Impact of geometry optimization on base-base stacking interaction energies in the canonical A- and B-forms of DNA.

ABSTRACT: Base stacking is known to make an important contribution to the stability of DNA and RNA, and accordingly, significant efforts are ongoing to calculate stacking energies using ab initio quantum mechanical methods. To date, impressive improvements have been made in the model chemistries used to perform stacking energy calculations, including extensions that include robust treatments of electron correlation with extended basis sets, as required to treat interactions where dispersion makes a significant contribution. However, those efforts typically use rigid monomer geometries when calculating the interaction energies. To overcome this, in the present work, we describe a novel internal coordinate definition that allows the relative, intermolecular orientation of stacked base monomers to be c

SUBMITTER: McDonald AR 

PROVIDER: S-EPMC3579007 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature