Melting of persistent double-stranded polymers.
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.
Rahi
Sahand Jamal
SJ
Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA. sjrahi@mit.edu
Hertzberg
Mark Peter
MP
Kardar
Mehran
M
D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011108:Polymers / Q000737:chemistry*; D013314:Stress, Mechanical; D013816:Thermodynamics
D004277:DNA, Single-Stranded; D011108:Polymers; D004247:DNA