Predicting sequence‐dependent melting stability of short duplex DNA oligomers

作者：Richard Owczarzy, Peter M. Vallone, Frank J. Gallo, Teodoro M. Paner, Michael J. Lane, Albert S. Benight · 发表于：Biopolymers · 年份：1997 · DOI：10.1002/(sici)1097-0282(1997)44:3<217::aid-bip3>3.3.co;2-k · 被引用次数：15 · 研究领域：DNA and Nucleic Acid Chemistry、RNA and protein synthesis mechanisms、Advanced biosensing and bioanalysis techniques

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 tm, 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 tm from the DNA sequence is demonstrated, and the ability of the nearest-neighbor parameters to provide accurate predictions of experimental tm's of short duplex DNA oligomers is assessed. © 1998 John Wiley & Sons, Inc. Biopoly 44: 217–239, 1997