Proofreading of DNA Polymerase: a new kinetic model with higher-order terminal effects

TL;DR

This paper introduces a comprehensive kinetic model for DNA polymerase fidelity that explicitly incorporates higher-order terminal effects, providing analytical insights into how these effects influence replication accuracy.

Contribution

The study develops a new kinetic model including higher-order terminal effects, offering a systematic and rigorous analysis of their role in DNA polymerase fidelity, unifying previous models.

Findings

Higher-order terminal effects significantly impact fidelity.

Fidelity expressions depend on only a few key parameters.

Model predictions align with experimental estimates.

Abstract

The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP which consists of both a polymerase site and an exonuclease (proofreading) site, there were quite few theoretical studies on the fidelity issue. The first model which explicitly considered both sites was proposed in 1970s' and the basic idea was widely accepted by later models. However, all these models did not systematically and rigorously investigate the dominant factor on DNAP fidelity, i.e, the higher-order terminal effects through which the polymerization pathway and the proofreading pathway coordinate to achieve high fidelity. In this paper, we propose a new and comprehensive kinetic model of DNAP based on some recent experimental observations, which includes previous models as special cases. We present a rigorous and unified treatment of the corresponding steady-state kinetic equations of any-order terminal effects, and derive analytical expressions for fidelity in terms of kinetic parameters under bio-relevant conditions. These expressions offer new insights on how the the higher-order terminal effects contribute substantially to the fidelity in an order-by-order way, and also show that the polymerization-and-proofreading mechanism is dominated only by very few key parameters. We then apply these results to calculate the fidelity of some real DNAPs, which are in good agreements with previous intuitive estimates given by experimentalists.