Bubble dynamics in double-stranded DNA.

  title={Bubble dynamics in double-stranded DNA.},
  author={Gr{\'e}goire Altan-Bonnet and Albert Libchaber and Oleg Krichevsky},
  journal={Physical review letters},
  volume={90 13},
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… 

Figures from this paper

Bubble dynamics in DNA

The dynamics of bubble formation in double-stranded DNA is studied in terms of a Fokker–Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland–Scheraga model.

The dynamics of intermittent strand separation in double-stranded DNA.

The transient rupture and reformation of hydrogen bonds between base pairs on distinct chains of double-stranded DNA ("bubble" dynamics) is modeled in terms of the fluctuating distance between the

Coupled dynamics of DNA breathing and of proteins that selectively bind to single-stranded DNA.

The effective free-energy landscape of the DNA bubble is determined and the system can be driven from undisturbed bubble fluctuations to full, binding-protein-induced denaturation by tuning the physical parameters.

Breathing dynamics in heteropolymer DNA.

The strong dependence on sequence, temperature and salt concentration for the breathing dynamics of DNA found here points at a good potential for nanosensing applications by utilizing short fluorophore-quencher dressed DNA constructs.

Dynamic Approach to DNA Breathing

A dynamical description of this DNA-bubble breathing in terms of a Fokker-Planck equation for the bubble size, based on the Poland-Scheraga free energy for DNA denaturation is presented.

Dynamics of the DNA duplex formation studied by single molecule force measurements.

Comparing different measurements, it is found that both DNA unzipping and the relaxation of tension in DNA are faster than the formation of the double helix.

Stochastic approach to DNA breathing dynamics

We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single-molecule time series. It is demonstrated that the model

A semiflexible chain model of local denaturation in double-stranded DNA.

The results show that the entropy associated with semiflexibility of DNA sensitively affects the size distribution and lifetime of bubble, and the lifetime grows with bubble size m as m(2.7) at temperature close to T(c), which is consistent with the analysis based on a stochastic model of bubble size dynamics.

Master equation approach to DNA breathing in heteropolymer DNA.

A dynamic description of this DNA breathing in a heteropolymer DNA with given sequence in terms of a master equation that governs the time evolution of the joint probability distribution for the bubble size and position along the sequence is established.

Strand diffusion-limited closure of denaturation bubbles in DNA

The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible



Nucleic Acids: Structures, Properties, and Functions

Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text is for those with only a basic


  • Natl. Acad. Sci. U.S.A. 95, 8602
  • 1998

DNA replication.

  • M. Gefter
  • Medicine
    Annual review of biochemistry
  • 1975

Phys. Rev. E

  • Phys. Rev. E
  • 2001


  • Rev. E 63, 21901
  • 2001

A direct link to this document may be found in the online article's HTML reference section

  • E-PRLTAO-90-028310 for full analytical derivation of formula

Nucleic Acids Res

  • 9, 5469
  • 1981


  • Rev. E 47, R44
  • 1993

J. Mol. Biol

  • J. Mol. Biol
  • 1992