G G A C A T A G T A C C

C G A G T T G T G G A C T G G C A C G C

STRAND DX5-20nt G C G T G C C A G T G G C T C A T C C G

STRAND DXBR1-20nt G C G A T C T A C A C C G T A T G C C

STRAND DXBR2-40nt C G G A t G A G C C T G A c G A G A C t

A T t G A t A A C C T G t A G A t C G C

6. Appendix 157

STRAND DXBR3-40nt T G G T A C T A T G T G G T T A T C A

A T A G T C T C G T C A C C A C A A C T C

STRAND DXBR-4-40nt C G G c A t A C G G A C A t A G t A C c

A G A G t T G t G G A C T G G c A c G C

STRAND CDBR5-20nt G C G T G C C A G T G G C T C A T C C

6.12.4 DNA Triangle Strands Designed by Prof. ChengDe

Mao

STRAND CDMT1-18nt G C T G C T A C A C C G T G T T C G

STRAND CDMT2-38nt C G T G A G C C T G A C G A G T G T C

A T T G A T A A C C T G T A G C A G C

STRAND CDMT3-42nt G G T A C T A T G T G G T T A T C A A

T G A C A C T C G T C A C C A C A A C T C G C

STRAND CDMT4-38nt C G A A C A C G G A C A T A G T A C C

G C G A G T T G T G G A C T G G C G C

STRAND CDM5-16nt G C G C C A G T G G C T C A C G

6. Appendix 158

6.12.5 DNA Strands for Gel-based studies of Triangles

STRAND CDM13-1-31nt C A G A C A G C C T G C T C T C G A T T G

G A C G A A G C C A

CDM-G2-18nt C C G C C A A G T G G C T G T C T G

STRAND CDM13-3-39nt C G A G A G C A C C G T C T A T T A

T C A C C T G A A C T C A C C A C C A A T

STRAND CDM13-4-31nt G A C T G T A C C T G G T G A G T T

C A G G A C G C T A C G A

STRAND CDM-G5-18nt T G G C T T C G T G G T A C A G T C

STRAND CDM13-6-31nt G G C A G T G C C T G A T A A T A G

A C G G A C T T G G C G G

CDM-G7-18nt T C G T A G C G T G G C A C T G C C

STRAND CDM14-1-32nt C A G A C A G C C T G C T C T C G C A

T T G G A C G A A G C C A

STRAND CDM14-3-42nt C G A G A G C A C C G T C A T A G C

A T C A C C T G T C A C T C A C C A C C A A T G

STRAND CDM14-4-32nt G A C T G T A C C T G G T G A G T G

A C A G G A C G C T A C G A

6. Appendix 159

STRAND CDM14-6-32nt G G C A G T G C C T G A T G C T A T

G A C G G A C T T G G C G G

STRAND CDM15-1-33nt C A G A C A G C C T G C T C T C G C A

T C T G G A C G A A G C C A

STRAND CDM15-3-45nt C G A G A G C A C C G T C A A G C T

T A T C A C C T G A A C A C T C A C C A C C A G A T G

STRAND CDM15-4-33nt G A C T G T A C C T G G T G A G T G

T T C A G G A C G C T A C G A

STRAND CDM15-6-33nt G G C A G T G C C T G A T A A G C T

T G A C G G A C T T G G C G

STRAND CDM17-1-35nt C A G A C A G C C T G C T C T C G G

A T C G A C G G A C G A A G C C A

STRAND CDM17-3-51nt C G A G A G C A C C G T C A A C C T

A T T A T C A C C T G A A C G T A C T C A C C A C C G T C G A

T C

STRAND CDM17-4-35nt G A C T G T A C C T G G T G A G T A

C G T T C A G G A C G C T A C G A

STRAND CDM17-6-35nt G G C A G T G C C T G A T A A T A G

6. Appendix 160

G T T G A C G G A C T T G G C G G

CDM18-1-36nt C A G A C A G C C T G C T C T C G G T A T C G

A C G G A C GA A G C C A

STRAND CDM18-3-54nt C G A G A G C A C C G T C A A C C A G A

T T A T C A C C T G A A C T C T A C T C A C C A C C G T C G A T A C

STRAND CDM18-4-36nt G A C T G T A C C T G G T G A G T A

G A G T T C A G G A C G C T A C G A

STRAND CDM18-6-36nt G G C A G T G C C T G A T A A T C T

G G T T G A C G G A C T T G G C G G

6.12.6 DNA Stands for 3D Triangle with 14nt per Edge

STRAND CDM3D-1-14A-42nt G T T C T G A T A G A C G A C C T G

C T G A C G C A T A G G A C G A T A G T C A T C

STRAND CDM3D-2-14A27nt T A G A T G T C C G A C A A G T G

G T C G T C T A T C

STRAND CDM3D-3-GEN-42nt G T C A G C A C C G T C A T A G

C A T C A C C T G T C G T A C A C C A C C T A T G C

STRAND CDM3D-4-14A-42nt C A T A C G T G A C T G T A C C T

G G T G T A C G A C A G G A C G C T A A C A C T G

6. Appendix 161

STRAND C5-14A-28nt A G A A C G A T G A C T A T C G T G G

T A C A G T C A C

STRAND C6-14A-42nt A T C T A C G A T T C A G T G C C T G

A T G C T A T G A C G G A C T T G T C G G A C

STRAND C7-14A-29 nt G T A T G C A G T G T T A G C G T G G

C A C T G A A T C G

STRAND C1-14B-40nt G C T A G A C G T G T C T C C T G C T

