Independent sets of DNA oligonucleotides for nanotechnology applications

IEEE Transactions on Nanobioscience

Volumn 9, Issue 1, 2010, Pages 38-43

  Yu, Weixia ^a   Lee, Ju Seok ^b   Johnson, Cole ^c   Kim, Jin Woo ^d   Deaton, Russell ^a,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF ARKANSAS   (United States)

^c WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

^d 3202 Bell Engineering Center   (United States)

Author keywords

DNA; Dynamic programming; Message passing; Nanotechnology

Indexed keywords

DNA DUPLEXES; DNA DYNAMICS; DNA OLIGONUCLEOTIDES; INDEPENDENT SET; SAMPLE SETS; SELF-ASSEMBLY OF NANOSTRUCTURES; SOFTWARE TOOL; THERMODYNAMIC MODEL;

DNA; DYNAMIC PROGRAMMING; MESSAGE PASSING; NANOTECHNOLOGY; OLIGONUCLEOTIDES;

GENES;

DNA; OLIGONUCLEOTIDE;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; METABOLISM; METHODOLOGY; NANOTECHNOLOGY; NUCLEIC ACID HYBRIDIZATION; POLYACRYLAMIDE GEL ELECTROPHORESIS; REPRODUCIBILITY; THERMODYNAMICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DNA; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MODELS, GENETIC; NANOTECHNOLOGY; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDES; REPRODUCIBILITY OF RESULTS; SOFTWARE; THERMODYNAMICS;

EID: 77950525510     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2009.2035446     Document Type: Article

References (22)

1. L. M. Adleman, "Molecular computation of solutions to combinatorial problems," Science, vol.266, pp. 1021-1024, 1994.
2. C. Mirkin, R. L. Letsinger, R. C. Mucic, and J. J. Storhoff, "A DNAbased method for rationally assembling nanoparticles into macroscopic materials," Nature, vol.382, pp. 607-609, 1996.
3. N. C. Seeman and P. S. Lukeman, "Nucleic acid nanostructures: Bottomup control of geometry on the nanoscale," Rep. Prog. Phys., vol.68, pp. 237-270, 2005.
4. E. Winfree, F. Liu, L. A. Wenzler, and N. C. Seeman, "Design and selfassembly of two-dimensional DNA crystals," Nature, vol.394, pp. 539- 544, 1998.
5. P. W. K. Rothemund, "Folding DNA to create nanoscale shapes and patterns," Nature, vol.440, pp. 297-302, 2006.
6. C. R. Cantor and P. R. Schimmel, Biophysical Chemistry-Part III: The Behavior of Biological Macromolecules. New York: Freeman, 1980.
7. R. Deaton, M. Garzon, J. A. Rose, D. R. Franceschetti, R. C. Murphy, and S. E. Stevens. Jr., "Reliability and efficiency of aDNAbased computation," Phys. Rev. Lett., vol.80, pp. 417-420, 1998.
8. A. G. Frutos, Q. Liu, A. J. Thiel, A. M. W. Sanner, A. E. Condon, L. M. Smith, and R. M. Corn, "Demonstration of a word design strategy for DNAcomputing on surfaces," Nucleic Acids Res., vol.25, pp. 4748-4757, 1997.
9. R. Deaton, J. Chen, H. Bi, and J. A. Rose, "A software tool for generating noncrosshybridizing libraries of DNA oligonucleotides," in DNA Computing: 8th International Workshop on DNA-Based Computers (Lecture Notes in Computer Science 2568), M. Hagiya and A. Ohuchi, Eds. Berlin, Germany: Springer-Verlag, 2003, pp. 252-261.
10. R. Deaton, J.-W. Kim, and J. Chen, "Design and test of noncrosshybridizing oligonucleotide building blocks for DNA computers and nanostructures," Appl. Phys. Lett., vol.82, pp. 1305-1307, 2003.
11. H.-H. Chou, A.-P. Hsia, D. L. Mooney, and P. S. Schnable, "PICKY: Oligo microarray design for large genomes," Bioinformatics, vol.20, pp. 2893-2902, 2004.
12. G. G. Leparc, T. T uchler,G. Striedner, K. Bayer, P. Sykacek, I. L.Hofacker, andD. P.Kreil, "Model-based probe set optimization for high-performance microarrays," Nucleic Acids Res., vol.37, pp. e18-e18, 2009.
13. L. Kaderali and A. Schliep, "Selecting signature oligonucleotides to indentify organisms using DNA arrays," Bioinformaitics, vol.18, pp. 1340- 1349, 2002.
14. J. A. Rose, R. J. Deaton, M. Hagiya, and A. Suyama, "The fidelity of the tag-antitag system," in DNA Computing: 7th International Meeting on DNA-Based Computers (Lecture Notes in Computer Science 2340), N. Jonoska and N. C. Seeman, Eds. Berlin, Germany: Springer-Verlag, 2002, pp. 138-149.
15. P. N. Borer, B. Dengler, I. Tinoco, Jr., and O. C. Uhlenbeck, "Stability of ribonucleic acid double-stranded helices," J. Mol. Biol., vol.86, pp. 843- 853, 1974.
16. J. SantaLucia, Jr., "A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics," Proc. Nat. Acad. Sci. USA, vol.95, pp. 1460-1465, 1998.
17. J. SantaLucia, Jr. and D. Hicks, "The thermodynamics of DNA structural motifs," Annu. Rev. Biophys. Biomol. Struct., vol.33, pp. 415-440, 2004.
18. T. F. Smith andM. S.Waterman, "The identification of commonmolecular subsequences," J. Mol. Biol., vol.147, pp. 195-197, 1981.
19. J. G. Wetmur, "Physical chemistry of nucleic acid hybridization," in DNA-Based Computers III (DIMACS series in Discrete Mathematics and Theoretical Computer Science), vol.48, H. Rubin and D. H. Wood, Eds. Providence, RI: American Mathematical Society, 1999, pp. 1-23.
20. R. Penchovsky and J. Ackermann, "DNA library design for molecular computation," J. Comput. Biol., vol.10, pp. 215-229, 2003.
21. P. O. Vardevanyan, A. P. Antonyan, M. A. Parsadanyan, H. G. Davtyan, and A. T. Karapetyan, "The binding of ethidium bromide with DNA: interaction with single- and double-stranded structures," Exp. Mol. Med., vol.35, pp. 527-533, 2003.
22. W. Yu, "Generating large libraries of non-crosshybridizing DNA oligonucleotides," Ph.D. dissertation, Dept. Comput. Sci. Comput. Eng., Univ. Arkansas, Fayetteville, AR, 2005.