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Nucleic Acids Research, 2001, Vol. 29, No. 20 4251-4256
© 2001 Oxford University Press

DNA exhibits multi-stranded binding recognition on glass microarrays

Shirley J. Shi, Alicia Scheffer, Erik Bjeldanes, Mark A. Reynolds and Lyle J. Arnold*

Incyte Genomics, Microarray Division, 6519 Dumbarton Circle, Fremont, CA 94555, USA

In the course of exploring the hybridization properties of glass DNA microarrays, multi-stranded DNA structures were observed that could not be accounted for by classical Watson–Crick base pairing. Non-denatured double-stranded DNA array elements were shown to hybridize to single-stranded (ss)DNA probes. Similarly, ssDNA array elements were shown to bind duplex DNA probes. This led to a series of experiments demonstrating the formation of multi-stranded DNA structures on the surface of microarrays. These structures were observed with a number of heterogeneous sequences, including both purine and pyrimidine bases, with shared sequence identity between the ssDNA and one of the duplex strands. Furthermore, we observed a strong binding preference near the ends of duplexes containing a 3'-homologous strand. We suggest that such binding interactions on cationic solid surfaces could serve as a model for a number of biological processes mediated through multi-stranded DNA.

* To whom correspondence should be addressed. Tel: +1 510 7392171; Fax: +1 510 739 2250; Email: larnold{at}incyte.com


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