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Related Concept Videos

Labeling DNA Probes03:31

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...

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Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope
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Probing DNA clamps with single-molecule force spectroscopy.

Lin Wang1, Xiaojun Xu, Ravindra Kumar

  • 1Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA and Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA.

Nucleic Acids Research
|June 21, 2013
PubMed
Summary

Investigating DNA clamps in bacteria and yeast using single-molecule force spectroscopy revealed distinct mechanical mechanisms for clamp opening. These findings illuminate how these essential proteins function differently across prokaryotic and eukaryotic systems.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biophysics

Background:

  • DNA clamps are essential sliding rings that encircle DNA, facilitating DNA replication and repair.
  • Prokaryotic (e.g., Escherichia coli) and eukaryotic (e.g., Saccharomyces cerevisiae) DNA clamps share functional similarities but may differ in their mechanical properties and regulation.

Purpose of the Study:

  • To elucidate the detailed mechanical mechanisms of DNA clamp opening in both prokaryotic and eukaryotic systems.
  • To compare the forces and energy landscapes governing clamp opening in Escherichia coli and Saccharomyces cerevisiae.

Main Methods:

  • Single-molecule force spectroscopy using optical tweezers to measure clamp opening forces.
  • Steered molecular dynamics simulations to analyze interface binding energies during clamp opening.
  • Molecular dynamics simulations to identify stabilizing contact networks within clamp subunits.

Main Results:

  • Quantified the precise mechanical forces required for Escherichia coli and Saccharomyces cerevisiae clamp opening at the single-molecule level.
  • Identified key interface binding energies and subunit contact networks critical for clamp stability in both organisms.
  • Revealed distinct mechanical principles governing clamp opening in prokaryotes versus eukaryotes.

Conclusions:

  • The study provides a comprehensive understanding of the mechanics and energy landscape of DNA clamp opening.
  • Demonstrates that prokaryotic and eukaryotic DNA clamps operate via fundamentally different mechanisms, despite conserved functions.
  • Highlights the utility of combining single-molecule biophysics and computational simulations for dissecting protein mechanics.