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Review
. 2022 Nov 1;24(11):1587.
doi: 10.3390/e24111587.

Structure and Dynamics of dsDNA in Cell-like Environments

Amar Singh  1 , Arghya Maity  1 , Navin Singh  1
Affiliations
Review

Structure and Dynamics of dsDNA in Cell-like Environments

Amar Singh et al. Entropy (Basel). .

Abstract

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.

Keywords: DNA dynamics; DNA encapsulation; DNA melting; confinement; crowding; dsDNA; ionic solution; phase transition; unzipping.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Schematic representation of the melting curve of a short, homogeneous DNA chain either experimentally (generally represented by UV absorbance, shown in blue) or theoretically (generally described by phase transitions with order parameters, i.e., fraction of open pairs, shown in red). The nature of these curves depends on many other factors, e.g., DNA sequence, length, mismatch, etc. [18].
Figure 2
Figure 2
(a) Cumulative number of DNA structures from the year 1981 to 2022. (b) Fraction of different types of DNA structures released in every five years. Data taken from the Nucleic Acid Database: http://ndbserver.rutgers.edu/, accessed on 27 June 2022.
Figure 3
Figure 3
Illustration of the presence of cations (represented by black or gray spheres; not to scale) around the two negatively charged DNA strands. Cations, such as K+, Na+, Mg2+, etc., counteract the repulsion between the two strands as well as the potential distribution of extra cations that interact with one another.
Figure 4
Figure 4
Thermal melting of DNA molecules in the presence of molecular crowders (described in detail in [122]). The change in the fraction of intact pairs with increasing temperature is shown by the black curve, while the change in specific heat is represented by the red curve. To visualize the opening of individual base pairs, corresponding dsDNA or ssDNA chains are displayed and mapped based on the fraction of intact base pairs. The presence of crowders, shown with spheres along the DNA chain, restricts thermal fluctuations, and a further increase in temperature leads to the opening of crowded base pairs.
Figure 5
Figure 5
DNA molecule in examples of confined environments: protein channel and nanopore. The thermodynamic properties of DNA molecules highly depend on these confined spaces and on the solvent properties.
See this image and copyright information in PMC

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Grants and funding

Navin Singh acknowledges the financial support from the Department of Science and Technology, New Delhi (EMR/2017/002451).

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