Toward a full structural characterization of G-quadruplex DNA in aqueous solution: Molecular dynamics simulations of four G-quadruplex molecules

A systematic study on guanine (G) quadruplex DNA flexibility was performed by using extended explicit molecular dynamics (MD) simulations on four quadruplex molecules containing one dimeric and three monomeric G-quadruplexes with the most used and recent modified versions of AMBER force fields (parm99 and parmbsc0). The detailed analyses of general structure and basic structural parameters were done for the G-DNA structures. The results indicate that parmbsc0 provides a slightly better description for the G-DNA stems than parm99, and the situation is the opposite for the loops. Many backbone torsions located in the non-canonical regions are not retained in both simulations. Most of the glycosidic torsion angles of loop bases deviate largely from the experimental values. Many phase angles of pseudorotation of the sugar rings are transformed to other puckers. The transformation of structural parameters given by each force field is useful as direction for further improving force field of polynucleotide structures.