The structure of four-stranded DNA: a theoretical approach

Abstract

To find the structure of quadruple helix, a theoretical approach has been performed. By torsion angle rotation, energy minimization, and molecular dynamics, the conformations of quadruple helix have been explored and one model was selected for further analysis. The backbones have symmetry with those of the diagonally opposite side. The average distance between adjacent phosphates in one strand is 7.0 A in this quadruple helix while 6.5 A in B-DNA. This implies that the quadruple helix has backbone conformations which reduce phosphate group repulsions. This model has an average helix rise of 3.3 A and twist of 33.4°, the values between A- and B-DNA. The glycosyl angles have alternate anti개yn conformations, and the sugar puckers are C3' endo, C2' endo, and Ol' endo. The base-pairs are of Watson-Crick type and additional hydrogen bonds also exist The hydrogen bond of this model is very interesting. The orientation of two Watson-Crick base pairs of one layer repeats in alternate layers with the base pairs of neighboring layers in near-perpendicular orientation. This alternating base pair orientation may stabilize the quadruple structure by allowing equal interactions among neighboring strands.