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

Szu Ning Lin, Remus T. Dame*, Gijs J.L. Wuite

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review

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.

Original languageEnglish
Article number18492
Pages (from-to)1-10
Number of pages10
JournalScientific Reports
Volume11
Issue number1
Early online date16 Sep 2021
DOIs
Publication statusPublished - Dec 2021

Bibliographical note

Funding Information:
This work was supported by a Vici grant from the Netherlands Organization for Scientific Research (R.T.D.) and the FOM Foundation for Fundamental Research on Matter program [programme Grant number 140] (R.T.D. and G.J.L.W). The authors thank Ilias Zarguit for critical reading of the manuscript.

Publisher Copyright:
© 2021, The Author(s).

Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.

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