A unified Poland-Scheraga model of oligo- and polynucleotide DNA melting: salt effects and predictive power.

ABSTRACT: Key biological and nano-technological processes require the partial or complete association and dissociation of complementary DNA strands. We present a variant of the Poland-Scheraga model for DNA melting where we introduce a local, sequence-dependent salt correction of the nearest-neighbor parameters. Furthermore, our formulation accounts for capping and interfacial energies of helical and coiled chain sections. We show that the model reproduces experimental data for melting temperatures over the full experimental range of strand length, strand concentration, and ionic strength of the solution. In particular, we reproduce a phenomenological relation by Frank-Kamenetskii for very long chains using a parameterization based on melting curves for short oligomers. However, we also show that th

SUBMITTER: Jost D 

PROVIDER: S-EPMC2716684 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature