Probing the mechanical stability of bridged DNA-H-NS protein complexes by single-molecule AFM pulling

Yan Liang; Ramon A. van der Valk; Remus T. Dame; Wouter H. Roos; Gijs J. L. Wuite

doi:10.1038/s41598-017-15477-4

Probing the mechanical stability of bridged DNA-H-NS protein complexes by single-molecule AFM pulling

Yan Liang, Ramon A. van der Valk, Remus T. Dame, Wouter H. Roos, Gijs J. L. Wuite

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

Atomic force microscopy (AFM) has proven to be a powerful tool for the study of DNA-protein interactions due to its ability to image single molecules at the nanoscale. However, the use of AFM in force spectroscopy to study DNA-protein interactions has been limited. Here we developed a high throughput, AFM based, pulling assay to measure the strength and kinetics of protein bridging of DNA molecules. As a model system, we investigated the interactions between DNA and the Histone-like Nucleoid-Structuring protein (H-NS). We confirmed that H-NS both changes DNA rigidity and forms bridges between DNA molecules. This straightforward methodology provides a high-throughput approach with single-molecule resolution which is widely applicable to study cross-substrate interactions such as DNA-bridging proteins.

Original language	English
Article number	15275
Journal	Scientific Reports
Volume	7
Issue number	1
DOIs	https://doi.org/10.1038/s41598-017-15477-4
Publication status	Published - 10 Nov 2017

Funding

We thank Marian Baclayon, Maryam Shabestari, Mariska van Rosmalen, Kathy Chaurasiya and Daan Vorselen, for providing custom LabView and Matlab programs and support (Vrije Universiteit Amsterdam). We thank Geri Moolenaar for technical assistance in substrate preparation and Olga Kalmykowa for cloning and production of the H-NSC21S protein (Leiden University). GJLW and RTD acknowledge NWO for a VICI grant and the Dutch government and partners for a NanoNextNL grant, WHR and RTD acknowledge NWO for a VIDI grant, YL acknowledges the funding from the Construction Programme for “Taishan Scholarship” of Shandong Province of China (S41201203), National Natural Science Foundation of China (G31302233) and the State Scholarship of China.

Funders	Funder number
Shandong Province of China	S41201203
National Natural Science Foundation of China	G31302233
Nederlandse Organisatie voor Wetenschappelijk Onderzoek

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abstract = "Atomic force microscopy (AFM) has proven to be a powerful tool for the study of DNA-protein interactions due to its ability to image single molecules at the nanoscale. However, the use of AFM in force spectroscopy to study DNA-protein interactions has been limited. Here we developed a high throughput, AFM based, pulling assay to measure the strength and kinetics of protein bridging of DNA molecules. As a model system, we investigated the interactions between DNA and the Histone-like Nucleoid-Structuring protein (H-NS). We confirmed that H-NS both changes DNA rigidity and forms bridges between DNA molecules. This straightforward methodology provides a high-throughput approach with single-molecule resolution which is widely applicable to study cross-substrate interactions such as DNA-bridging proteins.",

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AU - Wuite, Gijs J. L.

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Probing the mechanical stability of bridged DNA-H-NS protein complexes by single-molecule AFM pulling

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