Role of loop entropy in the force induced melting of DNA hairpin

TL;DR

This study investigates how loop entropy influences the force-induced melting of DNA hairpins, revealing temperature-dependent transition mechanisms through Langevin dynamics simulations.

Contribution

It introduces a detailed simulation-based analysis of DNA hairpin melting, highlighting the significant role of loop entropy and elastic energy in force-temperature phase behavior.

Findings

High-temperature transition is entropy dominated with loop contribution.

Low-temperature transition is force driven from the stem side.

Phase diagram differs from theoretical lattice model predictions.

Abstract

Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction based on the lattice model. Probability analysis of the extreme bases of the stem revealed that at high temperature, the hairpin to coil transition is entropy dominated and the loop contributes significantly in its opening. However, at low temperature, the transition is force driven and the hairpin opens from the stem side. It is shown that the elastic energy plays a crucial role at high force. As a result, the phase diagram differs significantly with the theoretical prediction.