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Thermodynamically based DNA strand design

delete2005-09-06
delete56
delete
OA
AI
D
Dan Tulpan
A
Andronescu, M
C
Chang, SB
S
Shortreed, MR
A
Anne Condon
H
Holger H. Hoos
L
Lloyd M. Smith
DOI：10.1093/nar/gki773delete
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Abstract

Abstract

En 中文
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.
Keywords:
SECONDARY STRUCTURE PREDICTION
STOCHASTIC LOCAL SEARCH
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Journal

Nucleic Acids Research cover
Nucleic Acids Research
IF:
13.1
Papers:
3.6W
Citations:
29.0W

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