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Related Experiment Videos

A stochastic model for helix bending in B-DNA.

R E Dickerson1, M L Kopka, P Pjura

  • 1Molecular Biology Institute, University of California, Los Angeles 90024.

Journal of Biomolecular Structure & Dynamics
|December 1, 1983
PubMed
Summary

DNA bending primarily involves rolling base pairs, not energetically costly tilting. This "random walk" of base pair rolls creates the helix axis

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Structural Biology

Background:

  • DNA bending is crucial for packaging and function, particularly within nucleosomes.
  • Previous models suggested specific kinking mechanisms for DNA bending.
  • The energetic costs of DNA deformation influence bending mechanisms.

Purpose of the Study:

  • To elucidate the fundamental mechanism of double-helical B-DNA bending.
  • To investigate the role of base pair roll angles in DNA helix axis deformation.
  • To propose a new model for DNA bending based on stochastic base pair movements.

Main Methods:

  • Analysis of base pair roll angles along the DNA helix axis.
  • Examination of energetic constraints on DNA deformation (tilt vs. roll).
  • Modeling DNA bending as a series of "random walk" base pair steps.

Main Results:

  • DNA bending occurs primarily through rolling of adjacent base pairs, not tilting.
  • Roll angles can be positive (major groove compression) or negative (minor groove compression).
  • The series of base pair rolls follows a stochastic "random walk" pattern, resulting in net bending.

Conclusions:

  • DNA bending is a more stochastic process than previously assumed.
  • The "random walk" model explains observed DNA bending patterns, including periodicity around nucleosomes.
  • This mechanism accounts for localized and distributed bending, minimizing free energy.

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