G A C G C A T A G G A C A G A C C A T A C

STRAND C2-14B-26nt A C A G A G T C G C G T A G T G G A G

A C A C G T C

STRAND C4-14B-40nt G A T G T A G T T G C G A C C T G G T

G T A C G A C A G G A C G A T G A C T G C

STRAND C5-14B-26nt T A G C G T A T G G T C T G T G G T C

G C A A C T A

STRAND C6-14B-40nt C T G T G A G T G C A T A C C T G A T

G C T A T G A C G G A C T A C G C G A C T

STRAND C7-14B-26nt C A T C G C A G T C A T C G T G G T A

TGCACTC

6. Appendix 162

STRAND C1-14C-32nt G C T A G A T A G C C T G C T G A C G

C A T A G G A C G A TA C

STRAND C2-14C-18nt A C A G T C T G A G T G G C T A T C

STRAND C4-14C-32nt G A T G T C G C T C C T G G T G T A C

G A C A G G A C A T G G C

STRAND C5-14C-18nt T A G C G T A T C G T G G A G C G A

STRAND C6-14C-32nt C T G T G A G T A C C T G A T G C T A

T G A C G G A C T C AG A

STRAND C7-14C-18nt C A T C G C C A T G T G G T A C T C

STRAND C4-A1SE-42nt C G T G A C T G T A C C T G G T G T A

C G A C A G G A C G C T A A C A C T G C A T A

STRAND C1-B-BE-40nt G A C G T G T C T C C T G C T G A C G

C A T A G G A C A G A C C A T A C G C T A

STRAND C6-A-BE-42nt C G A T T C A G T G C C T G A T G C T

A T G A C G G A C T T G T C G G A C A T C T A

6. Appendix 163

6.12.7 DNA Strands for 6 Helix Bundle with Netropsin

Binding Sites

STRAND 6HBNE-1-20nt G C A G A A C C G T C C A T A C A T C C

STRAND 6HBNE-2-90nt C G C A T A G T A C G A C G T C C A

C T C G C T G G A G C T T T A A A T A G T C T A A T A T T T C

C A T T T A T T T G A G G C C G T G G C A T C C A G A G G T C

A C G G T T C T G C

STRAND 6HBNE-3-90nt G G T A C G A G C G G A T C T C C T

G C C G C A G A C C T C T G G A T G C C T G G C G C A G G T C

C T A G G C A

STRAND 6HBNE-4-36nt G C T G T T C G G T C A C G G T C G

A T T C G G A C G G C C T C A A A T

STRAND 6HBNE-5-36nt A A A T G G A A A T A T T A G A G A

A A T A A T A G G T A T T T T A T C A G A T A A T A T A G

STRAND 6HBNE-6-37nt G A T T A T A A A G G C T T A A T A

A T C G C T T T T A A T T C C A T A A

STRAND 6HBNE-7-54nt TA A A G C C T C T G A C C T A T G A G G

T C G A G T A C C T G A C G C A G G A C G T C G T A C T A T G C G

STRAND 6HBNE-8-55nt C G G A G T A G A T C G A A T G G A C T G A

C C T G T C T C C G G T G C T A A G C G A G T T C A C G T T G G C

6. Appendix 164

STRAND 6HBNE-9-37nt T C A T T A T A T T C C T A T T T A A

A G C T C C T A A T T T G G T A T A

STRAND 6HBNE-10-83nt T A T T G G C T A A T T A T T C G T

A A A T A T A C G C T A A A A T T T C C T T T A A T A T C A G G

A G G C G T A C G G T C T C A C G C G T T A A A A T T C T G C C G

STRAND 6HBNE-11-55nt A C C A T C G T G G A C C G C G T C

G C A C A A C A G A G C C T G C G A G T C A G C T C G A C T C

A C G T C C

STRAND 6HBNE-12-90nt G G A T G T A T G G T G C G G C A C

C A C G A T G G T C G G C A G A A T T T A T A C C T A T T A T

T T C G A A T A T A A T G A G C C A A C G T G A T G C G T C A

CCTTGACTGG

STRAND 6HBNE-13-20nt C C A G T C A A G G A G C A A C T G

C G

STRAND 6HBNE-14-90nt C G C A G T T G C T G G T A C T C G

A C C T C A C C T T T A T A A T C C T A T A T T A T C T G A T A

A A T A A C G C G T G A G A C C A C G C G G T G G A G A T C C

GCTCGTACC

STRAND 6HBNE-15-90nt G C G A T G A T G T G G C T C T G T

T G T G C G G T A C G C C T C C T G A T A T T A A A G G A A A

6. Appendix 165

T T T A A G C G A T T A T T A A G T A G G T C A C C A T T C G

A T C T A C T C C G

STRAND 6HBNE-16-20nt G C G G T G T C G G A C A T C A T C

G C

STRAND 6HBNE-17-90nt C C A G T A T C C T G G T C A G T G

A G G C T T T A T T A T G G A A T T A A T A G C G T A T A T T

T A C A C C G A A C A G C T G C C T A G G A C C A C T C G C A

C C G A C A C C G C

STRAND 6HBNE-18-90nt G G A C G T G A G T C G A G C T G T

G C G C C A C C G A A T C G A C C G T G G A A T A A T T A G C

C A A T A T A T A C C A A A T T A T A G C A C C G G A G A C A

C C A C T A G T C C

STRAND 6HBNE-19-20nt G G A C T A G T G G A G G A T A C T

G G

Strands for 90mer DNA Duplex control:

