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Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.

Shenghua Duan·David H Mathews·Douglas H Turner
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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.

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3' Untranslated RegionsAlgorithmsAnimalsBase PairingBase SequenceBombyxEscherichia coliHydrogen-Ion ConcentrationMagnesium ChlorideMolecular Sequence DataNucleic Acid ConformationOligonucleotide Array Sequence AnalysisRNA ProbesRNA, Ribosomal, 5SRetroelementsRibonuclease HSodium ChlorideThermodynamicsJournal ArticleResearch Support, N.I.H., Extramural

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Shenghua Duan, David H Mathews, Douglas H Turner. 2006-08-15. Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.. https://doi.org/10.1021/bi052618x

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