Bubble dynamics in double-stranded DNA.
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.
Altan-Bonnet
Grégoire
G
Center for Studies in Physics and Biology, The Rockefeller University, New York, New York 10021, USA.
Libchaber
Albert
A
Krichevsky
Oleg
O
D004247:DNA / Q000737:chemistry*; D005453:Fluorescence; D005456:Fluorescent Dyes / Q000737:chemistry; D007700:Kinetics; D009690:Nucleic Acid Conformation; D013050:Spectrometry, Fluorescence; D013696:Temperature; D013816:Thermodynamics
D005456:Fluorescent Dyes; D004247:DNA