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Mechanical Constraint Effect on DNA Persistence Length

Persistence length is a significant criterion to characterize the semi-flexibility of DNA molecules. The mechanical constraints applied on DNA chains in new single-molecule experiments play a complex role in measuring DNA persistence length; however, there is a difficulty in quantitatively character...

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Autores principales: Zhang, Cheng-Yin, Zhang, Neng-Hui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9696218/
https://www.ncbi.nlm.nih.gov/pubmed/36431871
http://dx.doi.org/10.3390/molecules27227769
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author Zhang, Cheng-Yin
Zhang, Neng-Hui
author_facet Zhang, Cheng-Yin
Zhang, Neng-Hui
author_sort Zhang, Cheng-Yin
collection PubMed
description Persistence length is a significant criterion to characterize the semi-flexibility of DNA molecules. The mechanical constraints applied on DNA chains in new single-molecule experiments play a complex role in measuring DNA persistence length; however, there is a difficulty in quantitatively characterizing the mechanical constraint effects due to their complex interactions with electrostatic repulsions and thermal fluctuations. In this work, the classical buckling theory of Euler beam and Manning’s statistical theories of electrostatic force and thermal fluctuation force are combined for an isolated DNA fragment to formulate a quantitative model, which interprets the relationship between DNA persistence length and critical buckling length. Moreover, this relationship is further applied to identify the mechanical constraints in different DNA experiments by fitting the effective length factors of buckled fragments. Then, the mechanical constraint effects on DNA persistence lengths are explored. A good agreement among the results by theoretical models, previous experiments, and present molecular dynamics simulations demonstrates that the new superposition relationship including three constraint-dependent terms can effectively characterize changes in DNA persistence lengths with environmental conditions, and the strong constraint-environment coupling term dominates the significant changes of persistence lengths; via fitting effective length factors, the weakest mechanical constraints on DNAs in bulk experiments and stronger constraints on DNAs in single-molecule experiments are identified, respectively. Moreover, the consideration of DNA buckling provides a new perspective to examine the bendability of short-length DNA.
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spelling pubmed-96962182022-11-26 Mechanical Constraint Effect on DNA Persistence Length Zhang, Cheng-Yin Zhang, Neng-Hui Molecules Article Persistence length is a significant criterion to characterize the semi-flexibility of DNA molecules. The mechanical constraints applied on DNA chains in new single-molecule experiments play a complex role in measuring DNA persistence length; however, there is a difficulty in quantitatively characterizing the mechanical constraint effects due to their complex interactions with electrostatic repulsions and thermal fluctuations. In this work, the classical buckling theory of Euler beam and Manning’s statistical theories of electrostatic force and thermal fluctuation force are combined for an isolated DNA fragment to formulate a quantitative model, which interprets the relationship between DNA persistence length and critical buckling length. Moreover, this relationship is further applied to identify the mechanical constraints in different DNA experiments by fitting the effective length factors of buckled fragments. Then, the mechanical constraint effects on DNA persistence lengths are explored. A good agreement among the results by theoretical models, previous experiments, and present molecular dynamics simulations demonstrates that the new superposition relationship including three constraint-dependent terms can effectively characterize changes in DNA persistence lengths with environmental conditions, and the strong constraint-environment coupling term dominates the significant changes of persistence lengths; via fitting effective length factors, the weakest mechanical constraints on DNAs in bulk experiments and stronger constraints on DNAs in single-molecule experiments are identified, respectively. Moreover, the consideration of DNA buckling provides a new perspective to examine the bendability of short-length DNA. MDPI 2022-11-11 /pmc/articles/PMC9696218/ /pubmed/36431871 http://dx.doi.org/10.3390/molecules27227769 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 Article
Zhang, Cheng-Yin
Zhang, Neng-Hui
Mechanical Constraint Effect on DNA Persistence Length
title Mechanical Constraint Effect on DNA Persistence Length
title_full Mechanical Constraint Effect on DNA Persistence Length
title_fullStr Mechanical Constraint Effect on DNA Persistence Length
title_full_unstemmed Mechanical Constraint Effect on DNA Persistence Length
title_short Mechanical Constraint Effect on DNA Persistence Length
title_sort mechanical constraint effect on dna persistence length
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9696218/
https://www.ncbi.nlm.nih.gov/pubmed/36431871
http://dx.doi.org/10.3390/molecules27227769
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