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Mol. Cells

Published online September 2, 2021

© The Korean Society for Molecular and Cellular Biology

Single-Molecule Methods for Investigating the Double-Stranded DNA Bendability

Sanghun Yeou1 and Nam Ki Lee2,*

1Department of Physics, Pohang University of Science and Technology, Pohang 37673, Korea, 2Department of Chemistry, Seoul National University, Seoul 08826, Korea

Correspondence to : namkilee@snu.ac.kr

Received: July 9, 2021; Revised: July 19, 2021; Accepted: July 20, 2021

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.

Abstract

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

Keywords atomic force microscopy, DNA bending, DNA cyclization assay, D-shaped DNA, fluorescence resonance energy transfer, magnetic tweezers, optical tweezers, single-molecule, tethered particle motion

Article

On-line First

Mol. Cells

Published online September 2, 2021

Copyright © The Korean Society for Molecular and Cellular Biology.

Single-Molecule Methods for Investigating the Double-Stranded DNA Bendability

Sanghun Yeou1 and Nam Ki Lee2,*

1Department of Physics, Pohang University of Science and Technology, Pohang 37673, Korea, 2Department of Chemistry, Seoul National University, Seoul 08826, Korea

Correspondence to:namkilee@snu.ac.kr

Received: July 9, 2021; Revised: July 19, 2021; Accepted: July 20, 2021

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.

Abstract

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

Keywords: atomic force microscopy, DNA bending, DNA cyclization assay, D-shaped DNA, fluorescence resonance energy transfer, magnetic tweezers, optical tweezers, single-molecule, tethered particle motion

Mol. Cells
Dec 31, 2021 Vol.44 No.12, pp. 861~919
COVER PICTURE
Structure of the fly peripheral neurons in the fly head. Flies have basic sensory organs including eyes for vision, antennae and maxillary palps for olfaction, and proboscis (magenta) for gustation which can be labelled with monoclonal antibody 22C10. The figure is a 3D reconstructed image with 30 slices of confocal sections with 3 μm interval. It shows that the proboscis is required for sensing attractive carboxylic acids such as glycolic acid, citric acid, and lactic acid (Shrestha and Lee, pp. 900-910).

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