Demonstration of a universal surface DNA computer

Nucleic Acids Research

Volumn 32, Issue 10, 2004, Pages 3115-3123

  Su, Xingping ^a   Smith, Lloyd M ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ANTISENSE OLIGONUCLEOTIDE; DNA DIRECTED DNA POLYMERASE; LIGASE; LOCKED NUCLEIC ACID;

ARTICLE; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; COMPUTER SYSTEM; CONTROLLED STUDY; DNA DETERMINATION; EQUIPMENT DESIGN; INFORMATION SCIENCE; LOGIC; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROBLEM SOLVING; BIOSYNTHESIS; DNA DENATURATION; GENETICS; METABOLISM; MOLECULAR COMPUTER; PHOSPHORYLATION; REPRODUCIBILITY;

COMPUTERS, MOLECULAR; DNA; DNA-DIRECTED DNA POLYMERASE; LIGASES; NUCLEIC ACID DENATURATION; OLIGONUCLEOTIDES, ANTISENSE; PHOSPHORYLATION; REPRODUCIBILITY OF RESULTS;

EID: 2942652933     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh635     Document Type: Article

References (20)

1. Adleman,L.M. (1994) Molecular computation of solutions to combinatorial problems. Science, 266, 1021-1024.
2. Liu,Q., Wang,L., Frutos,A., Condon,A.E. and Smith,L.M. (2000) DNA computing on surfaces. Nature, 413, 175-179.
3. Yoshida,H. and Suyama,A. (2000) DIMACS: Series in Discrete Mathematics and Theoretical Computer Science. Solution to 3-SAT by Breadth First Search. American Mathematical Society, Providence, RI, Vol. 54, pp. 9-20.
4. Sakamoto,K., Gouzu,H., Komiya,K., Kiga,D., Yokoyama,S., Yokomori,T. and Hagiya,M. (2000) Molecular computation by DNA hairpin formation. Science, 288, 1223-1226.
5. Faulhammer,D., Cukras,A.R., Lipton,R.J. and Landweber,L.F. (2000) Molecular computation: RNA solutions to chess problems. Proc. Natl Acad. Sci. USA, 97, 1385-1389.
6. Braich,R.S., Chelyapov,N., Johnson,C., Rothemund,P.W.K. and Adleman,L.M. (2002) Solution of a 20-variable 3-SAT problem on a DNA computer. Science, 296, 499-502.
7. Gifford,D.K. (1994) On the path to computation with DNA. Science, 266, 993-994.
8. Boneh,D., Dunworth,C., Lipton,R.J. and Sgall,J. (1996) On the computational power of DNA. Discrete Appl. Math., 71, 79-94.
9. Winfree,E. (2000) Algorithmic self-assembly of DNA: theoretical motivations and 2D assembly experiments. J. Biomol. Struct. Dyn., 11, 263-270.
10. Benenson,Y., Paz-Elizur, T, Adar,R., Keinan,Z.L. and Shapiro,E. (2001) Programmable and autonomous computing machine made of biomolecules. Nature, 414, 430-434.
11. Stojanovic,M. and Stefanovic,D. (2003) A deoxyribozyme-based molecular automaton. Nat. Biotechnol., 21, 1069-1074.
12. Frutos,A.G., Liu,Q., Thiel,A.J., Sanner,A.M.W., Condon,A.E., Smith,L.M. and Corn,R.M. (1997) Demonstration of a word design strategy for DNA computing on surfaces. Nucleic Acids Res., 25, 4748-4757.
13. Wang,L., Liu,Q., Corn,R.M., Condon,A.E. and Smith,L.M. (2000) Multiple word DNA computing on surfaces. J. Am. Chem. Soc., 122, 7435-7440.
14. Cai,W., Condon,A.E., Corn,R.M., Glaser,E., Fei,Z., Frutos,T., Guo,Z., Lagally,M.G., Liu,Q., Smith,L.M. and Thiel,A. (1997) The power of surface-based DNA computation. Paper presented at the Proceedings of The First Annual International Conference on Computational Molecular Biology (Recomb 97), Saute Fe, NM, January, pp. 67-74.
15. Ralston,A., Reilly,E.D. and Hemmendinger,D. (2000) Encyclopedia of Computer Science, 4th Edn, Nature Publishing Group, London, UK.
16. Petersen,M. and Wengel,J. (2003) LNA: a versatile tool for therapeutics and genomics. Trends Biotechnol., 21, 74-81.
17. Brockman,J.M., Frutos,A.G. and Corn,R.M. (1999) A multi-step chemical modification procedure to create DNA arrays on gold surfaces for the study of protein-DNA interaction with surface plasmon resonance imaging. J. Am. Chem. Soc., 121, 8044-8051.
18. Chen,Y., Shortreed,M.R., Peelen,D., Lu, M and Smith,L.M. (2004) Surface amplification of invasive cleavage products. J. Am. Chem. Soc., 126, 3016-3017.
19. Vainrub,A. and Pettitt,B.M. (2000) Thermodynamics of association to a molecule immobilized in an electric double layer. Chem. Phys. Lett., 323, 160-166.
20. Di Giusto,D.A. and King,G.C. (2004) Strong positional preference in the interaction of LNA oligonucleotides with DNA polymerase and proofreading exonuclease activities: implications for genotyping assays. Nucleic Acids Res., 32, e32.