Kinetics of conformational fluctuations in DNA hairpin-loops
- Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York NY 10021
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Communicated by Hans Frauenfelder, Los Alamos National Laboratory, Los Alamos, NM (received for review April 8, 1998)
Abstract
The kinetics of DNA hairpin-loop fluctuations has been investigated by using a combination of fluorescence energy transfer and fluorescence correlation spectroscopy. We measure the chemical rates and the activation energies associated with the opening and the closing of the hairpin for different sizes and sequences of the loop and for various salt concentrations. The rate of unzipping of the hairpin stem is essentially independent of the characteristics of the loop, whereas the rate of closing varies greatly with the loop length and sequence. The closing rate scales with the loop length, with an exponent 2.6 ± 0.3. The closing rate is increased at higher salt concentrations. For hairpin closing, a loop of adenosine repeats leads to smaller rates and higher activation energies than a loop with thymine repeats.
Footnotes
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↵ † To whom reprint requests should be addressed. e-mail: libchbr{at}rockvax.rockefeller.edu.
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↵ ‡ A similar approach has been applied by Wennmalm et al. (15) to study the conformational fluctuations of an M13 DNA, taking advantage of the quenching capabilities of the guanine base. In our system, however, the quencher is more efficient than guanine, giving better signal/background ratio.
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↵ § At very short lag times (below 1 μs), G*(t) indicates another kinetic process, possibly related to transitions in the stacking of DNA bases (8, 14). In this range of lag times correlation functions are too noisy to extract reliable rates, and we do not consider this fast kinetics further in this paper.
- ABBREVIATION:
- FCS,
- fluorescence correlation spectroscopy
- Copyright © 1998, The National Academy of Sciences
