Bubble dynamics in double-stranded DNA

Phys Rev Lett. 2003 Apr 4;90(13):138101. doi: 10.1103/PhysRevLett.90.138101. Epub 2003 Apr 1.

Abstract

We report the first measurement of the dynamics of bubble formation in double-stranded DNA. Fluctuations of fluorescence of a synthetic DNA construct, internally tagged with a fluorophore and a quencher, are monitored by fluorescence correlation spectroscopy. The relaxation dynamics follow a multistate relaxation kinetics, with a characteristic time scale of 50 microseconds. A simple model of bubble dynamics based on constant zipping-unzipping rates is proposed to account for our experimental data. The role of different secondary structures stabilizing the open bubble is tested.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry*
  • Fluorescence
  • Fluorescent Dyes / chemistry
  • Kinetics
  • Nucleic Acid Conformation
  • Spectrometry, Fluorescence
  • Temperature
  • Thermodynamics

Substances

  • Fluorescent Dyes
  • DNA