Thermodynamics of G.A mispairs in DNA: continuum electrostatic model

TL;DR

This paper investigates the thermodynamic stability of G.A mispairs in DNA duplexes using a continuum electrostatic model, revealing how sequence and conformation influence melting behavior.

Contribution

It introduces a detailed electrostatic analysis of G.A mispair conformations and their impact on DNA duplex stability, highlighting differences from canonical base pairs.

Findings

G(anti).A(syn) and G(anti).A(anti) conformations have thermodynamic properties similar to canonical pairs.

Sheared conformation shows significant thermodynamic differences from canonical pairs.

Duplex stability depends on both sequence context and G.A mispair conformation.

Abstract

An analysis of the stability of a duplex containing G.A mispairs or G.A/A.G tandem during DNA melting has revealed that duplex stability depends on both DNA sequences and on the conformations of the G.A mispairs. The thermodynamics of single pair opening for G(anti).A(syn) and G(anti).A(anti) conformations adopted by G.A mispairs is found to strongly correlate with that of the canonical base pairs, while for sheared conformation a significant difference is observed.