Correlated local bending of DNA double helix and its effect on the cyclization of short DNA fragments

TL;DR

This paper introduces a correlated worm-like chain model for DNA that accounts for local bend angle correlations, explaining the higher cyclization probability of short DNA fragments compared to traditional models.

Contribution

The study develops a new theoretical model incorporating local bend correlations, improving predictions of DNA flexibility at short lengths over traditional models.

Findings

The model predicts increased flexibility of short DNA fragments.

It explains higher cyclization probabilities observed experimentally.

Persistence length becomes length-dependent in the new model.

Abstract

We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the persistence length of DNA l_P~150 base pairs) cannot be described by the traditional worm-like chain (WLC) model, e.g., the observed ring closure probability is much higher than predicted. To explain these observations, DNA flexibility is investigated with explicit considerations of a new length scale l_D~10 base pairs, over which DNA local bend angles are correlated. In this correlated worm-like chain (C-WLC) model, a finite length correction term is analytically derived and the persistence length is found to be contour length dependent. While our model reduces to the traditional worm-like chain model when treating long DNA at length scales much larger than l_P, it predicts that DNA becomes much more flexible at shorter sizes, which helps explain recent cyclization measurements of short DNA fragments around 100 base pairs.