Charge transport-mediated recruitment of DNA repair enzymes

TL;DR

This paper models how charge transport along DNA influences the recruitment and localization of DNA repair enzymes, revealing mechanisms that optimize enzyme concentration at damage sites.

Contribution

It introduces a stochastic model of electron dynamics along DNA, demonstrating how charge transport guides repair enzymes to lesions more efficiently.

Findings

Charge transport suppresses enzyme buildup on intact DNA regions.

Electrons are absorbed by lesions, aiding enzyme localization.

Model enables simulations of enzyme redistribution near DNA damage.

Abstract

Damaged or mismatched bases in DNA can be repaired by Base Excision Repair (BER) enzymes that replace the defective base. Although the detailed molecular structures of many BER enzymes are known, how they colocalize to lesions remains unclear. One hypothesis involves charge transport (CT) along DNA [Yavin, {\it et al.}, PNAS, {\bf 102}, 3546, (2005)]. In this CT mechanism, electrons are released by recently adsorbed BER enzymes and travel along the DNA. The electrons can scatter (by heterogeneities along the DNA) back to the enzyme, destabilizing and knocking it off the DNA, or, they can be absorbed by nearby lesions and guanine radicals. We develop a stochastic model to describe the electron dynamics, and compute probabilities of electron capture by guanine radicals and repair enzymes. We also calculate first passage times of electron return, and ensemble-average these results over guanine radical distributions. Our statistical results provide the rules that enable us to perform implicit-electron Monte-Carlo simulations of repair enzyme binding and redistribution near lesions. When lesions are electron absorbing, we show that the CT mechanism suppresses wasteful buildup of enzymes along intact portions of the DNA, maximizing enzyme concentration near lesions.