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Nucleic Acids Research, 2001, Vol. 29, No. 24 5163-5168
© 2001 Oxford University Press

The effect of surface probe density on DNA hybridization

Alexander W. Peterson, Richard J. Heaton and Rosina M. Georgiadis*

Department of Chemistry, 590 Commonwealth Avenue, Metcalf Center for Science and Engineering, Boston University, Boston MA 02215, USA

The hybridization of complementary strands of DNA is the underlying principle of all microarray-based techniques for the analysis of DNA variation. In this paper, we study how probe immobilization at surfaces, specifically probe density, influences the kinetics of target capture using surface plasmon resonance (SPR) spectroscopy, an in situ label-free optical method. Probe density is controlled by varying immobilization conditions, including solution ionic strength, interfacial electrostatic potential and whether duplex or single stranded oligonucleotides are used. Independent of which probe immobilization strategy is used, we find that DNA films of equal probe density exhibit reproducible efficiencies and reproducible kinetics for probe/target hybridization. However, hybridization depends strongly on probe density in both the efficiency of duplex formation and the kinetics of target capture. We propose that probe density effects may account for the observed variation in target-capture rates, which have previously been attributed to thermodynamic effects.

* To whom correspondence should be addressed. Tel: +1 617 353 7218; Fax: +1 617 353 6466; Email: rgeorgia{at}bu.edu Richard J. Heaton, deceased


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