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Published online 28 April 2004

Nucleic Acids Research, 2004, Vol. 32, No. 8 2372-2377
© 2004 Oxford University Press

Mismatching base-pair dependence of the kinetics of DNA–DNA hybridization studied by surface plasmon fluorescence spectroscopy

Keiko Tawa1,2 and Wolfgang Knoll*,1

1 Max-Planck-Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany and 2 Research Institute for Cell Engineering, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan

*To whom correspondence should be addressed. Tel: +49 6131 379160; Fax: +49 6131 379360; Email: knoll{at}mpip-mainz.mpg.de

Received January 19, 2004; Accepted April 7, 2004

Two single-stranded DNAs consisting of complementary base pairs except for one mismatching base pair (MM1) can form double-stranded DNA by molecular recognition. This type of duplex is not as stable as that formed by MM0. In order to add to a better understanding of the physical mechanism of the hybridization and dissociation processes at sensor (chip) surfaces, we studied the kinetics of the MM1 hybridization by surface plasmon fluorescence spectroscopy. Target DNA strands labelled with a fluorescent molecule Cy5 at the 5' end and hybridizing with the surface-attached probe DNA can be excited by the strong optical field of a surface plasmon resonance mode. The emitted fluorescence can be detected with high sensitivity. The affinity of a duplex was found to depend on the chemical nature, i.e. G–G, G–T etc., and on the position of the mismatching base pair along the 15mer duplex.


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