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 C C 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. 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Cover Design: KünkelLopka, Werbeagentur, Heidelberg Typesetting: by the Editors Production: LE-T E X Jelonek, Schmidt & Vöckler GbR, Leipzig Printed on acid-free paper 45/3142/YL – 5 4 3 2 1 0 Editors Junghuei Chen Department of Chemistry and Biochemistry University of Delaware Newark, DE 19716, USA Nataša Jonoska Department of Mathematics University of South Florida 4202 E. Fowler Av., PHY114 Tampa, FL 33620-5700, USA Grzegorz Rozenberg Leiden University Leiden Institute for Advanced Computer Science Niels Bohrweg 1 2333 CA Leiden, The Netherlands Series Editors G. Rozenberg (Managing Editor) rozenber@liacs.nl Th. Bäck, J.N. Kok, H.P. Spaink Leiden Institute of Advanced Computer Science 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 Preface Nanotechnology is slowly and steadily entering more and more aspects of our life. It is becoming a base for developing new materials as well as a base for developing novel methods of computing. As natural computing is concerned with information processing taking place in or inspired by nature, the ideas coming from basic interactions between atoms and molecules naturally become part 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 com- pletely new way of looking at this molecule of life. Starting with the synthesis of the first immobile Holliday junction, now referred to as J1, through the double and triple cross-over molecules, Ned has shown that DNA is a pow- erful and versatile molecule which is ideal for building complex structures at the nanometer scale. Through the years, Ned has used some of the basic DNA motif struc- 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 and demonstrated originally in Ned’s lab, but then all these ideas and designs were followed up by many other researchers around the world. Adleman’s seminal paper from 1994 provided a proof of principle that computing at a molecular level, with DNA, is possible. This led to a real explosion of research on molecular computing, and very quickly Ned’s ideas concerning the design and construction of nanoscale structures from DNA had a profound influence on the development of both the theoretical and the experimental 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 always considered 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 for almost 30 years and is still providing valuable insights into the DNA and RNA biophysical and topological properties as well as the mechanism of homologous recombination between two chromosomal DNAs. Ned’s enormous influence extends also to service to the scientific com- munity. Here one has to mention that Ned is the founding president of the International Society for Nanoscale Science, Computation and Engineering (ISNSCE). The respect that Ned enjoys is also manifested through various honors and awards that he has received — among others the Feynman Prize in Nanotechnology and the Tulip Award in DNA Computing. 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 of DNA-based nanostructures! Ned is an excellent lecturer and has given talks around the world, thereby instigating significant interest and research in DNA nanotechnology and computing. With this volume, which presents many aspects of research in basic sci- ence, application, theory and computing with DNA molecules, we celebrate a scientist who has been a source of inspiration to many researchers all over the world, and to us a mentor, a scientific collaborator, and a dear friend. December 2005 Junghuei Chen Nataˇsa Jonoska Grzegorz Rozenberg Contents 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 X Contents Test Tube Selection of Large Independent Sets of DNA Oligonucleotides Russell Deaton, Junghuei Chen, Jin-Woo Kim, Max H. Garzon, David H. Wood 147 Part III DNA Nanodevices DNA-Based Motor Work at Bell Laboratories Bernard Yurke 165 Nanoscale Molecular Transport by Synthetic DNA Machines 1 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 ChristofM.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 1 Adapted with permission (Table 1, Figs 1–3, and associated text) from J. Am. 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, Gheorghe P˘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 [...]... understand the advantages and disadvantages of different approaches Within the DNA nanotechnology paradigm, designs may be classified by how they are built up from component strands, being (1) composed entirely of short oligonucleotide strands as in Fig 1c, (2) composed of one long “scaffold strand” (black) and numerous short “helper strands” (colored) as in Fig 1d, or (3) composed of one long strand and. .. region outside of the network For example, the network in Fig 8a has 21 holes (small hexagons), and the molecular designs in Fig 8b,c both have 21 helper joins The network in Fig 8d has 19 holes (18 small hexagons and 1 large interior hexagonal void) and the designs in Fig 8e,f both have 19 helper joins The relationship J = S + H = N 1+ H is just a restatement of Euler’s theorem for planar graphs V −E... binary 1 s a new set of labeled helper strands is constructed; so far, they have been labeled with extra DNA hairpins To create a desired pattern (say Fig 4c), the appropriate complementary sets of strands are drawn from the original helper strands and the labeled helper strands Everywhere the pattern has a ‘0’, an original helper strand is used; everywhere the pattern has a 1 , a new helper strand is... replacing each geometrical 3-star 12 P.W.K Rothemund with one of the DNA 3-stars diagrammed in Fig 6b .1 In each DNA 3-star, the black strand is intended to be the scaffold strand of a DNA origami, and the colored strands are helper strands, each 32 nucleotides long DNA 3-stars are classified by the number of “open ends” that they have, i.e the number of breaks in the scaffold strand as it travels around the... Several folding paths (top) drawn without helper strands, and predicted structures (bottom) that use an ∼7000-base-long scaffold Colors indicate the base position on the scaffold, from 1 (red–orange) to 7000 (purple) Arrows indicate seams, which are bridged by helper strands for mechanical stability Scale bar, 10 0 nm As reported in [11 ], the method is general and scales quite well to large origami (Fig 3)... proportions of the various component strands, then incomplete structures form and purification may be required Because, for large and complex designs, a structure missing one strand is not very different from a complete structure, purification can be difficult and may have to be performed in multiple steps Single-stranded origami such as William Shih’s octahedron [19 ] cannot, by definition, suffer from this... sidesteps the problem of equalizing strand ratios by allowing an excess of helpers to be used As long as each scaffold strand gets one of each 6 a P.W.K Rothemund b Fill the shape with helices and a periodic array of crossovers Raster fill helices with a single long scaffold strand = 1 helical turn: y x c Add helper strands to bind the scaffold together seam Special helper strands ( ) bridge the seam Fig 2... joined the party, mixing their own ideas with Ned’s paradigm of “DNA as Tinkertoys” to create nanomechanical systems such as DNA tweezers [26] and walkers [25, 17 , 20] DNA nanotechnology has taken on a life of its own since Ned’s original vision of DNA fish flying in an extended Escherian lattice [14 ], and we look forward to a new “DNA world” in which an all-DNA “bacterium” wriggles, reproduces, and computes... allow double crossovers to assemble into large extended lattices [22], and nanotubes [12 ] Scaffolded DNA Origami a 5 b 2 AGTCGAGG ACGGATCG>3 TCAGCTCC TGCCTAGCTCACT4 TCTATCGT CCGATGAC . Rozenberg (Eds.) 12 3 Nanotechnology: Science and Computation With 12 6 Figures and 10 Tables Library of Congress Control Number: 2005936799 ACM Computing Classification (19 98): F .1, G.2.3, I .1, I.2, I.6,. permission (Table 1, Figs 1 3, and associated text) from J. Am. Chem. Soc. 2004, 12 6, 10 834 10 835. Copyright 2004 American Chemical Society. Contents XI Part VI Biomolecular Computational Models Computing. oligonucleotide strands as in Fig. 1c, (2) composed of one long “scaffold strand” (black) and numerous short “helper strands” (colored) as in Fig. 1d, or (3) composed of one long strand and few or no