Nanotechnology Science and Computation part 1 potx

As natural computing is concernedwith information processing taking place in or inspired by nature, the ideascoming from basic interactions between atoms and molecules naturally becomepa

Series Editors: G Rozenberg

Th Bäck A.E Eiben J.N Kok H.P Spaink

Leiden Center for Natural Computing

Advisory Board: S Amari G Brassard K.A De Jong

C.C.A.M Gielen T Head L Kari L Landweber T Martinetz

Z Michalewicz M.C Mozer E Oja Gh Paun J Reif H Rubin

A Salomaa M Schoenauer H.-P Schwefel C Torras

D Whitley E Winfree J.M Zurada

°

Natural Computing Series

N

Junghuei Chen · Nataša Jonoska

Grzegorz Rozenberg (Eds.)

123

Nanotechnology: Science and

Computation

With 126 Figures and 10 Tables

Library of Congress Control Number: 2005936799

ACM Computing Classification (1998): F.1, G.2.3, I.1, I.2, I.6, J.3

ISBN-10 3-540-30295-6 Springer Berlin Heidelberg New York

ISBN-13 978-3-540-30295-7 Springer Berlin Heidelberg New York

This work is subject to copyright All rights are reserved, whether the whole or part of the material

is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer Violations are liable for prosecution under the German Copyright Law.

Springer is a part of Springer Science+Business Media

Cover Design: KünkelLopka, Werbeagentur, Heidelberg

Typesetting: by the Editors

Production: LE-TEX Jelonek, Schmidt & Vöckler GbR, Leipzig

Printed on acid-free paper 45/3142/YL – 5 4 3 2 1 0

University of South Florida

4202 E Fowler Av., PHY114

Leiden University Niels Bohrweg 1

2333 CA Leiden, The Netherlands

A.E Eiben Vrije Universiteit Amsterdam The Netherlands

This book is dedicated to Nadrian C Seeman

on the occasion of his 60th birthday

This image was created by DADARA

Nanotechnology is slowly and steadily entering more and more aspects of ourlife It is becoming a base for developing new materials as well as a base fordeveloping novel methods of computing As natural computing is concernedwith information processing taking place in or inspired by nature, the ideascoming from basic interactions between atoms and molecules naturally becomepart of these novel ways of computing

While nanotechnology and nanoengineering have flourished in recent years,the roots of DNA nanotechnology go back to the pioneering work of Nadrian(Ned) C Seeman in the 1980s Many of the original designs and constructions

of nanoscale structures from DNA developed in Ned’s lab provided a pletely new way of looking at this molecule of life Starting with the synthesis

com-of the first immobile Holliday junction, now referred to as J1, through thedouble and triple cross-over molecules, Ned has shown that DNA is a pow-erful and versatile molecule which is ideal for building complex structures atthe nanometer scale

Through the years, Ned has used some of the basic DNA motif tures as ‘tinkertoy’ or ‘lego’ units to build a cube, two-dimensional arrays,and various three-dimensional structures, such as Borromean rings, nanome-chanical devices, nano-walkers (robots), etc All of them were designed anddemonstrated originally in Ned’s lab, but then all these ideas and designs werefollowed up by many other researchers around the world

struc-Adleman’s seminal paper from 1994 provided a proof of principle thatcomputing at a molecular level, with DNA, is possible This led to a realexplosion of research on molecular computing, and very quickly Ned’s ideasconcerning the design and construction of nanoscale structures from DNAhad a profound influence on the development of both the theoretical and theexperimental foundations of this research area

Ned is a scientist and a chemist in the first place Although Ned can

be considered the founder of the DNA nanoengineering field, he has alwaysconsidered himself as a chemist who is interested in basic science Therefore,

he is still very interested in the basic physical properties of DNA and enzymes

VIII Preface

that interact with nucleic acids Ned has been continuously funded by NIH foralmost 30 years and is still providing valuable insights into the DNA and RNAbiophysical and topological properties as well as the mechanism of homologousrecombination between two chromosomal DNAs

Ned’s enormous influence extends also to service to the scientific munity Here one has to mention that Ned is the founding president of theInternational Society for Nanoscale Science, Computation and Engineering(ISNSCE) The respect that Ned enjoys is also manifested through varioushonors and awards that he has received — among others the Feynman Prize

com-in Nanotechnology and the Tulip Award com-in DNA Computcom-ing

Besides science, Ned is very much interested in the world around him, e.g.,

in art Amazingly, some of this interest has also influenced his scientific work:

by studying the work of Escher he got some specific ideas for constructions ofDNA-based nanostructures! Ned is an excellent lecturer and has given talksaround the world, thereby instigating significant interest and research in DNAnanotechnology and computing

With this volume, which presents many aspects of research in basic ence, application, theory and computing with DNA molecules, we celebrate ascientist who has been a source of inspiration to many researchers all over theworld, and to us a mentor, a scientific collaborator, and a dear friend

