Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary Structure: Application to the 3‘ End of Bombyx mori R2 RNA†
Identifieur interne : 000947 ( Istex/Checkpoint ); précédent : 000946; suivant : 000948Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary Structure: Application to the 3‘ End of Bombyx mori R2 RNA†
Auteurs : Shenghua Duan ; David H. Mathews ; Douglas H. Turner [États-Unis]Source :
- Biochemistry [ 0006-2960 ] ; 2006.
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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DOI: 10.1021/bi052618x
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Structure: Application to the 3‘ End of <hi rend="italic">Bombyx mori</hi> R2 RNA<ref type="bib" target="#bi052618xAF2">†</ref></title><author><name sortKey="Duan, Shenghua" sort="Duan, Shenghua" uniqKey="Duan S" first="Shenghua" last="Duan">Shenghua Duan</name><affiliation></affiliation><affiliation><wicri:noCountry code="no comma"> Department of Chemistry.</wicri:noCountry></affiliation></author><author><name sortKey="Mathews, David H" sort="Mathews, David H" uniqKey="Mathews D" first="David H." last="Mathews">David H. Mathews</name><affiliation></affiliation><affiliation></affiliation><affiliation><wicri:noCountry code="subField">Dentistry.</wicri:noCountry></affiliation></author><author><name sortKey="Turner, Douglas H" sort="Turner, Douglas H" uniqKey="Turner D" first="Douglas H." last="Turner">Douglas H. Turner</name><affiliation></affiliation><affiliation></affiliation><affiliation></affiliation><affiliation wicri:level="1"><country wicri:rule="url">États-Unis</country></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Biochemistry</title><title level="j" type="abbrev">Biochemistry</title><idno type="ISSN">0006-2960</idno><idno type="eISSN">1520-4995</idno><imprint><publisher>American Chemical Society</publisher><date type="e-published">2006</date><date type="published">2006</date><biblScope unit="vol">45</biblScope><biblScope unit="issue">32</biblScope><biblScope unit="page" from="9819">9819</biblScope><biblScope unit="page" to="9832">9832</biblScope></imprint><idno type="ISSN">0006-2960</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0006-2960</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="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.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Duan, Shenghua" sort="Duan, Shenghua" uniqKey="Duan S" first="Shenghua" last="Duan">Shenghua Duan</name><name sortKey="Mathews, David H" sort="Mathews, David H" uniqKey="Mathews D" first="David H." last="Mathews">David H. Mathews</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Turner, Douglas H" sort="Turner, Douglas H" uniqKey="Turner D" first="Douglas H." last="Turner">Douglas H. Turner</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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