STRAND 90m46hb1-90 G G A T G T G G T A T C G T G A T T G A C

G A C G A T T G C G T A T C C G A G G A T G C A A G C G T T G

A T A C A G C C A G T G G A G A C T A T G C G G T A C T T G G

A T G A A C G

STRAND 90m46hb2-90 C G T T C A T C C A A G T A C C G C A

T A G T C T C C A C T G G C T G T A T C A A C G C T T G C A T

6. Appendix 166

C C T C G G A T A C G C A A T C G T C G T C A A T C A C G A T

ACCACATCC

6.12.8 DNA Strands for the TXDX Triangle Motif

STRAND TXDXtri-1-22 C T C G A A G T G G C G T A T C T C G T T G

STRAND TXDXtri-2A-41 G C A C T G G A T C T A A C G A C A

G C C T C G A T G G A C G C C T G C A T A C C

STRAND TXDXtri-2B-73 G A G C T T C A C A G T A T C C T C

T A G T T G A C A T C C G A G T G C C A T A G A C C T G A C C

T G G A A C A C T T A C G C G A T C T T A G C T

STRAND TXDXtri-2C-43 G T A C T T G G A T T G C T C C A G

A C G T A G A C T T G A C T T C G A G C A C A G C

STRAND TXDXtri-3A-48 G A G C T G C C T A G T A T T G T T

G C A T C A T G C C G T G G A G T G T A G C T C T C G A C G

STRAND TXDXtri-3B-46 C T T A G A G C G A T A T A C T C A

C G T T G C T G T C G T T A G A T G G A G A C T A G C C

STRAND TXDXtri-3C-50 G C T G G T A G C A C C A T C G A G

C G T G A G T G G T C T A T G C G T A C A C A C A A G T C T A C

STRAND TXDXtri-3D-77 G T C T G G A G C A A T G G T C A A

6. Appendix 167

T A T C G C T C T A A G C G T C G A G A G C T A C T A A T C T

A T C C G G T G T A T G T C C T G C G G A C C A A C G A

STRAND TXDXtri-4-20 G T C C G C A C C T A C T C G C T G T

STRAND TXDXtri-5-22 G A G A T T G T G G C A G C T C C G C T A C

STRAND TXDXtri-6A-41 G A G T A G G A A T A G T T C T C A

A C C A T G T A G G A C T C C T C G C G T A A

STRAND TXDXtri-6B-73 G T G T T C C A C C A A G T A C A G

C T A A G A A C G G C A T G A T G C C A G C A T C C T G T C C

T G A C T G T A G A G T A A C A C A T A T T C T

STRAND TXDXtri-6C-43 G T A T A G T G A C G C G G C A A G

C G A C G G T G C A G A C A A T C T C C G T C A G

STRAND TXDXtri-7A-51 G G A T C A C C T G T A A C C G T T

G C T A T C G G T C G T G G C G T G A A T G C C T G A G T C T

T G

STRAND TXDXtri-7B-43 C G A A T C A A T G A C T A C C G T

T G T T G A G A A C T A T T G G A C A T A C A C C

STRAND TXDXtri-7C-51 G G A T A G A T T A C C T A C A T G

C G G T A G T G G A T G C T G C A A T A C T A C T G C A C C G

6. Appendix 168

T C

STRAND TXDXtri-7D-76 G C T T G C C G C G T G G A C A C A

T T G A T T C G C A A G A C T C A G G C A T T C T T C G C G C

T A G A C G G C T C A A G C T G A G A C C G T A G C G

