Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations.

ABSTRACT: Explicit solvent molecular dynamics simulations have been used to complement preceding experimental and computational studies of folding of guanine quadruplexes (G-DNA). We initiate early stages of unfolding of several G-DNAs by simulating them under no-salt conditions and then try to fold them back using standard excess salt simulations. There is a significant difference between G-DNAs with all-anti parallel stranded stems and those with stems containing mixtures of syn and anti guanosines. The most natural rearrangement for all-anti stems is a vertical mutual slippage of the strands. This leads to stems with reduced numbers of tetrads during unfolding and a reduction of strand slippage during refolding. The presence of syn nucleotides prevents mutual strand slippage; therefore, the antip

SUBMITTER: Stadlbauer P 

PROVIDER: S-EPMC3737530 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature