Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions

Abstract Architectural DNA–binding proteins are involved in many important DNA transactions by virtue of their ability to change DNA conformation. Histone-like protein from E. coli strain U93, HU, is one of the most studied bacterial architectural DNA–binding proteins. Nevertheless, there is still a...

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Autores principales:	Szu-Ning Lin, Remus T. Dame, Gijs J. L. Wuite
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fd07cee0f0fd48a4b18836862b76e6ba
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spelling	oai:doaj.org-article:fd07cee0f0fd48a4b18836862b76e6ba2021-12-02T17:24:02ZDirect visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions10.1038/s41598-021-97763-w2045-2322https://doaj.org/article/fd07cee0f0fd48a4b18836862b76e6ba2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97763-whttps://doaj.org/toc/2045-2322Abstract Architectural DNA–binding proteins are involved in many important DNA transactions by virtue of their ability to change DNA conformation. Histone-like protein from E. coli strain U93, HU, is one of the most studied bacterial architectural DNA–binding proteins. Nevertheless, there is still a limited understanding of how the interactions between HU and DNA are affected by ionic conditions and the structure of DNA. Here, using optical tweezers in combination with fluorescent confocal imaging, we investigated how ionic conditions affect the interaction between HU and DNA. We directly visualized the binding and the diffusion of fluorescently labelled HU dimers on DNA. HU binds with high affinity and exhibits low mobility on the DNA in the absence of Mg2+; it moves 30-times faster and stays shorter on the DNA with 8 mM Mg2+ in solution. Additionally, we investigated the effect of DNA tension on HU–DNA complexes. On the one hand, our studies show that binding of HU enhances DNA helix stability. On the other hand, we note that the binding affinity of HU for DNA in the presence of Mg2+ increases at tensions above 50 pN, which we attribute to force-induced structural changes in the DNA. The observation that HU diffuses faster along DNA in presence of Mg2+ compared to without Mg2+ suggests that the free energy barrier for rotational diffusion along DNA is reduced, which can be interpreted in terms of reduced electrostatic interaction between HU and DNA, possibly coinciding with reduced DNA bending.Szu-Ning LinRemus T. DameGijs J. L. WuiteNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Szu-Ning Lin Remus T. Dame Gijs J. L. Wuite Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions
description	Abstract Architectural DNA–binding proteins are involved in many important DNA transactions by virtue of their ability to change DNA conformation. Histone-like protein from E. coli strain U93, HU, is one of the most studied bacterial architectural DNA–binding proteins. Nevertheless, there is still a limited understanding of how the interactions between HU and DNA are affected by ionic conditions and the structure of DNA. Here, using optical tweezers in combination with fluorescent confocal imaging, we investigated how ionic conditions affect the interaction between HU and DNA. We directly visualized the binding and the diffusion of fluorescently labelled HU dimers on DNA. HU binds with high affinity and exhibits low mobility on the DNA in the absence of Mg2+; it moves 30-times faster and stays shorter on the DNA with 8 mM Mg2+ in solution. Additionally, we investigated the effect of DNA tension on HU–DNA complexes. On the one hand, our studies show that binding of HU enhances DNA helix stability. On the other hand, we note that the binding affinity of HU for DNA in the presence of Mg2+ increases at tensions above 50 pN, which we attribute to force-induced structural changes in the DNA. The observation that HU diffuses faster along DNA in presence of Mg2+ compared to without Mg2+ suggests that the free energy barrier for rotational diffusion along DNA is reduced, which can be interpreted in terms of reduced electrostatic interaction between HU and DNA, possibly coinciding with reduced DNA bending.
format	article
author	Szu-Ning Lin Remus T. Dame Gijs J. L. Wuite
author_facet	Szu-Ning Lin Remus T. Dame Gijs J. L. Wuite
author_sort	Szu-Ning Lin
title	Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions
title_short	Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions
title_full	Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions
title_fullStr	Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions
title_full_unstemmed	Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions
title_sort	direct visualization of the effect of dna structure and ionic conditions on hu–dna interactions
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/fd07cee0f0fd48a4b18836862b76e6ba
work_keys_str_mv	AT szuninglin directvisualizationoftheeffectofdnastructureandionicconditionsonhudnainteractions AT remustdame directvisualizationoftheeffectofdnastructureandionicconditionsonhudnainteractions AT gijsjlwuite directvisualizationoftheeffectofdnastructureandionicconditionsonhudnainteractions
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Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions

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