The Contribution of Backbone Electrostatic Repulsion to DNA Mechanical Properties is Length-Scale-Dependent.

Abstract

The mechanics of DNA bending is crucially related to many vital biological processes. Recent experiments reported anomalous flexibility for DNA on short length scales, calling into doubt the validity of the harmonic worm-like chain (WLC) model in this region. In the present work, we systematically probed the bending dynamics of DNA at different length scales. In contrast to the remarkable deviation from the WLC description for DNA duplexes of less than three helical turns, our atomistic studies indicate that the neutral "null isomer" behaves in accord with the ideal elastic WLC and exhibits a uniform decay for the directional correlation of local bending. The backbone neutralization weakens the anisotropy in the effective bending preference and the helical periodicity of bend correlation that have previously been observed for normal DNA. The contribution of electrostatic repulsion to stretching cooperativity and the mechanical properties of DNA strands is length-scale-dependent: the phosphate neutralization increases the stiffness of DNA below two helical turns, but it is decreased for longer strands. We find that DNA rigidity is largely determined by base pair stacking, with electrostatic interactions contributing only around 10% of the total persistence length.