Melting of confined DNA: static and dynamic properties

Abstract

We study dsDNA (double strand DNA) melting in detail within varying strip-like confinement in a two-dimensional lattice model. The interplay between reduced configurational entropy and attractive base-pairing energy results non-monotonic...

Force induced DNA melting in the presence of an attractive surface

“…Base pairing interactions are restricted to native contacts (diagonal), where the i-th monomer of one strand interacts with the i-th monomer of the other strand only. 18,36,37 Since the model developed here is on the square lattice, only one strand (say, strand-I) will lie over the surface, while the other strand (strand-II) will be on top of strand-I, and hence strand-II will have no contact with the surface in the zipped state, or vice versa. This indicates that only one strand will be in contact with the surface.…”

“…The generation of dsDNA follows a specific procedure: strand-I is generated to its full extent, and then strand-II is generated, taking into account the available space restricted by the surface and strand-I. 18 The total number of conformations grows exponentially 43 with the chain length. Therefore, we have restricted ourselves to a finite length chain N = 15.…”

“…14,15 Recently, a few experiments have been performed to study DNA denaturation or melting along with adsorption on gold nanoparticles (Au-NPs). 16,17 DNA melting 18 in the presence of attractive surfaces has biological significance, such as DNA replication in the presence of a cell membrane. 19 In gene therapy, targeted drug delivery is facilitated through DNA adsorption-desorption on oppositely charged liposomes.…”

Solvent effect on equilibrium organization of confined polymers

“…Generally whenever polymers are set inside confinement (of size D) that has a dimension less than the size of the molecule (radius of gyration R g o D), then the equilibrium properties and dynamics of the polymers change significantly from the free-polymer solution. 4,21,22 The entropic and enthalpic contributions of the confined polymers compete with each other, where entropic loss due to confinement always results in an increase in free energy, but the enthalpy of the polymers due to surface-polymer interactions and non-bonded nearest neighbours can increase or decrease the free energy, depending on the solvent quality. [23][24][25] While small particles (like gases) favour mixing to maximize the entropy, long molecules like polymers demix (partition) due to the excluded-volume effect, lower configurational entropy of overlapping conformations, and steric repulsion between chains.…”