DNA thermal denaturation by polymer field theory approach: effects of the environment

TL;DR

This paper investigates how environmental factors like solvent quality and crowded surroundings affect the DNA denaturation transition, revealing significant influences on transition strength and conformational scaling laws through a polymer field theory approach.

Contribution

It introduces a polymer field theory analysis of DNA denaturation, incorporating environmental effects and extending the Poland-Scheraga model with resummation techniques and quantum gravity mappings.

Findings

Environmental factors significantly influence the first order transition.

Resummation techniques improve convergence of the epsilon expansion.

Extended impenetrable regions strengthen the transition.

Abstract

We analyse the effects of the environment (solvent quality, presence of extended structures - crowded environment) that may have impact on the order of the transition between denaturated and bounded DNA states and lead to changes in the scaling laws that govern conformational properties of DNA strands. We find that the effects studied significantly influence the strength of the first order transition. To this end, we re-consider the Poland-Scheraga model and apply a polymer field theory to calculate entropic exponents associated with the denaturated loop distribution. For the $d = 3$ case, the corresponding diverging $\epsilon = 4-d$ expansions are evaluated by restoring their convergence via the resummation technique. For the space dimension $d = 2$, the exponents are deduced from mapping the polymer model onto a two-dimensional random lattice, i.e., in the presence of quantum gravity. We also show that the first order transition is further strengthened by the presence of extended impenetrable regions in a solvent that restrict the number of the macromolecule configurations.