On the rupture of DNA molecule

Force-induced unzipping of DNA in the presence of solvent molecules

The melting of double-stranded DNA (dsDNA) in the presence of solvent molecules is a fundamental process with significant implications for understanding the thermal and mechanical behavior of DNA and its interactions with the surrounding environment. The solvents play an essential role in the structural transformation of DNA subjected to a pulling force. In this study, we simulate the thermal and force induced denaturation of dsDNA and elucidate the solvent dependent melting behavior, identifying key factors that influence the stability of DNA melting in presence of solvent molecules. Using a statistical model, we first find the melting profile of short heterogeneous DNA molecules in the presence of solvent molecules in Force ensemble. We also investigate the effect of solvent's strengths on the melting profile of DNA. In the force ensemble, we consider two homogeneous DNA chains and apply the force on different locations along the chain in the presence of solvent molecules. Different pathways manifest the melting of the molecule in both ensembles, and we found several interesting features of melting DNA in a constant force ensemble, such as lower critical force when the chain is pulled from the base pair close to a solvent molecule. The results provide new insights into the force-induced unzipping of DNA and could be used to develop new methods for controlling the unzipping process. By providing a better understanding of melting and unzipping of dsDNA in the presence of solvent molecules, this study provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA nanostructures.

Appearance of de Gennes length in force-induced transitions

Using Langevin dynamic simulations, a simple coarse-grained model of a DNA protein construct is used to study the DNA rupture and the protein unfolding. We identify three distinct states: (i) zipped DNA and collapsed protein, (ii) unzipped DNA and stretched protein, and (iii) unzipped DNA and collapsed protein. Here, we find a phase diagram that shows these states depending on the size of the DNA handle and the protein. For a less stable protein, unfolding is solely governed by the size of the linker DNA, whereas if the protein's stability increases, complete unfolding becomes impossible because the rupture force for DNA has reached a saturation regime influenced by the de Gennes length. We show that unfolding occurs via a few intermediate states by monitoring the force-extension curve of the entire protein. We extend our study to a heterogeneous protein system, where similar intermediate states in two systems can lead to different protein unfolding paths.

Structure and Dynamics of dsDNA in Cell-like Environments

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.

Opening of DNA chain due to force applied on different locations

We consider a homogeneous DNA molecule and investigate the effect of random force applied on the unzipping profile of the molecule. How the critical force varies as a function of the chain length or number of base pairs is the objective of this study. In general, the ratio of the critical forces that is applied on the middle of the chain to that which is applied on one of the ends is two. Our study shows that this ratio depends on the length of the chain. This means that the force which is applied to a point can be experienced by a section of the chain. Beyond a length, the base pairs have no information about the applied force. In the case when the chain length is shorter than this length, this ratio may vary. Only in the case when the chain length exceeds a critical length, this ratio is found to be two. Based on the de Gennes formulation, we developed a method to calculate these forces at zero temperature. The exact results at zero temperature match numerical calculations.

Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors

The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article, we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed force sensors and nanotechnological devices. We argue that rupture must be understood as an activated process, where the duplex state is metastable and the strands will separate in a finite time that depends on the duplex length and the force applied. Thus, the critical shearing force required to rupture a duplex depends strongly on the time scale of observation. We use simple models of DNA to show that this approach naturally captures the observed dependence of the force required to rupture a duplex within a given time on duplex length. In particular, this critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the long length limit. The prevailing approach, based on identifying when the presence of each additional base pair within the duplex is thermodynamically unfavorable rather than allowing for metastability, does not predict a time-scale-dependent critical force and does not naturally incorporate a critical force of zero for the shortest duplexes. We demonstrate that our findings have important consequences for the behavior of a new force-sensing nanodevice, which operates in a mixed mode that interpolates between shearing and unzipping. At a fixed time scale and duplex length, the critical force exhibits a sigmoidal dependence on the fraction of the duplex that is subject to shearing.