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Related Experiment Video

Updated: Jan 4, 2026

Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage
06:51

Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage

Published on: May 6, 2020

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Single-molecule manipulation quantification of site-specific DNA binding.

Xiaodan Zhao1, Shiwen Guo2, Chen Lu2

  • 1Department of Physics, National University of Singapore, Singapore 117542, Singapore.

Current Opinion in Chemical Biology
|November 3, 2019
PubMed
Summary
This summary is machine-generated.

This review covers fluorescence-label-free single-molecule methods for quantifying DNA-protein interactions. These techniques precisely measure ligand binding kinetics and affinities to DNA, crucial for understanding biological functions.

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Last Updated: Jan 4, 2026

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06:51

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4.3K
Visualizing the Interaction Between the Qdot-labeled Protein and Site-specifically Modified λ DNA at the Single Molecule Level
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Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions
14:43

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

Published on: August 27, 2014

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biophysics

Background:

  • DNA-protein interactions are essential for biological functions and depend on sequence and structure.
  • Accurate quantification of binding affinity and kinetics is vital for understanding molecular mechanisms.
  • Single-molecule manipulation technologies offer nanometer resolution for real-time measurements.

Purpose of the Study:

  • To review recently developed fluorescence-label-free single-molecule methods.
  • To provide a systematic overview of applications in quantifying site-specific DNA binding by ligands.
  • To demonstrate the broad applicability of these methods using diverse examples.

Main Methods:

  • Single-molecule manipulation techniques applying mechanical constraints to DNA.
  • Real-time measurement of end-to-end extension changes with nanometer resolution.
  • Label-free quantification of ligand binding to DNA (dsDNA and ssDNA).

Main Results:

  • Several recently developed fluorescence-label-free single-molecule methods are presented.
  • These methods enable accurate quantification of DNA-ligand interactions.
  • Examples showcase applications for both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) binding sites.

Conclusions:

  • Fluorescence-label-free single-molecule techniques are powerful tools for studying DNA-ligand interactions.
  • These methods provide critical insights into binding kinetics and affinities.
  • The reviewed approaches have wide-ranging applications in molecular biology and biophysics.