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Nucleic Acids Research Advance Access originally published online on April 20, 2009
Nucleic Acids Research 2009 37(11):3756-3765; doi:10.1093/nar/gkp230
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Nucleic Acids Research, 2009, Vol. 37, No. 11 3756-3765
© 2009 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.

Chemistry and Synthetic Biology

Kinetics and thermodynamics of DNA hybridization on gold nanoparticles

Chunlai Chen, Wenjuan Wang, Jing Ge and Xin Sheng Zhao*

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 February 1, 2009. Revised March 23, 2009. Accepted March 24, 2009.

Hybridization of single-stranded DNA immobilized on the surface of gold nanoparticles (GNPs) into double stranded DNA and its subsequent dissociation into ssDNA were investigated. Melting curves and rates of dissociation and hybridization were measured using fluorescence detection based on hybridization-induced fluorescence change. Two distribution functions, namely the state distribution and the rate distribution, were proposed in order to take interfacial heterogeneity into account and to quantitatively analyze the data. Reaction and activation enthalpies and entropies of DNA hybridization and dissociation on GNPs were derived and compared with the same quantities in solution. Our results show that the interaction between GNPs and DNA reduces the energetic barrier and accelerates the dissociation of adhered DNA. At low surface densities of ssDNA adhered to GNP surface, the primary reaction pathway is that ssDNA in solution first adsorbs onto the GNP, and then diffuses along the surface until hybridizing with an immobilized DNA. We also found that the secondary structure of a DNA hairpin inhibits the interaction between GNPs and DNA and enhances the stability of the DNA hairpin adhered to GNPs.


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