Reparametrizing loop entropy weights: Effect on DNA melting curves

TL;DR

This paper improves DNA melting curve models by incorporating the embedded loop closure exponent, revealing a higher cooperativity parameter and suggesting a reduced persistence length during melting.

Contribution

It introduces a reparametrization of loop entropy weights based on the embedded loop closure exponent, enhancing the accuracy of DNA melting simulations.

Findings

The cooperativity parameter is an order of magnitude larger with the new model.

The embedded loop closure exponent better explains melting behavior of long DNA sequences.

DNA persistence length decreases significantly in the melting region.

Abstract

Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior loop melting. So far, in the modeling of DNA melting, the entropy of denaturated loops has been estimated from the number of configurations of a closed self-avoiding walk. It is well understood now that a loop embedded in a chain is characterized by a loop closure exponent c which is higher than that of an isolated loop. Here we report an analysis of DNA melting curves for sequences of a broad range of lengths (from 10 to 10^6 base pairs) calculated with a program based on the algorithms underlying MELTSIM. Using the embedded loop exponent we find that the cooperativity parameter is one order of magnitude bigger than current estimates. We argue that in the melting region the double helix persistence length is greatly reduced compared to its room temperature value, so that the use of the embedded loop closure exponent for real DNA sequences is justified.