The effect of pore geometry on the denaturation of a DNA molecule during translocation
The recent years witnessed significant advances in nanopore technology and the DNA sequencing. Translocation of DNA in biological processes involves many constraints, and among them, the pore through which it translocates is worthy of attention. In this manuscript, we construct two different shaped confining wall, a cone-shaped and a cylindrical shaped, and investigate the denaturation of DNA molecule during various stages of translocation in a thermal ensemble. For the conically shaped confinement, we study the effect of the cone angle (θ) and the pore diameter (δ) on the melting profile of a DNA molecule. Similarly, for the cylindrically shaped confinement, we investigate the effect of pore diameter (r) on the melting profile of a DNA molecule. By varying the fraction of pairs (φ) that are on either side of a pore, we study the melting behaviour of DNA molecule in these two confinement geometries.
Presence of molecular crowders & effect on the melting profile of DNA
This is a known fact that about 15-20% of the total volume of cell is occupied by the molecular crowders. The crowders that surround the DNA molecule are randomly distributed along the molecule. Hence we consider the base pairs that are surrounded by crowders randomly. The presence of these crowders, reduces the free volume for the base pairs, hence the movement of base pairs is restricted. We study the thermal melting of a homogeneous DNA molecule using PBD model. The presence of crowders in the model is realized through the potential term. Using the equilibrium statistical calculations we find the melting profile and the melting probabilities of the chain. We also find a correlation between the melting temperature and the crowder density of the solution. The power law behaviour shows that the melting temperature scale linearly with the crowder density. The opening of a DNA molecule in presence of these crowders is shown through the density plots. The results display interesting features of opening of DNA molecule.
We have studied the separation of a double stranded DNA (dsDNA), which is driven by either the temperature or force. By monitoring the probability of opening of entire base pairs along the chain, we show that the opening of a dsDNA depends not only on the sequence but also on the constraints on the chain in the experimental setups. Our results clearly demonstrate that the force-induced melting of dsDNA, whose one of the ends is constrained, is significantly different from the thermal melting, when both ends are free.
http://link.aip.org/link/doi/10.1063/1.3563633
Phase diagram of unzipping of DNA: role of salt concentration
The cations, in form of salt, present in the solution containing DNA play a crucial role in the opening of two strands of DNA. We use a simple non linear model and investigate the role of these cations on the mechanical unzipping of DNA. The Hamiltonian is modified in terms of cations present in the solution. We calculate the melting temperature as well as the critical force that is required to unzip the DNA molecule as a function of salt concentration of the solution. The phase diagrams are found to be in close agreement with the experimental phase diagrams.