Thermodynamics of Twisted DNA with Solvent Interaction
arXiv:1108.1788 · doi:10.1063/1.3631564
Abstract
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base pairs stacked along the molecule backbone. The base pair displacements are described by an ensemble of temperature dependent paths thus incorporating those fluctuational effects which shape the multisteps thermal denaturation. By summing over base pair paths, a large number of double helix configurations is taken into account consistently with the physical requirements of the model potential. The partition function is computed as a function of the twist. It is found that the equilibrium twist angle, peculiar of B-DNA at room temperature, yields the stablest helicoidal geometry against thermal disruption of the base pair hydrogen bonds. This result is corroborated by the computation of thermodynamical properties such as fractions of open base pairs and specific heat.
The Journal of Chemical Physics (2011) in press
References in corpus (15)
- Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation
- Sequence sensitivity of breathing dynamics in heteropolymer DNA
- Bubbles and denaturation in DNA
- Denaturation transition of stretched DNA
- Modelling DNA at the mesoscale: a challenge for nonlinear science?
- Thermal denaturation of fluctuating finite DNA chains: the role of bending rigidity in bubble nucleation
- The thermal denaturation of DNA studied with neutron scattering
- Thermal Denaturation of Fluctuating DNA Driven by Bending Entropy
- 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
- Statistical physics of the melting of inhomogeneous DNA
- Dependence on temperature and GC content of bubble length distributions in DNA
- Dynamical versus statistical mesoscopic models for DNA denaturation
Cited by in corpus (23)
- Effect of salt concentration on the stability of heterogeneous DNA
- Helix untwisting and bubble formation in circular DNA
- Twist versus Nonlinear Stacking in Short DNA Molecules
- End-to-end distance and contour length distribution functions of DNA helices
- J-factors of short DNA molecules
- Flexibility of short DNA helices under mechanical stretching
- Twisting and Bending Stress in DNA Minicircles
- DNA size in confined environments
- Entropic Penalties in Circular DNA Assembly
- Phase diagram of mechanically stretched DNA: The salt effect
- Base pair fluctuations in helical models for nucleic acids
- Twisting short dsDNA with applied tension
- Anharmonic stacking in supercoiled DNA
- First-passage probability: a test for DNA Hamiltonian parameters
- Short DNA persistence length in a mesoscopic helical model
- Twist-stretch profiles of DNA chains
- Stretching DNA in hard-wall potential channels
- Mesoscopic helical models for DNA
- Modeling DNA Dynamics by Path Integrals
- Mesoscopic model for nano-channel confined DNA
- Statistical method for A-RNA and B-DNA
- Helical Disruptions in Small Loops of DNA
- Mechanical response to tension and torque of molecular chains via statistically interacting particles associated with extension, contraction, twist, and supercoiling