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

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.