title: Predicting sequence-dependent melting stability of short duplex DNA oligomers.
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 tm of short duplex DNA oligomers (approximately 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.
authors.affiliation: Department of Chemistry, University of Illinois, Chicago 60607, USA.
authors.forename: R
authors.initials: R
authors.lastname: Owczarzy
authors.forename: P M
authors.initials: PM
authors.lastname: Vallone
authors.forename: F J
authors.initials: FJ
authors.lastname: Gallo
authors.forename: T M
authors.initials: TM
authors.lastname: Paner
authors.forename: M J
authors.initials: MJ
authors.lastname: Lane
authors.forename: A S
authors.initials: AS
authors.lastname: Benight
mesh_terms: D001483:Base Sequence; D001699:Biometry; D004247:DNA / Q000737:chemistry*; D004355:Drug Stability; D008956:Models, Chemical; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D009838:Oligodeoxyribonucleotides; D004247:DNA