# Kinetic discrimination of a polymerase in the presence of obstacles

## TL;DR

This paper models how a polymerase enzyme's fidelity in copying RNA is affected by obstacles, revealing that fidelity depends on kinetic factors and can inform about junction dynamics without detailed interaction specifics.

## Contribution

It introduces a model analyzing how obstacles influence polymerase fidelity and demonstrates fidelity's independence from interaction details, aiding junction kinetics investigation.

## Key findings

- Fidelity depends on kinetic parameters and dissipation.
- Obstacle presence alters polymerase speed and accuracy.
- Fidelity analysis reveals junction kinetics independently of interaction nature.

## Abstract

One of the causes of high fidelity of copying in biological systems is kinetic discrimination. In this mechanism larger dissipation and copying velocity result in improved copying accuracy. We consider a model of a polymerase which simultaneously copies a single stranded RNA and opens a single- to double-stranded junction serving as an obstacle. The presence of the obstacle slows down the motor, resulting in a change of its fidelity, which can be used to gain information about the motor and junction dynamics. We find that the motor's fidelity does not depend on details of the motor-junction interaction, such as whether the interaction is passive or active. Analysis of the copying fidelity can still be used as a tool for investigating the junction kinetics.