Self-Assembled DNA Nanostructures and DNA Devices

This chapter overviews the past and current state of the emerging research area in the field of nanoscience that make use of synthetic DNA to self-assemble into DNA nanostructures and to make operational molecular-scale devices. Recently there have been a series of quite astonishing experimental results which have taken the technology from a state of intriguing possibilities into demonstrated capabilities of quickly increasing scale and complexity. We discuss the design and demonstration of molecular-scale devices that make use of DNA nanostructures to achieve: molecular patterning, molecular computation, amplified sensing and nanoscale transport. We particularly emphasize molecular devices that make use of techniques that seem most promising, namely ones that are programmable (the tasks executed can be modified without entirely redesigning the nanostructure) and autonomous (executing steps with no external mediation after starting).

[1]  S. Murata,et al.  Substrate-assisted assembly of interconnected single-duplex DNA nanostructures. , 2009, Angewandte Chemie.

[2]  Erik Winfree,et al.  On the computational power of DNA annealing and ligation , 1995, DNA Based Computers.

[3]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[4]  C. Dwyer,et al.  Scalable, low-cost, hierarchical assembly of programmable DNA nanostructures , 2007 .

[5]  John H. Reif,et al.  The Design of Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA , 2002, DNA.

[6]  J. Reif,et al.  Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Thomas H. LaBean,et al.  Optimized fabrication and electrical analysis of silver nanowires templated on DNA molecules , 2006 .

[8]  Ashish Goel,et al.  Error Free Self-assembly Using Error Prone Tiles , 2004, DNA.

[9]  Hao Yan,et al.  Parallel molecular computations of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly. , 2003, Journal of the American Chemical Society.

[10]  K. Mullis,et al.  Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. , 1985, Science.

[11]  Nadrian C Seeman,et al.  Nanotechnology and the double helix. , 2004, Scientific American.

[12]  Sudheer Sahu,et al.  Autonomous Programmable Nanorobotic Devices Using DNAzymes , 2007, DNA.

[13]  Tong Wang,et al.  Structural DNA Nanotechnology: Molecular Construction and Computation , 2005, UC.

[14]  Shawn M. Douglas,et al.  DNA-nanotube-induced alignment of membrane proteins for NMR structure determination , 2007, Proceedings of the National Academy of Sciences.

[15]  Erik Winfree,et al.  Two computational primitives for algorithmic self-assembly: copying and counting. , 2005, Nano letters.

[16]  Chengde Mao,et al.  Cascade Signal Amplification for DNA Detection , 2006, Chembiochem : a European journal of chemical biology.

[17]  Erik Winfree,et al.  Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly , 2003, DNA.

[18]  E. Winfree,et al.  Toward reliable algorithmic self-assembly of DNA tiles: a fixed-width cellular automaton pattern. , 2008, Nano letters.

[19]  C. Mao,et al.  Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra , 2008, Nature.

[20]  Rashid Amin,et al.  ARTIFICIALLY DESIGNED DNA NANOSTRUCTURES , 2009 .

[21]  John H. Reif,et al.  Designs of Autonomous Unidirectional Walking DNA Devices , 2004, DNA.

[22]  P. Yin,et al.  A DNAzyme that walks processively and autonomously along a one-dimensional track. , 2005, Angewandte Chemie.

[23]  Erik Winfree,et al.  Programmable Control of Nucleation for Algorithmic Self-Assembly , 2009, SIAM J. Comput..

[24]  Robert M. Dirks,et al.  Triggered amplification by hybridization chain reaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[25]  E. Winfree,et al.  Algorithmic Self-Assembly of DNA Sierpinski Triangles , 2004, PLoS biology.

[26]  J. Kjems,et al.  Self-assembly of a nanoscale DNA box with a controllable lid , 2009, Nature.

[27]  Erik Winfree,et al.  Reducing facet nucleation during algorithmic self-assembly. , 2007, Nano letters.

[28]  Erik Winfree,et al.  Experimental progress in computation by self-assembly of DNA tilings , 1999, DNA Based Computers.

[29]  Hao Yan,et al.  DNA Nanotechnology: A Rapidly Evolving Field , 2006 .

[30]  G. Schmid The Nature of Nanotechnology , 2010 .

[31]  Jack Parker Computing with DNA , 2003, EMBO reports.

[32]  Ye Tian,et al.  A Fresh Look at DNA Nanotechnology , 2006, Nanotechnology: Science and Computation.