Nataˇsa JonoskaGrzegorz Rozenberg

Part I DNA Nanotechnology – Algorithmic Self-assembly

Scaffolded DNA Origami: from Generalized Multicrossovers

to Polygonal Networks

Paul W.K Rothemund 3

A Fresh Look at DNA Nanotechnology

Zhaoxiang Deng, Yi Chen, Ye Tian, Chengde Mao 23

DNA Nanotechnology: an Evolving Field

Hao Yan, Yan Liu 35

Self-healing Tile Sets

Erik Winfree 55

Compact Error-Resilient Computational DNA Tilings

John H Reif, Sudheer Sahu, Peng Yin 79

Forbidding −Enforcing Conditions in DNA Self-assembly of

Graphs

Giuditta Franco, Nataˇsa Jonoska 105

Part II Codes for DNA Nanotechnology

Finding MFE Structures Formed by Nucleic Acid Strands in

a Combinatorial Set

Mirela Andronescu, Anne Condon 121

Involution Solid Codes

Lila Kari, Kalpana Mahalingam 137

Part III DNA Nanodevices

DNA-Based Motor Work at Bell Laboratories

Bernard Yurke 165

Nanoscale Molecular Transport by Synthetic DNA Machines1

Jong-Shik Shin, Niles A Pierce 175

Part IV Electronics, Nanowire and DNA

A Supramolecular Approach to Metal Array Programming

Using Artificial DNA

Mitsuhiko Shionoya 191

Multicomponent Assemblies Including Long DNA and

Nanoparticles – An Answer for the Integration Problem?

Andreas Wolff, Andrea Csaki, Wolfgang Fritzsche 199

Molecular Electronics: from Physics to Computing

Yongqiang Xue, Mark A Ratner 215

Part V Other Bio-molecules in Self-assembly

Towards an Increase of the Hierarchy in the Construction

of DNA-Based Nanostructures Through the Integration of

Inorganic Materials

Bruno Samor`ı, Giampaolo Zuccheri, Anita Scipioni, Pasquale De Santis 249

Adding Functionality to DNA Arrays: the Development of

Semisynthetic DNA–Protein Conjugates

Christof M Niemeyer 261

Bacterial Surface Layer Proteins: a Simple but Versatile

Biological Self-assembly System in Nature

Dietmar Pum, Margit S´ara, Bernhard Schuster, Uwe B Sleytr 277

Chem Soc 2004, 126, 10834–10835 Copyright 2004 American Chemical Society.

Contents XI

Part VI Biomolecular Computational Models

Computing with Hairpins and Secondary Structures of DNA

Masami Hagiya, Satsuki Yaegashi, Keiichiro Takahashi 293

Bottom-up Approach to Complex Molecular Behavior

Milan N Stojanovic 309

Aqueous Computing: Writing on Molecules Dissolved in

Water

Tom Head, Susannah Gal 321

Part VII Computations Inspired by Cells

Turing Machines with Cells on the Tape

Francesco Bernardini, Marian Gheorghe, Natalio Krasnogor, GheorgheP˘aun 335

Insights into a Biological Computer: Detangling Scrambled

Genes in Ciliates

Andre R.O Cavalcanti, Laura F Landweber 349

Modelling Simple Operations for Gene Assembly

Tero Harju, Ion Petre, Grzegorz Rozenberg 361

Part VIII Appendix

Publications by Nadrian C Seeman

377

Part I

DNA Nanotechnology – Algorithmic

Self-assembly

Scaffolded DNA Origami: from Generalized Multicrossovers to Polygonal Networks

Ned’s DNA sculptures did turn out to have a relationship to tion In 1994, Len Adleman’s creation of a DNA computer [1] showed thatlinear DNA self-assembly, together with operations such as PCR, could tackleNP-complete computational problems Excited by this result, Erik Winfreequickly forged an amazing link that showed how the self-assembly of geo-metrical DNA objects, alone, can perform universal computation [21] Thedemonstration and exploration of this link have kept a small gaggle of com-puter scientists and mathematicians tangled up with Ned and his academicchildren for the last decade At an intellectual level, the technical achieve-ments of the resulting collaborations and interactions have been significant,among them the first two-dimensional DNA crystals [22] and algorithmic self-assembly of both linear [7] and two-dimensional [10] arrays By various otherpaths, a number of physicists have joined the party, mixing their own ideaswith Ned’s paradigm of “DNA as Tinkertoys” to create nanomechanical sys-tems such as DNA tweezers [26] and walkers [25, 17, 20] DNA nanotechnologyhas taken on a life of its own since Ned’s original vision of DNA fish flying

computa-in an extended Escherian lattice [14], and we look forward to a new “DNAworld” in which an all-DNA “bacterium” wriggles, reproduces, and computes

On a personal level, I and many others have gotten to find out exactlywhat kind of twisted genius Ned is Ned is a singular character He is atonce gruff and caring, vulgar and articulate, stubborn and visionary Ned

is generous both with his knowledge of DNA and his knowledge of life His

4 P.W.K Rothemund

life’s philosophy includes a strong tension between the abysmally negative(the general state of the world) and the just tolerably positive (that whichone can, with great effort, hope to achieve) To paraphrase and to whitewash,

