Melting of persistent double-stranded polymers

Abstract

Motivated by recent DNA-pulling experiments, we revisit the Poland-Scheraga model of melting a double-stranded polymer. We include distinct bending rigidities for both the double-stranded segments, and the single-stranded segments forming a bubble. There is also bending stiffness at the branch points between the two segment types. The transfer matrix technique for single persistent chains is generalized to describe the branching bubbles. Properties of spherical harmonics are then exploited in truncating and numerically solving the resulting transfer matrix. This allows efficient computation of phase diagrams and force-extension curves (isotherms). While the main focus is on exposition of the transfer matrix technique, we provide general arguments for a reentrant melting transition in stiff double strands. Our theoretical approach can also be extended to study polymers with bubbles of any number of strands, with potential applications to molecules such as collagen.

9 pages, 7 figures

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Cited by in corpus (8)

• Coarse-grained simulations of DNA overstretching
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• Competition for hydrogen bond formation in the helix-coil transition and protein folding
• Mesoscopic models for DNA stretching under force: new results and comparison to experiments
• Can a double stranded DNA be unzipped by pulling a single strand?: Phases of adsorbed DNA
• A three-state model with loop entropy for the over-stretching transition of DNA
• Cross-linked pair of polymer chains under strong tension
• Cavity approach for modeling and fitting polymer stretching