title: Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.
abstract: A method to deduce RNA secondary structure on the basis of data from microarrays of 2'-O-methyl RNA 9-mers immobilized in agarose film on glass slides is tested with a 249 nucleotide RNA from the 3' end of the R2 retrotransposon from Bombyx mori. Various algorithms incorporating binding data and free-energy minimization calculations were compared for interpreting the data to provide possible secondary structures. Two different methods give structures with 100 and 87% of the base pairs determined by sequence comparison. In contrast, structures predicted by free-energy minimization alone by Mfold and RNAstructure contain 52 and 72% of the known base pairs, respectively. This combination of high throughput microarray techniques with algorithms using free-energy calculations has potential to allow for fast determination of RNA secondary structure. It should also facilitate the design of antisense and siRNA oligonucleotides.
authors.affiliation: Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA.
authors.forename: Shenghua
authors.initials: S
authors.lastname: Duan
authors.forename: David H
authors.initials: DH
authors.lastname: Mathews
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D020413:3' Untranslated Regions / Q000737:chemistry* / Q000235:genetics; D000465:Algorithms; D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D012831:Bombyx / Q000737:chemistry*; D004926:Escherichia coli / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D015636:Magnesium Chloride / Q000494:pharmacology; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D015347:RNA Probes / Q000187:drug effects; D012341:RNA, Ribosomal, 5S / Q000737:chemistry; D018626:Retroelements / Q000235:genetics*; D016914:Ribonuclease H / Q000378:metabolism; D012965:Sodium Chloride / Q000494:pharmacology; D013816:Thermodynamics
chemical_list: D020413:3' Untranslated Regions; D015347:RNA Probes; D012341:RNA, Ribosomal, 5S; D018626:Retroelements; D015636:Magnesium Chloride; D012965:Sodium Chloride; D016914:Ribonuclease H