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Predicting sequence‐dependent melting stability of short duplex DNA oligomers
Author(s) -
Owczarzy Richard,
Vallone Peter M.,
Gallo Frank J.,
Paner Teodoro M.,
Lane Michael J.,
Benight Albert S.
Publication year - 1997
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/(sici)1097-0282(1997)44:3<217::aid-bip3>3.0.co;2-y
Subject(s) - duplex (building) , sequence (biology) , melting temperature , dna , chemistry , k nearest neighbors algorithm , base pair , stability (learning theory) , dna sequencing , chemical stability , thermodynamics , physics , materials science , computer science , biochemistry , artificial intelligence , organic chemistry , machine learning , composite material
Abstract Many important applications of DNA sequence‐dependent hybridization reactions have recently emerged. This has sparked a renewed interest in analytical calculations of sequence‐dependent melting stability of duplex DNA. In particular, for many applications it is often desirable to accurately predict the transition temperature, or t m , of short duplex DNA oligomers (∼ 20 base pairs or less) from their sequence and concentration. The thermodynamic analytical method underlying these predictive calculations is based on the nearest‐neighbor model. At least 11 sets of nearest‐neighbor sequence‐dependent thermodynamic parameters for DNA have been published. These sets are compared. Use of the nearest‐neighbor sets in predicting t m from the DNA sequence is demonstrated, and the ability of the nearest‐neighbor parameters to provide accurate predictions of experimental t m 's of short duplex DNA oligomers is assessed. © 1998 John Wiley & Sons, Inc. Biopoly 44: 217–239, 1997