Pulling short DNA molecules having defects on different locations

TL;DR

This study investigates how defects at various locations affect the thermal and mechanical stability of short DNA molecules, revealing insights into their denaturation behavior under different conditions.

Contribution

It introduces a modified statistical model to analyze the impact of defects on short DNA denaturation in thermal and force ensembles, considering different base pair compositions and distributions.

Findings

Defects influence the probability of DNA opening under force.

Distribution of AT and GC affects denaturation behavior.

Presence of defects alters stability and opening patterns.

Abstract

We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects that occurs anywhere in the molecule. For the investigation, we consider four different kinds of chains. Not only the ratio of AT to GC different in these molecules but also the distributions of AT and GC along the molecule are different. With suitable modifications in the statistical model to show the defect in a pair, we investigate the denaturation of short DNA molecules in thermal as well as constant force ensemble. In the force ensemble, we pulled the DNA molecule from each end (keeping other end free) and observed some interesting features of opening of the molecule in the presence of defects in the molecule. We calculate the probability of opening of the DNA molecule in the constant force ensemble to explain the opening of base pairs and hence the denaturation of molecules in the presence of defects.