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 struc...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-11-01
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| Series: | Entropy |
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| Online Access: | https://www.mdpi.com/1099-4300/24/11/1587 |
| _version_ | 1797468368665575424 |
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| author | Amar Singh Arghya Maity Navin Singh |
| author_facet | Amar Singh Arghya Maity Navin Singh |
| author_sort | Amar Singh |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T19:05:30Z |
| format | Article |
| id | doaj.art-7186e2d5da2b4988879913a9402525ba |
| institution | Directory Open Access Journal |
| issn | 1099-4300 |
| language | English |
| last_indexed | 2024-03-09T19:05:30Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Entropy |
| spelling | doaj.art-7186e2d5da2b4988879913a9402525ba2023-11-24T04:36:41ZengMDPI AGEntropy1099-43002022-11-012411158710.3390/e24111587Structure and Dynamics of dsDNA in Cell-like EnvironmentsAmar Singh0Arghya Maity1Navin Singh2Department of Physics, Birla Institute of Technology & Science, Pilani 333031, IndiaDepartment of Physics, Birla Institute of Technology & Science, Pilani 333031, IndiaDepartment of Physics, Birla Institute of Technology & Science, Pilani 333031, IndiaDeoxyribonucleic 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.https://www.mdpi.com/1099-4300/24/11/1587dsDNADNA dynamicsDNA meltingunzippingcrowdingconfinement |
| spellingShingle | Amar Singh Arghya Maity Navin Singh Structure and Dynamics of dsDNA in Cell-like Environments Entropy dsDNA DNA dynamics DNA melting unzipping crowding confinement |
| title | Structure and Dynamics of dsDNA in Cell-like Environments |
| title_full | Structure and Dynamics of dsDNA in Cell-like Environments |
| title_fullStr | Structure and Dynamics of dsDNA in Cell-like Environments |
| title_full_unstemmed | Structure and Dynamics of dsDNA in Cell-like Environments |
| title_short | Structure and Dynamics of dsDNA in Cell-like Environments |
| title_sort | structure and dynamics of dsdna in cell like environments |
| topic | dsDNA DNA dynamics DNA melting unzipping crowding confinement |
| url | https://www.mdpi.com/1099-4300/24/11/1587 |
| work_keys_str_mv | AT amarsingh structureanddynamicsofdsdnaincelllikeenvironments AT arghyamaity structureanddynamicsofdsdnaincelllikeenvironments AT navinsingh structureanddynamicsofdsdnaincelllikeenvironments |