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Detection of localized DNA flexibility

J D Kahn1, E Yun, D M Crothers

  • 1Department of Chemistry, Yale University, New Haven, Connecticut 06511.

Nature
|March 10, 1994
PubMed
Summary

DNA flexibility, particularly at internal loops, significantly impacts DNA bending and cyclization. Electrophoretic methods subtly detect this, while cyclization kinetics accurately quantify flexibility, revealing its role in base-pair opening.

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Methods for analyzing DNA bending.

Methods in molecular biology (Clifton, N.J.)·2003

Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • DNA bending and flexibility are crucial for DNA packaging, recombination, and transcription.
  • Electrophoretic methods (circular permutation, phasing analysis) and DNA cyclization are used to study DNA bending.
  • Discrepancies in bend angle measurements between methods are attributed to DNA flexibility.

Purpose of the Study:

  • To investigate the role of DNA flexibility in discrepancies observed between electrophoretic and cyclization assays for measuring DNA bending.
  • To use an internal DNA loop as a model flexible locus to test the interpretation of DNA flexibility.

Main Methods:

  • Circular permutation and helical phasing analysis (electrophoretic methods).
  • DNA cyclization kinetics experiments in solution.
  • Utilizing an internal loop as a model flexible DNA locus.

Main Results:

  • Electrophoretic assays showed only subtle effects of the internal loop on DNA bending measurements.
  • DNA cyclization kinetics detected and quantified significant increases in both torsional and bending flexibility due to the internal loop.
  • The study's findings support a functional role for DNA bending stress in promoting base-pair opening.

Conclusions:

  • DNA cyclization kinetics is a more sensitive and accurate method for quantifying DNA flexibility compared to electrophoretic assays.
  • DNA flexibility, influenced by structural elements like internal loops, plays a critical role in DNA dynamics.
  • Bending-induced stress in DNA may contribute to functional processes such as base-pair opening.

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