title: DNA exhibits multi-stranded binding recognition on glass microarrays.
abstract: 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.
authors.affiliation: Incyte Genomics, Microarray Division, 6519 Dumbarton Circle, Fremont, CA 94555, USA.
authors.forename: S J
authors.initials: SJ
authors.lastname: Shi
authors.forename: A
authors.initials: A
authors.lastname: Scheffer
authors.forename: E
authors.initials: E
authors.lastname: Bjeldanes
authors.forename: M A
authors.initials: MA
authors.lastname: Reynolds
authors.forename: L J
authors.initials: LJ
authors.lastname: Arnold
mesh_terms: D004247:DNA / Q000378:metabolism*; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000378:metabolism; D016133:Polymerase Chain Reaction
chemical_list: D009841:Oligonucleotides; D004247:DNA