Effect of Bending Anisotropy on the 3D Conformation of Short DNA Loops

TL;DR

This study investigates how bending anisotropy influences the 3D shapes of short DNA loops, revealing complex conformations including out-of-plane bending and kinks, with implications for protein-DNA interactions.

Contribution

It introduces an elastic model incorporating bending anisotropy to analyze short DNA loop conformations, highlighting nontrivial shapes and the impact of sequence inhomogeneity.

Findings

DNA loops adopt nonplanar shapes due to anisotropy

Sequence inhomogeneity enhances geometrical features

Bending out of planes and kinks are observed in non-integer pitch lengths

Abstract

The equilibrium three dimensional shape of relatively short loops of DNA is studied using an elastic model that takes into account anisotropy in bending rigidities. Using a reasonable estimate for the anisotropy, it is found that cyclized DNA with lengths that are not integer multiples of the pitch take on nontrivial shapes that involve bending out of planes and formation of kinks. The effect of sequence inhomogeneity on the shape of DNA is addressed, and shown to enhance the geometrical features. These findings could shed some light on the role of DNA conformation in protein--DNA interactions.