Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis.

ABSTRACT: The lengths of G-tracts and their connecting loop sequences determine G-quadruplex folding and stability. Complete understanding of the sequence-structure relationships remains elusive. Here, single-loop G-quadruplexes were investigated using explicit solvent molecular dynamics (MD) simulations to characterize the effect of loop length, loop sequence, and G-tract length on the folding topologies and stability of G-quadruplexes. Eight loop types, including different variants of lateral, diagonal, and propeller loops, and six different loop sequences [d0 (i.e., no intervening residues in the loop), dT, dT(2), dT(3), dTTA, and dT(4)] were considered through MD simulation and free energy analysis. In most cases the free energetic estimates agree well with the experimental observations. The wor

SUBMITTER: Cang X 

PROVIDER: S-EPMC3168932 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature