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 in DNA (Palmeri J, Manghi M and Destainville N 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.

25 pages, 30 figures

References in corpus (7)

• Denaturation transition of stretched DNA
• The Worm-Like Chain Theory And Bending Of Short DNA
• Thermal denaturation of fluctuating finite DNA chains: the role of bending rigidity in bubble nucleation
• Thermal Denaturation of Fluctuating DNA Driven by Bending Entropy
• Statistical mechanics of base stacking and pairing in DNA melting
• 1/f fluctuations of DNA temperature at thermal denaturation
• Theoretical investigation of finite size effects at DNA melting

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• DNA as a one-dimensional chiral material. II. Dynamics of the structural transition between B form and Z form
• Energy required to pinch a DNA plectoneme
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