Stacking Interactions in Denaturation of DNA Fragments
arXiv:1106.4207 · doi:10.1140/epje/i2011-11068-9
Abstract
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The size of the paths ensemble, which measures the degree of cooperativity of the system, is computed versus temperature consistently with the model potential physical requirements. It is shown that the ensemble size strongly varies with the molecule backbone stiffness providing a quantitative relation between stacking and features of the melting transition. The latter is an overall smooth crossover which begins from the \emph{adenine-thymine} rich portions of the fragment. The harmonic stacking coupling shifts, along the -axis, the occurrence of the multistep denaturation but it does not change the character of the crossover. The methods to compute the fractions of open base pairs versus temperature are discussed: by averaging the base pair displacements over the path ensemble we find that such fractions signal the multisteps of the transition in good agreement with the indications provided by the specific heat plots.
European Physical Journal E (2011) in press
References in corpus (32)
- Why is the DNA Denaturation Transition First Order?
- Denaturation of Heterogeneous 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
- Reparametrizing loop entropy weights: Effect on DNA melting curves
- DNA bubble dynamics as a quantum Coulomb problem
- Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation
- Bubble dynamics in DNA
- Sequence sensitivity of breathing dynamics in heteropolymer DNA
- Poland-Scheraga models and the DNA denaturation transition
- Bubbles and denaturation in DNA
- Denaturation transition of stretched DNA
- Thermal denaturation of fluctuating finite DNA chains: the role of bending rigidity in bubble nucleation
- The thermal denaturation of DNA studied with neutron scattering
- Melting of genomic DNA: predictive modeling by nonlinear lattice dynamics
- Healing Length and Bubble Formation in DNA
- The probability analysis of opening of DNA
- Exons, introns and DNA thermodynamics
- Path Integral Method for DNA Denaturation
- Denaturation Patterns in Heterogeneous DNA
- Statistical physics of the melting of inhomogeneous DNA
- Towards more realistic dynamical models for DNA secondary structure
- Dynamical versus statistical mesoscopic models for DNA denaturation
- Simplified Langevin approach to the Peyrard-Bishop-Dauxois model of DNA
- Theoretical investigation of finite size effects at DNA melting
- Path Integral of the Two Dimensional Su-Schrieffer-Heeger Model
- Phonon Thermodynamics versus Electron-Phonon Models
- Polaron Mass and Electron-Phonon Correlations in the Holstein Model
- Renormalisation group determination of the order of the DNA denaturation transition
- Non Local Electron-Phonon Correlations in a Dispersive Holstein Model
- Dynamical modelling of molecular constructions and setups for DNA unzipping
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- Thermodynamics of Twisted DNA with Solvent Interaction
- Twist versus Nonlinear Stacking in Short DNA Molecules
- Helix untwisting and bubble formation in circular DNA
- 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
- 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
- Twist-stretch profiles of DNA chains
- Short DNA persistence length in a mesoscopic helical model
- Mesoscopic helical models for DNA
- Twist-stretch relations in nucleic acids
- 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