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

We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri et al 2007 Phys. Rev. Lett. 99 088103). Our discrete helical wormlike chain model takes explicitly into account the three elastic degrees of freedom, namely stretching, bending and torsion of the polymer. By integrating out these external variables, the conformational entropy contributes to bubble nucleation (opening of base-pairs), which sheds light on the DNA melting mechanism. Because the values of monomer length, bending and torsional moduli differ significantly in dsDNA and ssDNA, these effects are important. Moreover, we explore in this context the role of an additional 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.