Stability of DNA passing through different geometrical pores

Abstract

The recent years witnessed significant advances in nanopore technology and the DNA sequencing. One of the efficient methods for DNA sequencing is denaturation mapping of the DNA molecule that is trapped inside a cylindrical geometry. In this paper, we investigate the denaturation of homogeneous as well as heterogeneous DNA molecules which are confined in a conical as well as cylindrical geometric space. For the conically shaped confinement, we study the effect of the cone angle and the pore width on the melting profile of homogeneous DNA molecules. Similarly, for the cylindrically shaped confinement, we investigate the effect of the cylinder diameter on the melting profile of homogeneous and heterogeneous DNA molecules. We consider the conditions when DNA is partially inside the confined space and partially outside the confined space. For the investigation, we vary the fraction of base pairs that remains inside the space and calculate the denaturation profile of DNA molecules in each condition.

Structural Analysis of DNA molecule in a confined shell

“…next part of the study, we have used Gromacs package, version 4.0.4, to study the change in the average size of the 1 BNA molecule with the changing size (radius) of the cylinder.With the change in the cylinder's size (radius only), we have calculated the RMSD (root mean square deviation) values of the confined DNA at different temperatures. The RMSD calculations showed that the molecule is more stable when it is placed inside a cylinder.The results are trivial and well in agreement with the first part of the current investigation and our earlier work[1,2]. The reason for the stability is as follows: the decrease in the cylinder's radius, the confining wall becomes closer, which suppresses the molecule's entropy and hence the RMSD value decreases.…”

“…Several researchers have extended the model to three-dimensions [17,18]. The PBD model has been extended to study the effect of molecular crowders as well as the effect of confinement on the thermal stability of DNA molecule [1,2,17]. The mathematical form of the model that contains N base pairs, is as follows:…”

“…In the current manuscript, we extend the work study the effect of confinement on the thermal stability and the structural properties of duplex DNA. The present work is an extension of our previous research works [1,2]. For our study we have considered a 1 BNA chain that is confined in a cylindrical geometry.…”

Melting of DNA in confined geometry

“…In the present manuscript, motivated by all these different kinds of experiments in different geometries, we attempt to understand the thermal stability of a DNA molecule that is confined in different geometries through a statistical model. The present manuscript is an following work of our recent published research work [32]. It helps to understand confinement effect more immensely.…”

Structure and Dynamics of dsDNA in Cell-like Environments

“…This method opens up new possibilities for predicting the genome sequence by fusing the experimental approach with a computer simulation built on the Poland–Scheraga model [ 23 ], which assesses the sequence-dependent melting probability. In recent research, Maity et al [ 185 ] expanded these ground-breaking studies and made an effort to comprehend how DNA that is completely or partially confined in a nanochannel melts. They studied the melting of homogenous DNA in two distinct geometries: conical and cylindrical.…”