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...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-09-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-97763-w |
| _version_ | 1818993722731266048 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-20T20:46:35Z |
| format | Article |
| id | doaj.art-fd07cee0f0fd48a4b18836862b76e6ba |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-20T20:46:35Z |
| publishDate | 2021-09-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-fd07cee0f0fd48a4b18836862b76e6ba2022-12-21T19:27:01ZengNature PortfolioScientific Reports2045-23222021-09-0111111010.1038/s41598-021-97763-wDirect visualization of the effect of DNA structure and ionic conditions on HU–DNA interactionsSzu-Ning Lin0Remus T. Dame1Gijs J. L. Wuite2Leiden Institute of Chemistry, Leiden UniversityLeiden Institute of Chemistry, Leiden UniversityDepartment of Physics and Astronomy, Vrije Universiteit AmsterdamAbstract 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.https://doi.org/10.1038/s41598-021-97763-w |
| spellingShingle | 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 Scientific Reports |
| title | 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_short | 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 |
| url | https://doi.org/10.1038/s41598-021-97763-w |
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