Simulating a burnt-bridges DNA motor with a coarse-grained DNA model

TL;DR

This study uses a coarse-grained DNA model to simulate a burnt-bridges DNA motor, revealing how stator spacing affects stepping efficiency and suggesting a method to enhance motor decision-making.

Contribution

It demonstrates the application of a coarse-grained DNA model to simulate a DNA motor and explores how stator spacing influences its stepping behavior.

Findings

Increased stator distance suppresses successful steps due to tension.

Varying stator spacing can improve signal-to-noise ratios.

The model accurately captures the physics of DNA nanomachines.

Abstract

We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a `burnt-bridges' DNA motor consisting of a single-stranded cargo that steps processively along a track of single-stranded stators. We demonstrate that the model is able to simulate such a system, and investigate the sensitivity of the stepping process to the spatial separation of stators, finding that an increased distance can suppress successful steps due to the build up of unfavourable tension. The mechanism of suppression suggests that varying the distance between stators could be used as a method for improving signal-to-noise ratios for motors that are required to make a decision at a junction of stators.