A statistical thermodynamic model for investigating the stability of DNA sequences from oligonucleotides to genomes.

ABSTRACT: We describe the development and testing of a simple statistical mechanics methodology for duplex DNA applicable to sequences of any composition and extensible to genomes. The microstates of a DNA sequence are modeled in terms of blocks of basepairs that are assumed to be fully closed (paired) or open. This approach generates an ensemble of bubblelike microstates that are used to calculate the corresponding partition function. The energies of the microstates are calculated as additive contributions from hydrogen bonding, basepair stacking, and solvation terms parameterized from a comprehensive series of molecular dynamics simulations including solvent and ions. Thermodynamic properties and nucleotide stability constants for DNA sequences follow directly from the partition function. The meth

SUBMITTER: Khandelwal G 

PROVIDER: S-EPMC4052264 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature