Design of an Autonomous DNA Nanomechanical Device Capable of Universal Computation and Universal Translational Motion

Intelligent nanomechanical devices that operate in an autonomous fashion are of great theoretical and practical interest. Recent successes in building large scale DNA nano-structures, in constructing DNA mechanical devices, and in DNA computing provide a solid foundation for the next step forward: designing autonomous DNA mechanical devices capable of arbitrarily complex behavior. One prototype system towards this goal can be an autonomous DNA mechanical device capable of universal computation, by mimicking the operation of a universal Turing machine. Building on our prior theoretical design and prototype experimental construction of an autonomous unidirectional DNA walking device moving along a linear track, we present here the design of a nanomechanical DNA device that autonomously mimics the operation of a 2-state 5-color universal Turing machine. Our autonomous nanomechanical device, called an Autonomous DNA Turing Machine (ADTM), is thus capable of universal computation and hence complex translational motion, which we define as universal translational motion.

[1]  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.

[2]  A. Turberfield,et al.  DNA fuel for free-running nanomachines. , 2003, Physical review letters.

[3]  John H. Reif,et al.  Paradigms for Biomolecular Computation , 1998 .

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

[5]  Jean-Louis Mergny,et al.  DNA duplex–quadruplex exchange as the basis for a nanomolecular machine , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Floyd E Romesberg,et al.  Beyond A, C, G and T: augmenting nature's alphabet. , 2003, Current opinion in chemical biology.

[7]  Hao Yan,et al.  Directed Nucleation Assembly of Barcode Patterned DNA Lattices , 2003 .

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

[9]  N. Seeman,et al.  Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy , 1999 .

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

[11]  Shi V. Liu.  Debating controversies can enhance creativity , 2000, Nature.

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

[13]  Paul W. K. Rothemund,et al.  A DNA and restriction enzyme implementation of Turing machines , 1995, DNA Based Computers.

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

[15]  Lloyd M. Smith,et al.  DNA computing on surfaces , 2000, Nature.

[16]  Gerry White,et al.  The Past , 2000 .

[17]  E. Shapiro,et al.  Programmable and autonomous computing machine made of biomolecules , 2001, Nature.

[18]  Warren D. Smith.  DNA computers in vitro and vivo , 1995, DNA Based Computers.

[19]  N. Seeman.  DNA in a material world , 2003, Nature.

[20]  Ehud Shapiro,et al.  DNA molecule provides a computing machine with both data and fuel , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Bernard Yurke,et al.  A DNA-based molecular device switchable between three distinct mechanical states , 2002 .

[22]  Edward M. Scott,et al.  Beyond A.A. , 1986 .

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

[24]  Stephen Wolfram,et al.  A New Kind of Science , 2003, Artificial Life.

[25]  Laura F. Landweber,et al.  The past, present and future of molecular computing , 2000, Nature Reviews Molecular Cell Biology.

[26]  A. Turing.  On Computable Numbers, with an Application to the Entscheidungsproblem. , 1937 .

[27]  Shirley Dex,et al.  JR 旅客販売総合システム（マルス）における運用及び管理について , 1991 .

[28]  N. Seeman,et al.  A nanomechanical device based on the B–Z transition of DNA , 1999, Nature.

[29]  John H. Reif,et al.  Parallel molecular computation , 1995, SPAA '95.

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

[31]  J. Reif,et al.  A unidirectional DNA walker that moves autonomously along a track. , 2004, Angewandte Chemie.

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

[33]  N. Seeman,et al.  A robust DNA mechanical device controlled by hybridization topology , 2002, Nature.

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

[35]  Weihong Tan,et al.  A Single DNA Molecule Nanomotor , 2002 .

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

[37]  J. Reif,et al.  A two-state DNA lattice switched by DNA nanoactuator. , 2003, Angewandte Chemie.

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

[39]  L F Landweber,et al.  Molecular computation: RNA solutions to chess problems , 2000, Proc. Natl. Acad. Sci. USA.

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

[41]  Richard J. Lipton,et al.  DNA²DNA Computations: A Potential "Killer App"? , 1997, ICALP.

[42]  A. Church.  Review: A. M. Turing, On Computable Numbers, with an Application to the Entscheidungsproblem , 1937 .

[43]  R J Lipton,et al.  DNA solution of hard computational problems. , 1995, Science.

[44]  P D Kaplan,et al.  DNA solution of the maximal clique problem. , 1997, Science.

[45]  F. Simmel,et al.  Using DNA to construct and power a nanoactuator. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[46]  S. Balasubramanian,et al.  A proton-fuelled DNA nanomachine. , 2003, Angewandte Chemie.

[47]  A. Turing,et al.  On Computable Numbers, with an Application to the Entscheidungsproblem. A Correction , 1938 .