Comparison of Molecular Contours for Measuring Writhe in Atomistic Supercoiled DNA

Abstract

DNA molecular center-lines designed from atomistic-resolution structures are compared for the evaluation of the writhe in supercoiled DNA using molecular dynamics simulations of two sets of minicircles with 260 and 336 base pairs. We present a new method called WrLINE that systematically filters out local (i.e., subhelical turn) irregularities using a sliding-window averaged over a single DNA turn and that provides a measure of DNA writhe that is suitable for comparing atomistic resolution data with those obtained from measurements of the global molecular shape. In contrast, the contour traced by the base-pair origins defined by the 3DNA program largely overestimates writhe due to the helical periodicity of DNA. Nonetheless, this local modulation of the molecular axis emerges as an internal mechanism for the DNA to confront superhelical stress, where the adjustment between low and high twist is coupled to a high and low local periodicity, respectively, mimicking the different base-stacking conformational space of A and B canonical DNA forms.