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Kinetics of conformational fluctuations in DNA hairpin-loops
Open accessAbstract
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.
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Cites
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Zazopoulos, E., Lalli, E., Stocco, D. M., & Sassone-Corsi, P. (1997) · Nature · doi:10.1038/36899 · Cited by 433
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Meller, A., Nivon, L., Brandin, E., Golovchenko, J., & Branton, D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.3.1079 · Cited by 937
Rapid spontaneous accessibility of nucleosomal DNA
Li, G., Levitus, M., Bustamante, C., & Widom, J. (2005) · Nature Structural & Molecular Biology · doi:10.1038/nsmb869 · Cited by 649
Woodside, M. T., Behnke-Parks, W. M., Larizadeh, K., Travers, K., Herschlag, D., & Block, S. M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0511048103 · Cited by 474
Fluorescence Correlation Spectroscopy: Past, Present, Future
Elson, E. L. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.11.012 · Cited by 438
McNally, B., Singer, A., Yu, Z., Sun, Y., Weng, Z., & Meller, A. (2010) · Nano Letters · doi:10.1021/nl1012147 · Cited by 270
Metadata
- Authors
- Bonnet, G., Krichevsky, O., & Libchaber, A.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 1998-07-21
- Volume
- 95
- Issue
- 15
- Pages
- 8602-8606
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2067008143
- Cited by
- 537
- References
- 1
- FWCI
- 4.61
- Type
- journal article
- Language
- en
- Open access
- green
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- Bonnet, G., Krichevsky, O., & Libchaber, A. (1998). Kinetics of conformational fluctuations in DNA hairpin-loops. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.95.15.8602
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
