First-passage problems in DNA replication: effects of template tension on stepping and exonuclease activities of a DNA polymerase motor

TL;DR

This paper develops a stochastic kinetic model of DNA replication under tension, predicting how mechanical forces influence polymerase and exonuclease activities, with results aligning qualitatively with experimental data.

Contribution

It introduces a novel kinetic model incorporating first-passage time analysis and nine conditional dwell times to describe DNA polymerase behavior under tension.

Findings

Model agrees qualitatively with experimental force dependence data.

Introduces nine new conditional dwell times for DNA polymerase.

Provides exact analytical distributions for dwell times, testable by experiments.

Abstract

A DNA polymerase (DNAP) replicates a template DNA strand. It also exploits the template as the track for its own motor-like mechanical movement. In the polymerase mode it elongates the nascent DNA by one nucleotide in each step. But, whenever it commits an error by misincorporating an incorrect nucleotide, it can switch to an exonuclease mode. In the latter mode it excises the wrong nucleotide before switching back to its polymerase mode. We develop a stochastic kinetic model of DNA replication that mimics an {\it in-vitro} experiment where a single-stranded DNA, subjected to a mechanical tension $F$, is converted to a double-stranded DNA by a single DNAP. The $F$-dependence of the average rate of replication, which depends on the rates of both polymerase and exonuclease activities of the DNAP, is in good qualitative agreement with the corresponding experimental results. We introduce 9 novel distinct {\it conditional dwell times} of a DNAP. Using the methods of first-passage times, we also derive the exact analytical expressions for the probability distributions of these conditional dwell times. The predicted $F$-dependence of these distributions are, in principle, accessible to single-molecule experiments.