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Bubble dynamics in double-stranded DNA.

Grégoire Altan-Bonnet1, Albert Libchaber, Oleg Krichevsky

  • 1Center for Studies in Physics and Biology, The Rockefeller University, New York, New York 10021, USA.

Physical Review Letters
|April 12, 2003
PubMed
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We measured DNA bubble dynamics for the first time using fluorescence correlation spectroscopy. Our findings reveal multistate relaxation kinetics with a characteristic time of 50 microseconds.

Area of Science:

  • Biophysics
  • Molecular Biology
  • Chemical Physics

Background:

  • DNA secondary structures are crucial for biological processes.
  • Understanding DNA bubble dynamics is key to comprehending DNA-protein interactions and replication.
  • Previous studies lacked direct measurements of DNA bubble formation kinetics.

Purpose of the Study:

  • To report the first quantitative measurement of DNA bubble formation dynamics.
  • To investigate the relaxation kinetics of DNA bubble formation.
  • To propose and test a model for DNA bubble dynamics.

Main Methods:

  • Utilized a synthetic double-stranded DNA construct internally tagged with a fluorophore and quencher.
  • Employed fluorescence correlation spectroscopy to monitor fluorescence fluctuations.

Related Experiment Videos

  • Analyzed relaxation dynamics using multistate relaxation kinetics.

    • Main Results:

    • Observed DNA bubble dynamics with a characteristic time scale of 50 microseconds.
    • Demonstrated that relaxation dynamics follow multistate relaxation kinetics.
    • Proposed a simple model of bubble dynamics based on zipping-unzipping rates that fits experimental data.
    • Investigated the influence of secondary structures on open bubble stability.

    Conclusions:

    • The study provides the first experimental measurement of DNA bubble dynamics.
    • A model based on zipping-unzipping rates successfully explains the observed DNA bubble dynamics.
    • The findings offer insights into the role of secondary structures in stabilizing DNA bubbles.