Anharmonic stacking in supercoiled DNA

Abstract

Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking anharmonicity stabilizes the double helix against thermal disruption of the hydrogen bonds. Twisting is essential in the model to capture the importance of nonlinear effects on the thermodynamical properties. In a ladder model with zero twist, anharmonic stacking scarcely affects the thermodynamics. Moderately untwisted helices, with respect to the equilibrium conformation, show an energetic advantage against the overtwisted ones. Accordingly moderately untwisted helices better sustain local fluctuational openings and make more unlikely the thermally driven complete strand separation.

In press

References in corpus (26)

• Why is the DNA Denaturation Transition First Order?
• Denaturation of Heterogeneous DNA
• Helicoidal model for DNA opening
• Statistical Mechanics of Torque Induced Denaturation of DNA
• Order of the phase transition in models of DNA thermal denaturation
• Roles of stiffness and excluded volume in DNA denaturation
• Theory of Bubble Nucleation and Cooperativity in DNA Melting
• Thermal denaturation of an helicoidal DNA model
• Localization of Denaturation Bubbles in Random DNA Sequences
• Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation
• Sequence sensitivity of breathing dynamics in heteropolymer DNA
• Denaturation transition of stretched DNA
• Thermodynamics of Twisted DNA with Solvent Interaction
• A composite model for DNA torsion dynamics
• Thermal Denaturation of Fluctuating DNA Driven by Bending Entropy
• The thermal denaturation of DNA studied with neutron scattering
• Melting of genomic DNA: predictive modeling by nonlinear lattice dynamics
• Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules
• The probability analysis of opening of DNA
• Path Integral Method for DNA Denaturation
• Denaturation Patterns in Heterogeneous DNA
• Stacking Interactions in Denaturation of DNA Fragments
• Dependence on temperature and GC content of bubble length distributions in DNA
• Dynamical versus statistical mesoscopic models for DNA denaturation
• DNA breathing dynamics: Analytic results for distribution functions of relevant Brownian functionals
• Renormalisation group determination of the order of the DNA denaturation transition

Cited by in corpus (9)

• End-to-end distance and contour length distribution functions of DNA helices
• J-factors of short DNA molecules
• Phase diagram of mechanically stretched DNA: The salt effect
• Base pair fluctuations in helical models for nucleic acids
• Short DNA persistence length in a mesoscopic helical model
• Twist-stretch profiles of DNA chains
• Stretching DNA in hard-wall potential channels
• Distribution of Base Pair Alternations in a Periodic DNA Chain: Application of Polya Counting to a Physical System
• Helical Disruptions in Small Loops of DNA