Published online 20 May 2004
Nucleic Acids Research, 2004, Vol. 32, No. 9 e75
© 2004 Oxford University Press
Oligonucleotide hybridization studied by a surface plasmon diffraction sensor (SPDS)
Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
*To whom correspondence should be addressed. Tel: +49 6131 379 160; Fax: +49 6131 379 360; Email: knoll{at}mpip-mainz.mpg.de
Received November 25, 2003; Revised February 1, 2004; Accepted April 15, 2004
A novel label-free biosensor concept based on surface plasmon-enhanced diffraction by micro- patterned interfaces was applied to the study of hybridization reactions of target DNA oligonucleotides (15mers and 75mers) from solution to probe DNA oligonucleotides attached via streptavidin to the sensor surface. The self-referencing and quadratic signal amplification mechanism of the sensor allowed highly sensitive detection of the hybridization process. Association and dissociation processes of DNA targets could be recorded in real time and used for the quantification of their binding affinities, which differ considerably with a single base pair mismatch. An equilibrium titration approach was also applied in order to obtain the binding affinities for 15mer targets, yielding similar affinity values. The hybridization efficiencies were found to be higher for the 15mers than for the 75mers, although the latter contained the same recognition sequences. The hybridization efficiency was shown to depend on the probe density and reached nearly 100% for the 15mer fully complementary targets at a probe density of 
1.2 x 1012 molecules/cm2. Using the assay as an end-point determination method, the lowest detectable coverage of a 15mer oligonucleotide was at least 1.1 x 1011 molecules/cm2. The diffraction sensing concept offers a completely novel way to integrate a reference channel in large-scale, label-free screening applications, to improve the stability and to enhance the sensitivity of microarray read-out systems.
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