A protrusion can "eclipse" looping of a long self-avoiding chain

TL;DR

This study uses Monte Carlo simulations to analyze how a protrusion affects the looping probability of long self-avoiding chains, revealing an eclipse mechanism that influences DNA regulation.

Contribution

It introduces a weighted-biased sampling Monte Carlo method to quantify protrusion effects on chain looping probabilities and models the eclipse mechanism theoretically.

Findings

Protrusions near chain termini decrease looping probability.

Larger protrusions further reduce looping probability.

The eclipse effect depends on protrusion size and position.

Abstract

We simulate long self-avoiding chains using a weighted-biased sampling Monte-Carlo algorithm, and compute the probabilities for chain looping with and without a protrusion. We find that a protrusion near one of the chain's termini reduces the probability of looping, even for chains much longer than the protrusion-chain-terminus distance. This effect increases with protrusion size, and decreases with protrusion-terminus distance. We model the simulated results theoretically by considering how the protrusion "eclipses" the chain terminus closer to the protrusion from the more distant chain terminus. This eclipse mechanism has implications for understanding the regulatory role of proteins bound to DNA.