Coulombic free energy and salt ion association per phosphate of all-atom models of DNA oligomer: dependence on oligomer size.

ABSTRACT: We investigate how the coulombic Gibbs free energy and salt ion association per phosphate charge of DNA oligomers vary with oligomer size (i.e. number of charged residues ∣Z_D∣) at 0.15 M univalent salt by non-linear Poisson Boltzmann (NLPB) analysis of all-atom DNA models. Calculations of these quantities ([Formula: see text], [Formula: see text]) are performed for short and long double-stranded (ds) and single-stranded (ss) DNA oligomers, ranging from 4 to 118 phosphates (ds) and from 2 to 59 phosphates (ss). Behaviors of [Formula: see text] and [Formula: see text] as functions of ∣Z_D∣ provide a measure of the range of the coulombic end effect and determine the size of an oligomer at which an interior region with the properties (per charge) of th

SUBMITTER: Shkel IA 

PROVIDER: S-EPMC4440516 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature