DNA Computation: Applications and Perspectives

The computational capability of living systems has intrigued researchers for years. Primarily, the focus has been on implementing aspects of living systems in computational devices. Computer literal peoples expand their hand to the molecular biologist and chemist to explore the potential for computation of biological molecules line Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA) which are information carrying molecules. In this context, DNA computation is basically a collection of specially selected DNA strands whose combinations will result in the solution to some problems. DNA computation rather DNA-based computing is at the intersection of several threads of research. Main advantages of DNA computation are miniaturization and parallelism over conventional silicon-based machines. The informationbearing capability of DNA molecules is a cornerstone of modern theories of genetics and molecular biology. In this paper we have tried to focus on some key issues regarding the used and implementation DNA-based devices in life science field. We have also tried to suggest its advantage over silicon computers.

[1]  H Wu.  An improved surface-based method for DNA computation. , 2001, Bio Systems.

[2]  T. Head.  Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors. , 1987, Bulletin of mathematical biology.

[3]  Chang-Biau Yang,et al.  Solving satisfiability problems using a novel microarray-based DNA computer , 2007, Biosyst..

[4]  Masanori Arita,et al.  Solid phase DNA solution to the Hamiltonian path problem , 1997, DNA Based Computers.

[5]  A. Kowald,et al.  Off-target activity of TNF-α inhibitors characterized by protein biochips , 2008, Analytical and bioanalytical chemistry.

[6]  P. Harbury,et al.  DNA Display I. Sequence-Encoded Routing of DNA Populations , 2004, PLoS biology.

[7]  Hui Ma,et al.  Parallel scan spectral surface plasmon resonance imaging. , 2008, Applied optics.

[8]  Gheorghe Paun,et al.  DNA computing based on splicing: universality results. , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[9]  John von Neumann,et al.  Theory Of Self Reproducing Automata , 1967 .

[10]  Rainer Schuler,et al.  Strategies for the development of a peptide computer , 2001, Bioinform..

[11]  Chang-Biau Yang,et al.  A DNA solution of SAT problem by a modified sticker model. , 2005, Bio Systems.

[12]  Wolfgang Banzhaf,et al.  Microarray-based in vitro evaluation of DNA oligomer libraries designed in silico. , 2004, Chemphyschem : a European journal of chemical physics and physical chemistry.

[13]  G. Węgrzyn,et al.  Rapid Identification of Shiga Toxin-producing Escherichia coli (STEC) Using Electric Biochips , 2008, Diagnostic molecular pathology : the American journal of surgical pathology, part B.

[14]  B. Nordén,et al.  Triplex addressability as a basis for functional DNA nanostructures. , 2007, Nano letters.

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

[16]  Lloyd M Smith,et al.  Demonstration of a universal surface DNA computer. , 2004, Nucleic acids research.

[17]  Anne Condon,et al.  A thermodynamic approach to designing structure-free combinatorial DNA word sets , 2005, Nucleic acids research.

[18]  Tom Quirk,et al.  There’s Plenty of Room at the Bottom , 2006, Size Really Does Matter.

[19]  Richard A Mathies,et al.  An integrated microfluidic processor for single nucleotide polymorphism-based DNA computing. , 2005, Lab on a chip.

[20]  Majid Darehmiraki.  A New Solution for Maximal Clique Problem based Sticker Model , 2009, Biosyst..

[21]  Patricia Rodriguez-Tomé,et al.  Accessing and distributing EMBL data using CORBA (common object request broker architecture) , 2000, Genome Biology.

[22]  Jin Xu,et al.  DNA Solution of a Graph Coloring Problem , 2002, J. Chem. Inf. Comput. Sci..

[23]  Z. Ibrahim,et al.  Hybridization-ligation versus parallel overlap assembly: an experimental comparison of initial pool generation for direct-proportional length-based DNA computing , 2006, IEEE Transactions on NanoBioscience.

[24]  Jin Xu,et al.  A Chinese Postman Problem Based on DNA Computing , 2002, J. Chem. Inf. Comput. Sci..

[25]  N. Seeman,et al.  Holliday junction crossover topology. , 1994, Journal of molecular biology.

[26]  A P Mills,et al.  Article for analog vector algebra computation. , 1999, Bio Systems.

[27]  Fumiaki Tanaka,et al.  Design of nucleic acid sequences for DNA computing based on a thermodynamic approach , 2005, Nucleic acids research.

[28]  I. Kulić,et al.  Evaluating polynomials on the molecular level--a novel approach to molecular computers. , 1998, Bio Systems.

[29]  J. M. Miret,et al.  Markov chains: computing limit existence and approximations with DNA. , 2005, Bio Systems.

[30]  Richard J. Lipton,et al.  Fidelity of Enzymatic Ligation for DNA Computing , 2000, J. Comput. Biol..

[31]  G. Cost.  Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA , 2007, Nature Protocols.

[32]  James L. Winkler,et al.  Accessing Genetic Information with High-Density DNA Arrays , 1996, Science.

[33]  Bin Fu,et al.  Molecular Computing, Bounded Nondeterminism, and Efficient Recursion , 1997, Algorithmica.

[34]  Grace Jordison.  Molecular Biology of the Gene , 1965, The Yale Journal of Biology and Medicine.

[35]  Erik Winfree,et al.  A Sticker-Based Model for DNA Computation , 1998, J. Comput. Biol..

[36]  Dafa Li,et al.  Hairpin formation in DNA computation presents limits for large NP-complete problems. , 2003, Bio Systems.

[37]  C Martín-Vide,et al.  New computing paradigms suggested by DNA computing: computing by carving. , 1999, Bio Systems.

[38]  Jun Gu,et al.  Algorithms for the satisfiability (SAT) problem: A survey , 1996, Satisfiability Problem: Theory and Applications.

[39]  Byoung-Tak Zhang,et al.  Solving traveling salesman problems with DNA molecules encoding numerical values. , 2004, Bio Systems.

[40]  Tom Head,et al.  Formal language theory and DNA: An analysis of the generative capacity of specific recombinant behaviors , 1987 .

[41]  Christof M Niemeyer,et al.  Design and Evaluation of Single-Stranded DNA Carrier Molecules for DNA-Directed Assembly , 2006, Journal of biomolecular structure & dynamics.

[42]  Qinghua Liu,et al.  A surface-based approach to DNA computation , 1996, DNA Based Computers.

[43]  Anne Condon,et al.  Designed DNA molecules: principles and applications of molecular nanotechnology , 2006, Nature Reviews Genetics.

[44]  Jing Li,et al.  Differential dependence on DNA ligase of type II restriction enzymes: a practical way toward ligase-free DNA automaton. , 2007, Biochemical and biophysical research communications.

[45]  N. Seeman.  Nucleic acid junctions and lattices. , 1982, Journal of theoretical biology.

[46]  A. Melkikh.  DNA Computing, Computation Complexity and Problem of Biological Evolution Rate , 2008, Acta biotheoretica.

[47]  Jonghwa Lee,et al.  "Smart" biopolymer for a reversible stimuli-responsive platform in cell-based biochips. , 2008, Langmuir : the ACS journal of surfaces and colloids.

[48]  J. McCaskill,et al.  End-specific covalent photo-dependent immobilisation of synthetic DNA to paramagnetic beads. , 2000, Nucleic acids research.

[49]  Grzegorz Rozenberg,et al.  DNA computing using single-molecule hybridization detection. , 2004, Nucleic acids research.

[50]  Dafa Li,et al.  Scalability of the surface-based DNA algorithm for 3-SAT. , 2006, Bio Systems.

[51]  A Salomaa,et al.  Bidirectional sticker systems. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[52]  Hui Wang,et al.  The perils of polynucleotides: The experimental gap between the design and assembly of unusual DNA structures , 1996, DNA Based Computers.

[53]  Yaw-Jen Chang,et al.  Dividable membrane with multi-reaction wells for microarray biochips. , 2008, Journal of bioscience and bioengineering.

[54]  A Suyama,et al.  Intelligent DNA chips: logical operation of gene expression profiles on DNA computers. , 2000, Genome informatics. Workshop on Genome Informatics.

[55]  R. Deaton,et al.  Estimating the sequence complexity of a random oligonucleotide population by using in vitro thermal melting and Cot analyses. , 2005, Nanomedicine : nanotechnology, biology, and medicine.

[56]  Dafa Li,et al.  The surface-based approach for DNA computation is unreliable for SAT. , 2005, Bio Systems.

[57]  N. Cozzarelli,et al.  Directed assembly of DNA molecules via simultaneous ligation and digestion. , 2007, BioTechniques.

[58]  N. Seeman,et al.  The construction of a trefoil knot from a DNA branched junction motif , 1994, Biopolymers.

[59]  N. Seeman,et al.  Construction of a DNA-Truncated Octahedron , 1994 .

[60]  Carlo C. Maley,et al.  DNA Computation: Theory, Practice, and Prospects , 1998, Evolutionary Computation.

[61]  John H. Holland,et al.  Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .

[62]  L F Landweber,et al.  The evolution of cellular computing: nature's solution to a computational problem. , 1999, Bio Systems.

[63]  Laurent Griscom,et al.  In situ micropatterning technique by cell crushing for co-cultures inside microfluidic biochips , 2008, Biomedical microdevices.

[64]  P. McEuen,et al.  Controlled assembly of dendrimer-like DNA , 2004, Nature materials.

[65]  Martyn Amos,et al.  DNA computation , 1997 .

[66]  Qinghua Liu,et al.  DNA Computing on Surfaces: Encoding Information at the Single Base Level , 1998, J. Comput. Biol..

[67]  Shinzi Ogasawara,et al.  Autonomous DNA computing machine based on photochemical gate transition. , 2008, Journal of the American Chemical Society.

[68]  Byoung-Tak Zhang,et al.  An evolutionary Monte Carlo algorithm for predicting DNA hybridization , 2008, Biosyst..

[69]  H. Hug,et al.  Measurement of the number of molecules of a single mRNA species in a complex mRNA preparation. , 2003, Journal of theoretical biology.

[70]  Jin Xu,et al.  Solving the 3-SAT Problem Based on DNA Computing , 2003, J. Chem. Inf. Comput. Sci..

[71]  Xu Jin,et al.  The general form of 0-1 programming problem based on DNA computing. , 2003, Bio Systems.

[72]  A. Condon,et al.  Surface-based DNA computing operations: DESTROY and READOUT. , 1999, Bio Systems.

[73]  Kazuto Tominaga,et al.  Modeling Molecular Computing Systems by an Artificial ChemistryIts Expressive Power and Application , 2007, Artificial Life.

[74]  Amit Marathe,et al.  On combinatorial DNA word design , 1999, DNA Based Computers.

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

[76]  Robert Penchovsky,et al.  DNA Library Design for Molecular Computation , 2003, J. Comput. Biol..

[77]  J.,et al.  Using DNA to Solve NP-Complete ProblemsRichard , 1995 .

[78]  P W Rothemund,et al.  Using lateral capillary forces to compute by self-assembly , 2000, Proc. Natl. Acad. Sci. USA.

[79]  M. Whelan,et al.  Fabrication of holographic diffractive optical elements for enhancing light collection from fluorescence-based biochips. , 2008, Optics letters.

[80]  Witold Pedrycz,et al.  DNA approach to solve clustering problem based on a mutual order , 2008, Biosyst..

[81]  Erliang Zeng,et al.  IEM: an algorithm for iterative enhancement of motifs using comparative genomics data. , 2007, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

[82]  Daming Zhu,et al.  DNA solution based on sequence alignment to the Minimum Spanning Tree problem , 2008, Int. J. Bioinform. Res. Appl..

[83]  Jin Xu,et al.  A new DNA computing model for the NAND gate based on induced hairpin formation. , 2004, Bio Systems.

[84]  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.

[85]  A. Condon,et al.  Demonstration of a word design strategy for DNA computing on surfaces. , 1997, Nucleic acids research.

[86]  Luigi Petraccone,et al.  Structure-based drug design: from nucleic acid to membrane protein targets. , 2009, Experimental and molecular pathology.

[87]  B Fu,et al.  Length bounded molecular computing. , 1999, Bio Systems.