[33]  E. Shapiro,et al.  An autonomous molecular computer for logical control of gene expression , 2004, Nature.

[34]  John H. Reif,et al.  Isothermal reactivating Whiplash PCR for locally programmable molecular computation , 2009, Natural Computing.

[35]  A. Turberfield,et al.  DNA nanomachines. , 2007, Nature nanotechnology.

[36]  Sudheer Sahu,et al.  Design of Autonomous DNA Cellular Automata , 2005, DNA.

[37]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[38]  John H. Reif,et al.  Self‐Assembling DNA Nanostructures for Patterned Molecular Assembly , 2007 .

[39]  J. Reif,et al.  Finite-size, fully addressable DNA tile lattices formed by hierarchical assembly procedures. , 2006, Angewandte Chemie.

[40]  Shawn M. Douglas,et al.  Folding DNA into Twisted and Curved Nanoscale Shapes , 2009, Science.

[41]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[42]  Erik Winfree,et al.  TileSoft: Sequence Optimization Software for Designing DNA Secondary Structures , 2004 .

[43]  Chengde Mao,et al.  An autonomous DNA nanomotor powered by a DNA enzyme. , 2004, Angewandte Chemie.

[44]  B H Robinson,et al.  The design of a biochip: a self-assembling molecular-scale memory device. , 1987, Protein engineering.

[45]  Erik Winfree,et al.  Universal computation via self-assembly of DNA: Some theory and experiments , 1996, DNA Based Computers.

[46]  Harry M. T. Choi,et al.  Programming biomolecular self-assembly pathways , 2008, Nature.

[47]  N. Seeman,et al.  A precisely controlled DNA biped walking device , 2004 .

[48]  Andrew J Turberfield,et al.  The single-step synthesis of a DNA tetrahedron. , 2004, Chemical communications.

[49]  Naftali Tishby,et al.  Stochastic computing with biomolecular automata , 2004, Proc. Natl. Acad. Sci. USA.

[50]  D. Y. Zhang,et al.  Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA , 2007, Science.

[51]  Robert L. Berger The undecidability of the domino problem , 1966 .

[52]  Shawn M. Douglas,et al.  Self-assembly of DNA into nanoscale three-dimensional shapes , 2009, Nature.

[53]  Sudheer Sahu,et al.  Compact Error-Resilient Computational DNA Tiling Assemblies , 2004, DNA.

[54]  J. Reif,et al.  Logical computation using algorithmic self-assembly of DNA triple-crossover molecules , 2000, Nature.

[55]  Chengde Mao,et al.  Self-assembly of hexagonal DNA two-dimensional (2D) arrays. , 2005, Journal of the American Chemical Society.

[56]  J. Reif,et al.  Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes , 2000 .

[57]  Yan Liu,et al.  DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires , 2003, Science.

[58]  Chengde Mao,et al.  Sequence symmetry as a tool for designing DNA nanostructures. , 2005, Angewandte Chemie.

[59]  D. Shank,et al.  Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Darko Stefanovic,et al.  A deoxyribozyme-based molecular automaton , 2003, Nature Biotechnology.

[61]  Hao Wang Proving theorems by pattern recognition — II , 1961 .

[62]  John H. Reif,et al.  Activatable Tiles: Compact, Robust Programmable Assembly and Other Applications , 2007, DNA.

[63]  P. Rothemund Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[64]  John H. Reif,et al.  The design of autonomous DNA nano-mechanical devices: Walking and rolling DNA , 2003, Natural Computing.

[65]  G. Walker,et al.  Strand displacement amplification--an isothermal, in vitro DNA amplification technique. , 1992, Nucleic acids research.

[66]  Thomas H. LaBean,et al.  Constructing novel materials with DNA , 2007 .

[67]  Leandro Nunes de Castro,et al.  Fundamentals of Natural Computing - Basic Concepts, Algorithms, and Applications , 2006, Chapman and Hall / CRC computer and information science series.

[68]  M. Hagiya,et al.  State transitions by molecules. , 1999, Bio Systems.

[69]  William M. Shih,et al.  A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron , 2004, Nature.

[70]  Pamela E. Constantinou,et al.  From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal , 2009, Nature.

[71]  Erik Winfree,et al.  The program-size complexity of self-assembled squares (extended abstract) , 2000, STOC '00.

[72]  R. Robinson Undecidability and nonperiodicity for tilings of the plane , 1971 .

[73]  Ehud Shapiro,et al.  Bringing DNA computers to life , 2006 .