Helicase activity on DNA as a propagating front

TL;DR

This paper models helicase activity on DNA as a propagating front, analyzing the transition between zipped and unzipped DNA states, and estimates helicase speeds based on local driving forces.

Contribution

It introduces a novel front analysis approach to model helicase activity, providing bounds and estimates for helicase speeds in different driving conditions.

Findings

Bounds on helicase speed derived from variational analysis

Different helicase behaviors characterized by drive nature

Model captures the transition between zipped and unzipped DNA states

Abstract

We develop a propagating front analysis, in terms of a local probability of zipping, for the helicase activity of opening up a double stranded DNA (dsDNA). In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front separates the zipped and unzipped phases of a dsDNA and a drive acts locally around the front. Bounds from variational analysis and numerical estimates for the speed of a helicase are obtained. Different types of helicase behaviours can be distinguished by the nature of the drive.