Thermal Denaturation of Fluctuating DNA Driven by Bending Entropy

Abstract

A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the fraction of denaturation bubbles and their correlation length is deduced. The thermal denaturation transition emerges naturally when the chain fluctuations are integrated out and is driven by the difference in bending (entropy dominated) free energy between broken and unbroken segments. Conformational properties of DNA, such as persistence length and mean-square-radius, are also explicitly calculated, leading, e.g., to a coherent explanation for the experimentally observed thermal viscosity transition.

4 pages, 1 figure

References in corpus (6)

• Why is the DNA Denaturation Transition First Order?
• Roles of stiffness and excluded volume in DNA denaturation
• DNA bubble dynamics as a quantum Coulomb problem
• Loop Dynamics in DNA Denaturation
• Distribution Functions, Loop Formation Probabilities and Force-Extension Relations in a Model for Short Double-Stranded DNA Molecules
• The bend stiffness of S-DNA

Cited by in corpus (25)

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• Thermodynamics of Twisted DNA with Solvent Interaction
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• Slow closure of denaturation bubbles in DNA: twist matters
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• Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide
• Coupling between denaturation and chain conformations in DNA: stretching, bending, torsion and finite size effects
• Mesoscopic models for DNA stretching under force: new results and comparison to experiments
• Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA
• Denaturation of Circular DNA: Supercoil Mechanism
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• DNA as a one-dimensional chiral material: Application to the structural transition between B form and Z form
• Strand diffusion-limited closure of denaturation bubbles in DNA
• Thermomechanics of DNA
• Anharmonic stacking in supercoiled DNA
• How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model
• Softening of DNA near Melting as Disappearance of an Emergent Property
• A three-state model with loop entropy for the over-stretching transition of DNA
• High-energy deformation of filaments with internal structure and localized torque-induced melting of DNA
• DNA as a one-dimensional chiral material. II. Dynamics of the structural transition between B form and Z form
• Thermomechanical Stability and Mechanochemical Response of DNA: a Minimal Mesoscale Model
• Statistical physics and mesoscopic modeling to interpret tethered particle motion experiments