Nucleic Acids Research Advance Access originally published online on April 11, 2007
Nucleic Acids Research 2007 35(9):2875-2884; doi:10.1093/nar/gkm177
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Nucleic Acids Research, 2007, Vol. 35, No. 9 2875-2884
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization
Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
*To whom correspondence should be addressed. Tel: +86-10-62751727; Fax: +86-10-62751708; Email: zhaoxs{at}pku.edu.cn
Received October 25, 2006. Revised March 12, 2007. Accepted March 12, 2007.
Hybridization of nucleic acids with secondary structure is involved in many biological processes and technological applications. To gain more insight into its mechanism, we have investigated the kinetics of DNA hybridization/denaturation via fluorescence resonance energy transfer (FRET) on perfectly matched and single-base-mismatched DNA strands. DNA hybridization shows non-Arrhenius behavior. At high temperature, the apparent activation energies of DNA hybridization are negative and independent of secondary structure. In contrast, when temperature decreases, the apparent activation energies of DNA hybridization change to positive and become structure dependent. The large unfavorable enthalpy of secondary structure melting is compensated for by concomitant duplex formation. Based on our results, we propose a reaction mechanism about how the melting of secondary structure influences the hybridization process. A significant point in the mechanism is that the rate-limiting step switches along with temperature variation in the hybridization process of structured DNA, because the free energy profile of hybridization in structured DNA varies with the variation in temperature.
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