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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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Autores principales: Singh, Amar, Maity, Arghya, Singh, Navin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9689892/
https://www.ncbi.nlm.nih.gov/pubmed/36359677
http://dx.doi.org/10.3390/e24111587
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author Singh, Amar
Maity, Arghya
Singh, Navin
author_facet Singh, Amar
Maity, Arghya
Singh, Navin
author_sort Singh, Amar
collection PubMed
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.
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spelling pubmed-96898922022-11-25 Structure and Dynamics of dsDNA in Cell-like Environments Singh, Amar Maity, Arghya Singh, Navin Entropy (Basel) Review 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. MDPI 2022-11-01 /pmc/articles/PMC9689892/ /pubmed/36359677 http://dx.doi.org/10.3390/e24111587 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Singh, Amar
Maity, Arghya
Singh, Navin
Structure and Dynamics of dsDNA in Cell-like Environments
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 Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9689892/
https://www.ncbi.nlm.nih.gov/pubmed/36359677
http://dx.doi.org/10.3390/e24111587
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