Melting of genomic DNA: predictive modeling by nonlinear lattice dynamics

TL;DR

This paper models DNA melting behavior using nonlinear lattice dynamics, successfully predicting melting curves and base-pair opening probabilities for various DNA sequences without adjustable parameters.

Contribution

It introduces a predictive nonlinear lattice dynamics model for DNA melting that accurately matches experimental data across different DNA sequences and conditions.

Findings

Model accurately predicts melting curves for multiple DNA sequences.

Predicted base-pair opening probabilities align with experimental measurements.

Model parameters depend on salt content, affecting melting behavior.

Abstract

The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to obtain model fits and determine parameter dependence on salt content. Melting curves predicted for the complete fd phage and the Y1 and Y2 fragments of the $\phi$X174 phage without any adjustable parameters are in good agreement with experiment. The calculated probabilities for single base-pair opening are consistent with values obtained from imino proton exchange experiments.