Physics – Condensed Matter – Soft Condensed Matter
Scientific paper
2008-09-02
J. Phys.: Condens. Matter 21 034104 (2009)
Physics
Condensed Matter
Soft Condensed Matter
25 pages, 30 figures
Scientific paper
10.1088/0953-8984/21/3/034104
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.
Destainville Nicolas
Manghi Manoel
Palmeri John
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