title: Rapid determination of RNA accessible sites by surface plasmon resonance detection of hybridization to DNA arrays.
abstract: RNA accessible sites are the regions in an RNA molecule that are available for hybridization with cDNA or RNA molecules. The identification of these accessible sites is a critical first step in identifying antisense-mediated gene suppression sites, as well as in a variety of other RNA-based analysis methods. Here, we present a rapid, hybridization-based, label-free method of identifying RNA accessible sites with surface plasmon resonance imaging (SPRi) on in situ synthesized oligonucleotide arrays prepared on carbon-on-metal substrates. The accessible sites of three pre-miRNAs, miRNA precursors of approximately 75 nt in length, were determined by hybridizing the RNA molecules to RNA-specific tiling arrays. An array composed of all possible 6mer oligonucleotide sequences was also utilized in this work, offering a universal platform capable of studying RNA molecules in a high throughput manner.
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Joshua B
authors.initials: JB
authors.lastname: Mandir
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Lockett
authors.forename: Margaret F
authors.initials: MF
authors.lastname: Phillips
authors.forename: Hatim T
authors.initials: HT
authors.lastname: Allawi
authors.forename: Victor I
authors.initials: VI
authors.lastname: Lyamichev
authors.forename: Lloyd M
authors.initials: LM
authors.lastname: Smith
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D035683:MicroRNAs / Q000378:metabolism; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000737:chemistry; D012313:RNA / Q000032:analysis*; D020349:Surface Plasmon Resonance / Q000379:methods*
chemical_list: D035683:MicroRNAs; D009841:Oligonucleotides; D012313:RNA