Effect of genome sequence on the force-induced unzipping of a DNA molecule

TL;DR

This study investigates how the specific sequence of bases in DNA influences the force required to unzip the molecule, revealing sequence-dependent variations in unzipping force and potential implications for understanding DNA mechanics.

Contribution

It introduces a model analyzing the effect of base sequence variations on DNA unzipping force in the constant extension ensemble, highlighting sequence-dependent force changes.

Findings

Force vs. extension curve shows maxima and minima.

Changing base pairs affects force by a few pN.

Effect range depends on temperature.

Abstract

We considered a dsDNA polymer in which distribution of bases are random at the base pair level but ordered at a length of 18 base pairs and calculated its force elongation behaviour in the constant extension ensemble. The unzipping force $F(y)$ vs. extension $y$ is found to have a series of maxima and minima. By changing base pairs at selected places in the molecule we calculated the change in $F(y)$ curve and found that the change in the value of force is of the order of few pN and the range of the effect depending on the temperature, can spread over several base pairs. We have also discussed briefly how to calculate in the constant force ensemble a pause or a jump in the extension-time curve from the knowledge of $F(y)$.