Dynamical modelling of molecular constructions and setups for DNA unzipping

TL;DR

This paper develops a dynamical model for DNA unzipping under force, incorporating the motion of the unzipping fork, traps, and polymer components, and compares it to existing equilibrium models.

Contribution

It introduces a comprehensive dynamical model that accounts for sequence-dependent DNA unzipping and compares it with simpler equilibrium-based models.

Findings

The model captures the dynamics of DNA unzipping more accurately.

Simulation results align with experimental data.

Different experimental setups are effectively tested with the model.

Abstract

We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the molecular construction (unzipped single strands of DNA, and linkers). Different setups are considered to test the model, and the outcome of the simulations is compared to simpler dynamical models existing in the literature where polymers are assumed to be at equilibrium.