Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength

The opening of DNA double strands is extremely relevant to several biological functions, such as replication and transcription or binding of specific proteins. Such opening phenomenon is particularly sensitive to the aqueous solvent conditions in which the DNA molecule is dispersed, as it can be obs...

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Main Authors:	Tempestini, Alessia, Cassina, Valeria, Brogioli, Doriano, Ziano, Roberto, Erba, Simona, Giovannoni, Roberto, Cerrito, Maria G., Salerno, Domenico, Mantegazza, Francesco
Format:	Online
Language:	English
Published:	Oxford University Press 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561983/

id	pubmed-3561983
recordtype	oai_dc
spelling	pubmed-35619832013-02-01 Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength Tempestini, Alessia Cassina, Valeria Brogioli, Doriano Ziano, Roberto Erba, Simona Giovannoni, Roberto Cerrito, Maria G. Salerno, Domenico Mantegazza, Francesco Structural Biology The opening of DNA double strands is extremely relevant to several biological functions, such as replication and transcription or binding of specific proteins. Such opening phenomenon is particularly sensitive to the aqueous solvent conditions in which the DNA molecule is dispersed, as it can be observed by considering the classical dependence of DNA melting temperature on pH and salt concentration. In the present work, we report a single-molecule study of the stability of DNA against denaturation when subjected to changes in solvent. We investigated the appearance of DNA instability under specific external applied force and imposed twist values, which was revealed by an increase in the temporal fluctuations in the DNA extension. These fluctuations occur in the presence of a continuous interval of equilibrium states, ranging from a plectonemic state to a state characterized by denaturation bubbles. In particular, we observe the fluctuations only around a characteristic force value. Moreover, this characteristic force is demonstrated to be notably sensitive to variations in the pH and ionic strength. Finally, an extension of a theoretical model of plectoneme formation is used to estimate the average denaturation energy, which is found to be linearly correlated to the melting temperature of the DNA double strands. Oxford University Press 2013-02 2012-12-15 /pmc/articles/PMC3561983/ /pubmed/23248010 http://dx.doi.org/10.1093/nar/gks1206 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Tempestini, Alessia Cassina, Valeria Brogioli, Doriano Ziano, Roberto Erba, Simona Giovannoni, Roberto Cerrito, Maria G. Salerno, Domenico Mantegazza, Francesco
spellingShingle	Tempestini, Alessia Cassina, Valeria Brogioli, Doriano Ziano, Roberto Erba, Simona Giovannoni, Roberto Cerrito, Maria G. Salerno, Domenico Mantegazza, Francesco Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength
author_facet	Tempestini, Alessia Cassina, Valeria Brogioli, Doriano Ziano, Roberto Erba, Simona Giovannoni, Roberto Cerrito, Maria G. Salerno, Domenico Mantegazza, Francesco
author_sort	Tempestini, Alessia
title	Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength
title_short	Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength
title_full	Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength
title_fullStr	Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength
title_full_unstemmed	Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength
title_sort	magnetic tweezers measurements of the nanomechanical stability of dna against denaturation at various conditions of ph and ionic strength
description	The opening of DNA double strands is extremely relevant to several biological functions, such as replication and transcription or binding of specific proteins. Such opening phenomenon is particularly sensitive to the aqueous solvent conditions in which the DNA molecule is dispersed, as it can be observed by considering the classical dependence of DNA melting temperature on pH and salt concentration. In the present work, we report a single-molecule study of the stability of DNA against denaturation when subjected to changes in solvent. We investigated the appearance of DNA instability under specific external applied force and imposed twist values, which was revealed by an increase in the temporal fluctuations in the DNA extension. These fluctuations occur in the presence of a continuous interval of equilibrium states, ranging from a plectonemic state to a state characterized by denaturation bubbles. In particular, we observe the fluctuations only around a characteristic force value. Moreover, this characteristic force is demonstrated to be notably sensitive to variations in the pH and ionic strength. Finally, an extension of a theoretical model of plectoneme formation is used to estimate the average denaturation energy, which is found to be linearly correlated to the melting temperature of the DNA double strands.
publisher	Oxford University Press
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561983/
_version_	1611951949687554048

Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength

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