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Related Experiment Videos

Bubble propagation in a helicoidal molecular chain.

A Campa1

  • 1Physics Laboratory, Istituto Superiore di Sanità and INFN Sezione di Roma1, Gruppo Collegato Sanità, Viale Regina Elena 299, 00161 Roma, Italy. campa@axiss.iss.infn.it

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|April 20, 2001
PubMed
Summary

Localized excitations, termed transcription bubbles, can propagate along DNA. These dynamic DNA bubbles facilitate genetic code access and can travel over 1000 base pairs, even with thermal noise.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Genetics

Background:

  • DNA's helicoidal structure influences localized excitations.
  • Transcription bubbles disrupt hydrogen bonds for genetic code access.
  • Previous models focused on low-amplitude solutions or DNA melting.

Purpose of the Study:

  • Investigate propagation of large-amplitude localized excitations in a DNA model.
  • Extend existing models to include heterogeneous DNA chains (A-T and G-C base pairs).
  • Explore the dynamics and mobility of transcription bubbles.

Main Methods:

  • Utilized a modified Barbi et al. model incorporating DNA helicoidal structure.
  • Employed molecular dynamics simulations.
  • Computed equilibrium configurations for uncoiled DNA chains.

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Main Results:

  • Identified static bubbles as equilibrium configurations in uncoiled DNA.
  • Demonstrated that generated bubbles can propagate along the DNA chain.
  • Showed that excitations travel over 1000 base pairs even in heterogeneous DNA with thermal noise.

Conclusions:

  • Large-amplitude localized excitations (transcription bubbles) are mobile in DNA.
  • The model provides a framework for studying DNA dynamics beyond simple kinks or breathers.
  • Findings contribute to understanding DNA accessibility and dynamics in biological systems.