Design of nucleic acid sequences for DNA computing based on a thermodynamic approach

Nucleic Acids Research

Volumn 33, Issue 3, 2005, Pages 903-911

  Tanaka, Fumiaki ^a   Kameda, Atsushi ^b   Yamamoto, Masahito ^a,b   Ohuchi, Azuma ^a,b  

^a HOKKAIDO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER MODEL; COMPUTER PROGRAM; DNA DETERMINATION; DNA SEQUENCE; MATHEMATICAL COMPUTING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; THERMODYNAMICS; BIOLOGY; EVALUATION; METHODOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; SEQUENCE ANALYSIS, DNA; SOFTWARE; THERMODYNAMICS; USER-COMPUTER INTERFACE;

EID: 13944261250     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki235     Document Type: Article

References (23)

1. Adleman,L.M. (1994) Molecular computation of solutions to combinatorial problems. Science, 266, 1021-1024.
2. Braich,R.S., Chelyapov,N., Johnson,C., Rothemund,P.W. and Adleman,L. (2002) Solution of a 20-variable 3-SAT problem on a DNA computer. Science, 296, 499-502.
3. 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.
4. Rouillard,J.M., Zuker,M. and Gulari,E. (2003) OligoArray 2.0: Design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res., 31, 3057-3062.
5. Bozdech,Z., Zhu,J., Joachimiak,M.P., Cohen,F.E., Pulliam,B. and DeRisi,J.L. (2003) Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol., 4, R9.
6. Kane,M.D., Jatkoe,T.A., Stumpf,C.R., Lu,J., Thomas,J.D. and Madore,S.J. (2000) Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res., 28, 4552-4557.
7. Winfree,E., Liu,F, Wenzler,L.A. and Seeman,N.C. (1998) Design and self-assembly of two-dimensional DNA crystals. Nature, 394, 539-544.
8. Shih,W.M., Quispe,J.D. and Joyce,G.F. (2004) A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427, 618-621.
9. Yan,H., Zhang,X., Shen,Z. and Seeman,N.C. (2002) A robust DNA mechanical device controlled by hybridization topology. Nature, 415, 62-65.
10. Arita,M. and Kobayashi, S. (2002) DNA sequence design using templates. New Gen. Comput., 20, 263-277.
11. Arita,M., Nishikawa,A., Hagiya,M., Komiya,K., Gouzu,H. and Sakamoto,K. (2000) Improving sequence design for DNA computing. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2000), July 8-12, Las Vegas, NV. Morgan Kaufmann, pp. 875-882.
12. Dirks,R.M., Lin,M., Winfree,E. and Pierce,N.A. (2004) Paradigms for computational nucleic acid design. Nucleic Acids Res., 32, 1392-1403.
13. Andronescu,M., Fejes,A.P., Hutter,F., Hoos,H.H. and Condon,A. (2004) A new algorithm for RNA secondary structure design. J. Mol. Biol., 336, 607-624.
14. Andronescu,M., Aguirre-Hernandez,R., Condon,A. and Hoos,H.H. (2003) RNAsoft: A suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res., 31, 3416-3422.
15. Hofacker,I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431.
16. Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
17. Zuker,M. and Stiegler,P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
18. SantaLucia,J.Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
19. Tanaka,F., Kameda,A., Yamamoto,M. and Ohuchi,A. (2004) Thermodynamic parameters based on a nearest-neighbor model for DNA sequences with a single-bulge loop. Biochemistry, 43, 7143-7150.
20. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
21. Peritz,A.E., Kierzek,R., Sugimoto,N. and Turner,D.H. (1991) Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops. Biochemistry, 30 6428-6436.
22. Bommarito,S., Peyret,N. and SantaLucia,J.,Jr (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res. 28, 1929-1934.
23. Lyngsø,R.B., Zuker,M. and Pedersen,C.N.S. (1999) Fast evaluation of internal loops in RNA secondary structure prediction. Bioinformatics 15, 440-445.