Statistical Mechanics of thermal denaturation of DNA oligomers

TL;DR

This paper investigates how constraining one end of a DNA oligomer affects its thermal denaturation profile, revealing significant differences from unconstrained DNA through a Peyrard-Bishop Hamiltonian model.

Contribution

It introduces a novel analysis of the impact of end constraints on DNA denaturation profiles using a specific Hamiltonian model.

Findings

Constrained DNA shows markedly different denaturation behavior.

The position of defect sites influences the denaturation profile.

Elasticity effects are significant in DNA stability.

Abstract

Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or intact) state. The effect of this constraint on the denaturation profile of the oligomer has been calculated using the Peyrard-Bishop Hamiltonian. The denaturation profile is found to be very different from the free (i.e. without the constraint) oligomer. We have also examined how this constraint affects the denaturation profile of the oligomer having a segment of defect sites located at different parts of the chain.