Intracellular positive ions neutralize negative charges on the phosphates of a DNA strand, conferring greater strength on the hydrogen bonds that connect complementary strands into a double helix and so confer enhanced stability. Beyond a certain value of salt concentration, the DNA molecule displays an unstable nature in vivo as well as in vitro. We consider a wide range of salt concentrations and study the stability of the DNA double helix using a statistical model. Through numerical calculations, we attempt to explain the different behavior exhibited by DNA molecules in this range. We compare our results with experimental data and find a close agreement.

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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.

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.

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