How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model

TL;DR

This study explores how nanochannel confinement influences DNA melting behavior within the Poland-Scheraga model, revealing that confinement lowers melting temperature and broadens the transition, with effects depending on DNA sequence and persistence lengths.

Contribution

It introduces a detailed analysis of confinement effects on DNA melting using the Poland-Scheraga model with an ideal Gaussian chain loop factor, including analytical estimates and numerical solutions.

Findings

Melting temperature decreases with decreasing channel diameter.

Confinement broadens the DNA melting transition.

Sequence heterogeneity affects transition width and behavior.

Abstract

When double-stranded DNA molecules are heated, or exposed to denaturing agents, the two strands get separated. The statistical physics of this process has a long history, and is commonly described in term of the Poland-Scheraga (PS) model. Crucial to this model is the configurational entropy for a melted region (compared to the entropy of an intact region of the same size), quantified by the loop factor. In this study we investigate how confinement affects the DNA melting transition, by using the loop factor for an ideal Gaussian chain. By subsequent numerical solutions of the PS model, we demonstrate that the melting temperature depends on the persistence lengths of single-stranded and double-stranded DNA. For realistic values of the persistence lengths the melting temperature is predicted to decrease with decreasing channel diameter. We also demonstrate that confinement broadens the melting transition. These general findings hold for the three scenarios investigated: namely 1. homo-DNA, i.e. identical basepairs along the DNA molecule; 2. random sequence DNA, and 3. "real" DNA, here T4 phage DNA. We show that cases 2 and 3 in general give rise to broader transitions than case 1. Case 3 exhibits a similar phase transition as case 2 provided the random sequence DNA has the same ratio of AT to GC basepairs. A simple analytical estimate for the shift in melting temperature is provided as a function of nanochannel diameter. For homo-DNA, we also present an analytical prediction of the melting probability as a function of temperature.