Distributions of free energy, melting temperature, and hybridization propensity for genomic DNA oligomers

Abstract

Many molecular biology techniques such as PCR, southern blotting, molecular beacon based assays, and DNA microarrays rely on the ability to design oligonucleotide probes possessing specific thermodynamic properties. Thermodynamic parameters for DNA duplex formation (melting temperature: Tm, free energy: /spl Delta/G/spl deg//sub /spl gamma//, and hybridization extent: Fb) are accurately predicted using the nearest-neighbor model for a range of physical conditions for oligonucleotides up to about 50 bases in length. The use of thermodynamic quantities is ubiquitous in probe design schemes, but invariably focus on achieving specific values for sequences in hand. This fails to provide general insights about how these quantities depend on sequence composition, length, and experimental conditions. Here we present Tm and Fb distributions calculated for genomic DNA samples of 10 to 50 bases.