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Nucleic Acids Research 2005 33(15):4951-4964; doi:10.1093/nar/gki773
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Published online 6 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Thermodynamically based DNA strand design

Dan Tulpan, Mirela Andronescu, Seo Bong Chang1, Michael R. Shortreed1, Anne Condon*, Holger H. Hoos and Lloyd M. Smith1

Department of Computer Science, University of British Columbia Vancouver, BC, V6T 1Z4, Canada 1Department of Chemistry, University of Wisconsin 1101 University Avenue, Madison, WI 53706-1396, USA

*To whom correspondence should be addressed. Tel: +1 604 221 0575; Fax: +1 604 822 5485; E-mail: condon{at}cs.ubc.ca

Received December 21, 2004. Revised July 2, 2005. Accepted August 1, 2005.

We describe a new algorithm for design of strand sets, for use in DNA computations or universal microarrays. Our algorithm can design sets that satisfy any of several thermodynamic and combinatorial constraints, which aim to maximize desired hybridizations between strands and their complements, while minimizing undesired cross-hybridizations. To heuristically search for good strand sets, our algorithm uses a conflict-driven stochastic local search approach, which is known to be effective in solving comparable search problems. The PairFold program of Andronescu et al. [M. Andronescu, Z. C. Zhang and A. Condon (2005) J. Mol. Biol., 345, 987–1001; M. Andronescu, R. Aguirre-Hernandez, A. Condon, and H. Hoos (2003) Nucleic Acids Res., 31, 3416–3422.] is used to calculate the minimum free energy of hybridization between two mismatched strands. We describe new thermodynamic measures of the quality of strand sets. With respect to these measures of quality, our algorithm consistently finds, within reasonable time, sets that are significantly better than previously published sets in the literature.

Correspondence may also be addressed to Lloyd M. Smith. Tel: +1 608 262 9207; Fax: +1 608 265-6780; E-mail: smith{at}chem.wisc.edu


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M. R. Shortreed, S. B. Chang, D. Hong, M. Phillips, B. Campion, D. C. Tulpan, M. Andronescu, A. Condon, H. H. Hoos, and L. M. Smith
A thermodynamic approach to designing structure-free combinatorial DNA word sets
Nucleic Acids Res., September 2, 2005; 33(15): 4965 - 4977.
[Abstract] [Full Text] [PDF]


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