Structural Analysis of DNA molecule in a confined shell

TL;DR

This paper investigates how confinement in a cylindrical geometry affects the structural stability and properties of DNA molecules using statistical and molecular dynamics models.

Contribution

It extends previous research by analyzing the impact of confinement geometry on DNA's structural and thermal stability using combined modeling approaches.

Findings

Confinement influences DNA opening and structural parameters.

The geometry of confinement affects DNA stability.

Results provide insights into DNA behavior in nano-channels.

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. 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.