PREDICTING SEQUENCE-DEPENDENT MELTING STABILITY OF SHORT DUPLEX DNA OLIGOMERS

Many important applications of DNA sequence-dependent hybridization re actions have recently emerged. This has sparked a renewed interest in analytical calculations of sequence-dependent melting stability of dup lex DNA, In particular, for many applications it is often desirable to accurately predict the transition temperature, or t(m), of short dupl ex DNA oligomers (similar to 20 base pairs or less) from their sequenc e and concentration. The thermodynamic analytical method underlying th ese predictive calculations is based on the nearest-neighbor model. Al least II sets of nearest-neighbor sequence-dependent thermodynamic pa rameters for DNA have been published. These sets are compared Use of t he nearest-neighbor sets in predicting t(m) from the DNA sequence is d emonstrated, and the ability of the nearest-neighbor parameters to pro vide accurate predictions of experimental t(m)'s of short duplex-DNA o ligomers is assessed. (C) 1998 John Wiley & Sons, Inc.