DNA thermal denaturation by polymer field theory approach: effects of the environment

Abstract

We analyse the effects of the environment (solvent quality, presence of extended structures - crowded environment) that may have impact on the order of the transition between denaturated and bounded DNA states and lead to changes in the scaling laws that govern conformational properties of DNA strands. We find that the effects studied significantly influence the strength of the first order transition. To this end, we re-consider the Poland-Scheraga model and apply a polymer field theory to calculate entropic exponents associated with the denaturated loop distribution. For the $d=3$ case, the corresponding diverging $\epsilon =4-d$ expansions are evaluated by restoring their convergence via the resummation technique. For the space dimension $d=2$, the exponents are deduced from mapping the polymer model onto a two-dimensional random lattice, i.e., in the presence of quantum gravity. We also show that the first order transition is further strengthened by the presence of extended impenetrable regions in a solvent that restrict the number of the macromolecule configurations.

arXiv commentSubmitted to Condensed Matter Physics Journal

References in corpus (24)

• Why is the DNA Denaturation Transition First Order?
• Roles of stiffness and excluded volume in DNA denaturation
• A Simple Model for the DNA Denaturation Transition
• Reparametrizing loop entropy weights: Effect on DNA melting curves
• Poland-Scheraga models and the DNA denaturation transition
• Polymers in long-range-correlated disorder
• Two-Dimensional Copolymers and Exact Conformal Multifractality
• Copolymer Networks and Stars: Scaling Exponents
• About the relevance of the fixed dimension perturbative approach to frustrated magnets in two and three dimensions
• Weak quenched disorder and criticality: resummation of asymptotic(?) series
• Melting and unzipping of DNA
• Copolymer Networks: Multifractal dimension spectra in polymer field theory
• Scaling in DNA unzipping models: denaturated loops and end-segments as branches of a block copolymer network
• Analysis of the 3d massive renormalization group perturbative expansions: a delicate case
• Critical exponents of the diluted Ising model between dimensions 2 and 4
• Entropy-induced separation of star polymers in porous media
• Disorder effects on the static scattering function of star branched polymers
• Star copolymers in porous environments: scaling and its manifestations
• Fractals Meet Fractals: Self-Avoiding Random Walks on Percolation Clusters
• How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model
• Scaling of star polymers: high order results
• Variety of Scaling Laws for DNA Thermal Denaturation
• Polymers in anisotropic environment with extended defects
• Unbinding of mutually avoiding random walks and two dimensional quantum gravity