DNA-binding proteins studied by mechanical manipulation and AFM imaging of single DNA molecules

Xiaodan Zhao; Xuyao Priscilla Liu; Jie Yan

doi:10.52601/bpr.2022.220015

Volume 8 Issue 4

Aug. 2022

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Xiaodan Zhao, Xuyao Priscilla Liu, Jie Yan. DNA-binding proteins studied by mechanical manipulation and AFM imaging of single DNA molecules[J]. Biophysics Reports, 2022, 8(4): 212-224. doi: 10.52601/bpr.2022.220015

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Xiaodan Zhao, Xuyao Priscilla Liu, Jie Yan. DNA-binding proteins studied by mechanical manipulation and AFM imaging of single DNA molecules[J]. Biophysics Reports, 2022, 8(4): 212-224. doi: 10.52601/bpr.2022.220015

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DNA-binding proteins studied by mechanical manipulation and AFM imaging of single DNA molecules

doi: 10.52601/bpr.2022.220015

Xiaodan Zhao^{1, 3},
Xuyao Priscilla Liu^{1, 3},
Jie Yan^{1, 2, 3
,
,}

1.
Department of Physics, National University of Singapore, Singapore 117542, Singapore
2.
Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
3.
Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore

More Information

Corresponding author: phyyj@nus.edu.sg (Jie Yan)
Received Date: 22 June 2022
Accepted Date: 17 July 2022

Available Online: 08 November 2022

Publish Date: 31 August 2022

Abstract

Abstract

The functions of DNA-binding proteins are dependent on protein-induced DNA distortion, the binding preference to special sequences, DNA secondary structures, the binding kinetics and the binding affinity. Recent rapid progress in single-molecule imaging and mechanical manipulation technologies have made it possible to directly probe the DNA binding by proteins, footprint the positions of the bound proteins on DNA, quantify the kinetics and the affinity of protein–DNA interactions, and study the interplay of protein binding with DNA conformation and DNA topology. Here, we review the applications of an integrated approach where the single-DNA imaging using atomic force microscopy and the mechanical manipulation of single DNA molecules are combined to study the DNA–protein interactions. We also provide our views on how these findings yield new insights into understanding the roles of several essential DNA architectural proteins.
- AFM imaging,
- Single-molecule manipulation,
- Magnetic tweezers,
- Optical tweezers,
- DNA–protein interactions,
- DNA supercoiling,
- DNA distortion

Xiaodan Zhao, Xuyao Priscilla Liu and Jie Yan declare that they have no conflict of interest.
This article does not contain any studies with human or animal subjects performed by any of the authors.

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References(86)

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