Statistical mechanics of a polymer chain attached to the interface of a cone-shaped channel

Chauhan

Bharadwaj

et al. 2023

IJMS

Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.

Section: Polymer Translocation: Highlights From Theoretical Developmentmentioning

confidence: 99%

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

Chauhan

Bharadwaj

et al. 2023

IJMS

“…In vivo, a DNA molecule is in a highly dense solvent environment and is confined in a limited space, such as a cell chamber or a channel [ 149 , 150 , 151 ] (see Figure 5 ). The solvent’s ionic charges make it easy for DNA polymers to slide through the confinement channel [ 152 ].…”

Section: Dna In Confined Geometrymentioning

confidence: 99%

“…However, solid-state nanopores have the advantage in terms of tunable size and shape. In addition to these studies, a study related to the stability of biopolymers, especially DNA molecules, when they passes through these pores also needs special attention [ 150 , 159 ]. The confined space of the cytoskeleton and cell organelles restricts the movement of DNA molecules and hence alters their stability.…”

Section: Translocation Of Dna (Dna Passing Through Pores)mentioning

confidence: 99%

Structure and Dynamics of dsDNA in Cell-like Environments

Maity

2022

Entropy

Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA’s structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.

“…Due to the restricted behaviour of DNA molecule during encapsulation, it is of deep interest to investigate the tube diameter's effect on the DNA molecule's stability. The confinement restricts the conformation and movement of DNA molecules in the cell due to which there is substantial changes in the thermodynamic properties of DNA molecules [9][10][11][12]. The DNA packing in eukaryotic chromosomes, viral capsids in the confined space are some examples that show the importance of the studies related to DNA in confined geometry.…”

Section: Introductionmentioning

confidence: 99%

Structural Analysis of DNA molecule in a confined shell

Maity¹,

Mathur²,

Imhof³

et al. 2022

Preprint

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.