Self-avoiding worm-like chain model for dsDNA loop formation

TL;DR

This study models double-stranded DNA loop formation considering excluded volume effects using a self-avoiding worm-like chain model, revealing significant differences from traditional models and potential explanations for experimental anomalies.

Contribution

First application of a self-avoiding worm-like chain model to DNA looping, quantifying excluded volume effects on the J-factor across different regimes.

Findings

Power-law decay of -1.92 in the entropic regime confirms theoretical predictions.

Excluded volume increases the J-factor by about half an order of magnitude.

Anisotropic end-to-end distribution in the elastic regime influences looping probabilities.

Abstract

We compute for the first time the effects of excluded volume on the probability for double-stranded DNA to form a loop. We utilize a Monte-Carlo algorithm for generation of large ensembles of self- avoiding worm-like chains, which are used to compute the J-factor for varying lengthscales. In the entropic regime, we confirm the scaling-theory prediction of a power-law drop off of -1.92, which is significantly stronger than the -1.5 power-law predicted by the non-self-avoiding worm-like chain model. In the elastic regime, we find that the angle-independent end-to-end chain distribution is highly anisotropic. This anisotropy, combined with the excluded volume constraints, lead to an increase in the J-factor of the self-avoiding worm-like chain by about half an order of magnitude relative to its non-self-avoiding counterpart. This increase could partially explain the anomalous results of recent cyclization experiments, in which short dsDNA molecules were found to have an increased propensity to form a loop.