STRAND TXDXtri-8-20 G G T C T C A C C G A A C G C T G A C

STRAND TXDXtri-9-22 C G A C G T G T G G T G A T C C G C C A T C

STRAND TXDXtri-10A-41 C G T T C G G A G T T A C G A A G C

G C C A G T A C G G A C G C C T G T T A C T C

STRAND TXDXtri-10B-73 T A C A G T C A C A C T A T A C A G

A A T A T G A C G A C C G A T A G C C A A T C A T C T G A C C

T G A A G C T C G G T A T G C A C A A C T A G A

STRAND TXDXtri-10C-43 G G T A T G C A C A A C T A G A G G

A T A C T G A C C G C T C A T A C G A T G A G T T C G A C A C

G T C G G C A G T C

STRAND TXDXtri-11A-48 G A T A C G C C T G T G T A C G T T

G C A C T C G G A T G T G G C G T G G T A C G A C G A G T C

STRAND TXDXtri-11B-44 G A T C A G T C T G A G G A C G C A

C G T T G C G C T T C G T A A C T G C T T G A G C C

6. Appendix 169

STRAND TXDXtri-11C-53 G T C T A G C G C G A A C C G T A C

T G C G T G C G T G A T G A T T G C G G T T A C A C G A A C T

C A T C

STRAND TXDXtri-11D-76 G T A T G A G C G G T G G T C A C C

T C A G A C T G A T C G A C T C G T C G T A C C T G C T A C C

A G C G G C T A G T C T C C T G T C A T G G A T G G C

STRAND TXDXtri-12-20 C A T G A C A C C A G T G C G A C T

G C

STRAND TXDXtri-1BE-22 G C T G T G C T C G A A G T G G C

G T A T C

STRAND TXDXtri-4BE-20 T C G T T G G T C C G C A C C T A C

T C

STRAND TXDXtri-5BE-22 C T G A C G G A G A T T G T G G C

A G C T C

STRAND TXDXtri-8BE-20 C G C T A C G G T C T C A C C G A A

C G

STRAND TXDXtri-9BE-22 G A C T G C C G A C G T G T G G T

G A T C C

6. Appendix 170

STRAND TXDXtri-12BE-20 G C C A T C C A T G A C A C C A G

T G C

6. Appendix 171

6.13 Lebenslauf - Curriculum Vitae

Name: Jens Kopatsch

Geburtsdatum: 3. September 1972

Geburtsort: Salm¨unster

1979-1983 Philipp-Reis Grundschule, Gelnhausen

1983-1985 Rudolf-Steiner Schule, Loheland

1985-1993 Grimmelshausen Gymnasium, Gelnhausen

06/1993 Abitur am Grimmelshausen Gymnasium, Gelnhausen

10/1993 Aufnahme des Studiums der Biotechnologie an der TU Berlin

07/1997-11/1997 Studienarbeit an der Dongseo University in S¨ud Korea

(Pusan) ¨uber kontinuieriche Kultivierung von Mikroalgen

04/1998-10/1998 Diplomarbeit an der New York University im Institut f¨ur

Chemie ¨uber Self Assembly of 2-dimensional DNA Arrays

10/1999 Abschluss des Studiums an der TU Berlin als

Diplom Ingenieur Fachrichtung Biotechnologie

09/2004 Promotion an der TU Berlin, Fakul¨at f¨ur Prozesswissenschaften.

Die Forschungsarbeit wurde an der der New York University im Institut

f¨ur Chemie bei Prof. Dr. Nadrian C. Seeman durchgef¨uhrt. Betreuer an der

TU Berlin war Prof. Dr. Ulf Stahl.