Paper detail

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

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.