“In a world full of execrable excrescences, there is always a fetid coprostasis

of an idea to make your own.” Once one is correctly calibrated to Ned, thissuperficially gloomy counsel becomes positively bright and Ned’s success withDNA nanotechnology serves as an example for the young scientist In fact,Ned’s education of young scientists reveals a latent optimism As an advisorNed plots a strategic course, giving graduate students projects with risks andpayoffs calculated to help them succeed at every stage — from confidencebuilders in their first years to high-risk/high-gain projects in later years.Ned’s own relationship with science is equally telling of his character He ishealthily (and vocally) paranoid about Nature’s determination to screw up hisexperiments To combat this, he practices a capricious paganism, frequentlyswitching between gods in the hope that one will answer his prayers for ahighly-ordered three-dimensional DNA crystal (A habit which he attemptedunsuccessfully to break when he abandoned crystallography.) Such supersti-tion is tongue-in-cheek, however, and Ned is one of the most careful scientiststhat I know He is ever-mindful that, as Peter Medawar wrote, “research issurely the art of the soluble” and, while his highly imaginative research isconstructive and nonreductionist in its goals, Ned makes sure that it rests onfalsifiable Popperian bedrock

In celebration of Ned the character, as well as the box of Tinkertoys andLegos that he has created, I cover two topics First, I review the recent gener-alization of Ned’s geometry of parallel crossovers to the creation of arbitraryshapes and patterns via a method called scaffolded DNA origami I give anexample pattern with roughly 200 pixels spaced 6 nm apart Second, I propose

a new method for using scaffolded DNA origami to make arbitrary nal networks, both two-dimensional planar stick figures and three-dimensionalpolyhedra

polygo-1 Scaffolded DNA Origami for Parallel Multicrossovers

Fig 1a,b show one of the most successful of Ned’s noncanonical DNA motifs,

a “double-crossover” molecule [4] fashioned from two parallel double helicaldomains that comprise four distinct strands of DNA Each DNA strand windsalong one helix for a number of bases before switching to the other helix bypassing through a structure called a “crossover” (small black triangles) Be-cause strands reverse direction at the crossovers, the crossovers are termed

“antiparallel” It is the juxtaposition of two crossovers that holds the helices

in their parallel arrangement (isolated crossovers assume an equilibrium gle of roughly 60◦), and it is their juxtaposition that also holds the helices

an-rigidly together (isolated crossovers are floppy) These properties allow doublecrossovers to assemble into large extended lattices [22], and nanotubes [12]

Scaffolded DNA Origami 5

C T G A

C A G

C G C C

T

T T T

T T T T

single-stranded origami

c

G A C T G

C T G A C

C A G T

C C G C C C

A G T

G G C T T

C C G A A

C C

G G C G

G G C

T A

A T

2<GATGGCGT CCGTTTAC AGTCGAGG ACGGATCG>3

1>TCACTCTACCGCA GGCAAATG TCAGCTCC TGCCTAGCTCACT<4

1<TAGAGGTAAGACC TGCGGTAT AGATAGCA GGCTACTGGAGAT>4

2>CATTCTGG ACGCCATA TCTATCGT CCGATGAC<3

1

4

Fig 1 Double-crossover molecules, and flavors of DNA design.

The idea of holding helical domains in a parallel arrangement via thejuxtaposition of antiparallel crossovers has become a general principle in DNAnanotechnology, used in at least a dozen constructions For example, it hasbeen extended to molecules with three parallel helices [6], and it has beenused to attach triangles rigidly to a nanomechanical device [23]

A key question is how to create generalized multicrossover molecules withparallel helices To answer this question, it is necessary to understand theadvantages and disadvantages of different approaches Within the DNA nan-otechnology paradigm, designs may be classified by how they are built upfrom component strands, being (1) composed entirely of short oligonucleotidestrands as in Fig 1c, (2) composed of one long “scaffold strand” (black) andnumerous short “helper strands” (colored) as in Fig 1d, or (3) composed

of one long strand and few or no helpers as in Fig 1e Here these designapproaches are termed “multistranded”, “scaffolded”, and “single-stranded”,respectively The last two are termed “DNA origami” because a single longstrand is folded, whether by many helpers or by self-interactions

Multistranded designs (such as Ned’s original cube) suffer from the ficulty of getting the ratios of the component short strands exactly equal Ifthere are not equal proportions of the various component strands, then in-complete structures form and purification may be required Because, for largeand complex designs, a structure missing one strand is not very differentfrom a complete structure, purification can be difficult and may have to beperformed in multiple steps Single-stranded origami such as William Shih’soctahedron [19] cannot, by definition, suffer from this problem Scaffoldedorigami sidesteps the problem of equalizing strand ratios by allowing an ex-cess of helpers to be used As long as each scaffold strand gets one of each