DNA exhibits multi-stranded binding recognition on glass microarrays

In the course of exploring the hybridization properties of glass DNA microa rrays, multi-stranded DNA structures were observed that could not be accoun ted for by classical Watson-Crick base pairing. Non-denatured double-strand ed DNA array elements were shown to hybridize to single-stranded (ss)DNA pr obes. Similarly, ssDNA array elements were shown to bind duplex DNA probes. This led to a series of experiments demonstrating the formation of multi-s tranded DNA structures on the surface of microarrays. These structures were observed with a number of heterogeneous sequences, including both purine a nd pyrimidine bases, with shared sequence identity between the ssDNA and on e of the duplex strands. Furthermore, we observed a strong binding preferen ce 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.