Single-molecule DNA-flow stretching assay as a versatile hybrid tool for investigating DNA-protein interactions

Authors

Sadaf Shehzad, The University of Texas Rio Grande Valley
HyeongJun Kim, The University of Texas Rio Grande ValleyFollow

Document Type

Article

Publication Date

1-24-2025

Abstract

Single-molecule techniques allow researchers to investigate individual molecules and obtain unprecedented details of the heterogeneous nature of biological entities. They play instrumental roles in studying DNA-protein interactions due to the ability to visualize DNA or proteins and to manipulate individual DNA molecules by applying force or torque. Here, we describe single-molecule DNA-flow stretching assays as hybrid tools that combine forces with fluorescence. We also review how widely these assays are utilized in elucidating working mechanisms of DNA-binding proteins. Additionally, we provide a brief explanation of various efforts to prepare DNA substrates with desired internal protein-binding sequences. More complicated needs for DNA-protein interaction research have led to improvements in single-molecule DNA flow-stretching techniques. Several DNA flow-stretching variants such as DNA curtain, DNA motion capture assays, and protein-induced fluorescence enhancement (PIFE) are introduced in this mini review. Single-molecule DNA flow-stretching assays will keep contributing to our understanding of how DNA-binding proteins function due to their multiplexed, versatile, and robust capabilities.

Comments

© Korean Society for Biochemistry and Molecular Biology. All rights reserved.

This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Recommended Citation

Shehzad, Sadaf, and HyeongJun Kim. "Single-molecule DNA-flow stretching assay as a versatile hybrid tool for investigating DNA-protein interactions." BMB reports 58, no. 1 (2025): 41-51. https://doi.org/10.5483/BMBRep.2024-0177

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License

First Page

41

Last Page

51

Publication Title

BMB Reports

DOI

10.5483/BMBRep.2024-0177