Coupling between denaturation and chain conformations in DNA: stretching, bending,torsion and finite size effects

Abstract

We develop further a statistical model coupling denaturation and chain conformations inDNA (Palmeri et al 2007 Phys. Rev. Lett. 99 088103). Our discrete helical wormlike chainmodel takes explicitly into account the three elastic degrees of freedom, namely stretching,bending and torsion of the polymer. By integrating out these external variables, theconformational entropy contributes to bubble nucleation (opening of base-pairs), whichsheds light on the DNA melting mechanism. Because the values of monomerlength, bending and torsional moduli differ significantly in dsDNA and ssDNA,these effects are important. Moreover, we explore in this context the role of anadditional loop entropy and analyze finite size effects in an experimental context,where polydA–polydT is clamped by two G–C strands, as well as for free polymers.