Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide

TL;DR

This study adapts a coarse-grain DNA model to accurately simulate thermal and mechanical denaturation, aligning well with experimental data and providing insights into DNA-protein interactions.

Contribution

The paper introduces an adjusted coarse-grain DNA model that accurately predicts denaturation properties and critical forces, enhancing understanding of DNA behavior.

Findings

Critical temperatures match experimental data

Denaturation exhibits a step-like behavior in long sequences

Critical force at room temperature is about 10 pN

Abstract

In this paper, we show that the coarse grain model for DNA, which has been proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys. 126, 084901 (2007)), can be adapted to describe the thermal and mechanical denaturation of long DNA sequences by adjusting slightly the base pairing contribution. The adjusted model leads to (i) critical temperatures for long homogeneous sequences that are in good agreement with both experimental ones and those obtained from statistical models, (ii) a realistic step-like denaturation behaviour for long inhomogeneous sequences, and (iii) critical forces at ambient temperature of the order of 10 pN, close to measured values. The adjusted model furthermore supports the conclusion that the thermal denaturation of long homogeneous sequences corresponds to a first-order phase transition and yields a critical exponent for the critical force equal to sigma=0.70. This model is both geometrically and energetically realistic, in the sense that the helical structure and the grooves, where most proteins bind, are satisfactorily reproduced, while the energy and force required to break a base pair lie in the expected range. It therefore represents a promising tool for studying the dynamics of DNA-protein specific interactions at an unprecedented detail level.