Structural Analysis of DNA molecule in a confined shell

Abstract

Recent advances in operating and manipulating DNA have provided unique experimental possibilities in many fields of DNA research, especially in gene therapy. Researchers have deployed many techniques, experimental and theoretical, to study the DNA structure changes due to external perturbation. It is crucial to understand the structural and dynamical changes in the DNA molecules in a confined state to understand and control the self-assembly of DNA confined in a chamber or nano-channel for various applications. 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. How the geometry of the confinement affects the opening and other structural parameters of DNA molecule is the objective of this manuscript. We have used a statistical model(PBD model) and Molecular dynamics simulations for our purpose.

Structure and Dynamics of dsDNA in Cell-like Environments

“…The stability of DNA molecules during encapsulation is a field of earnest research. Maity et al [ 180 , 181 ] have studied the thermal stability of double-stranded DNA molecules of different lengths in a confined space. Using the PBD model and molecular dynamics simulations, they evaluated the melting profile of DNA of different lengths in two geometries: conical and cylindrical.…”