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Predicting sequence-dependent melting stability of short duplex DNA oligomers

✍ Scribed by Richard Owczarzy; Peter M. Vallone; Frank J. Gallo; Teodoro M. Paner; Michael J. Lane; Albert S. Benight

Publisher
Wiley (John Wiley & Sons)
Year
1997
Tongue
English
Weight
263 KB
Volume
44
Category
Article
ISSN
0006-3525

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✦ Synopsis

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 (Ç 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.

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