Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary Structure: Application to the 3‘ End of Bombyx mori R2 RNA†
Identifieur interne : 000368 ( Istex/Corpus ); précédent : 000367; suivant : 000369Interpreting 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. TurnerSource :
- 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><mods:affiliation>Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, and Center for Pediatric BiomedicalResearch, Department of Pediatrics, and Department of Biochemistry and Biophysics, University of Rochester School ofMedicine and Dentistry, Rochester, New York, 14642</mods:affiliation></affiliation><affiliation><mods:affiliation> Department of Chemistry.</mods:affiliation></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><mods:affiliation>Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, and Center for Pediatric BiomedicalResearch, Department of Pediatrics, and Department of Biochemistry and Biophysics, University of Rochester School ofMedicine and Dentistry, Rochester, New York, 14642</mods:affiliation></affiliation><affiliation><mods:affiliation> Center for Pediatric Biomedical Research, Department of Pediatrics.</mods:affiliation></affiliation><affiliation><mods:affiliation> Department of Biochemistry and Biophysics, University ofRochester School of Medicine and Dentistry.</mods:affiliation></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><mods:affiliation>Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, and Center for Pediatric BiomedicalResearch, Department of Pediatrics, and Department of Biochemistry and Biophysics, University of Rochester School ofMedicine and Dentistry, Rochester, New York, 14642</mods:affiliation></affiliation><affiliation><mods:affiliation> Department of Chemistry.</mods:affiliation></affiliation><affiliation><mods:affiliation> Center for Pediatric Biomedical Research, Department of Pediatrics.</mods:affiliation></affiliation><affiliation><mods:affiliation> To whom correspondence should be addressed. Telephone: (585)275-3207. Fax: (585) 276-0205. E-mail: turner@chem.rochester.edu.</mods:affiliation></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. 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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></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>American Chemical Society</publisher><availability><licence>Copyright © 2006 American Chemical Society</licence><p>American Chemical Society</p></availability><date type="published">2006</date><date type="Copyright" when="2006">2006</date></publicationStmt><notesStmt><note type="content-type" source="research-article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</note><note type="publication-type" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note></notesStmt><sourceDesc><biblStruct type="article"><analytic><title level="a" type="main">Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary
Structure: Application to the 3‘ End of <hi rend="italic">Bombyx mori</hi> R2 RNA<ref type="bib" target="#bi052618xAF2">†</ref></title><author xml:id="author-0000"><persName><surname>Duan</surname><forename type="first">Shenghua</forename></persName><affiliation><orgName type="institution">Department of Chemistry</orgName><orgName type="institution">University of Rochester</orgName><address><addrLine>Rochester</addrLine><addrLine>New York 14627-0216</addrLine><addrLine>and Center for Pediatric Biomedical Research</addrLine><addrLine>Department of Pediatrics</addrLine><addrLine>and Department of Biochemistry and Biophysics</addrLine><addrLine>University of Rochester School of Medicine and Dentistry</addrLine><addrLine>Rochester</addrLine><addrLine>New York</addrLine><addrLine>14642</addrLine></address></affiliation><note place="foot" n="bi052618xAF3"><ref>‡</ref><p>
Department of Chemistry.</p></note></author><author xml:id="author-0001"><persName><surname>Mathews</surname><forename type="first">David H.</forename></persName><note place="foot" n="bi052618xAF4"><ref>§</ref><p>
Center for Pediatric Biomedical Research, Department of Pediatrics.
</p></note><note place="foot" n="bi052618xAF5"><ref>‖</ref><p>
Department of Biochemistry and Biophysics, University of
Rochester School of Medicine and Dentistry.</p></note></author><author xml:id="author-0002" role="corresp"><persName><surname>Turner</surname><forename type="first">Douglas H.</forename></persName><note place="foot" n="bi052618xAF3"><ref>‡</ref><p>
Department of Chemistry.</p></note><note place="foot" n="bi052618xAF4"><ref>§</ref><p>
Center for Pediatric Biomedical Research, Department of Pediatrics.
</p></note><affiliation role="corresp"> To whom correspondence should be addressed. Telephone: (585) 275-3207. Fax: (585) 276-0205. E-mail: turner@chem.rochester.edu.</affiliation></author><idno type="istex">961BE605853C8968681415ECE22FAFABE448C8CB</idno><idno type="ark">ark:/67375/TPS-CR0P76RD-4</idno><idno type="DOI">10.1021/bi052618x</idno></analytic><monogr><title level="j" type="main">Biochemistry</title><title level="j" type="abbrev">Biochemistry</title><idno type="acspubs">bi</idno><idno type="coden">bichaw</idno><idno type="pISSN">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></monogr></biblStruct></sourceDesc></fileDesc><encodingDesc><schemaRef type="ODD" url="https://xml-schema.delivery.istex.fr/tei-istex.odd"></schemaRef><appInfo><application ident="pub2tei" version="1.0.41" when="2020-04-06"><label>pub2TEI-ISTEX</label><desc>A set of style sheets for converting XML documents encoded in various scientific publisher formats into a common TEI format.
<ref target="http://www.tei-c.org/">We use TEI</ref></desc></application></appInfo></encodingDesc><profileDesc><abstract><p><graphic url="bi052618xn00001.tif"></graphic></p><p>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 <hi rend="italic">Bombyx mori</hi>. 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.
</p></abstract><textClass ana="subject"><keywords scheme="document-type-name"><term>Article</term></keywords></textClass><langUsage><language ident="en"></language></langUsage></profileDesc><revisionDesc><change when="2020-04-06" who="#istex" xml:id="pub2tei">formatting</change></revisionDesc></teiHeader></istex:fulltextTEI></fulltext><metadata><istex:metadataXml wicri:clean="corpus acs not found" wicri:toSee="no header"><istex:xmlDeclaration>version="1.0" encoding="UTF-8"</istex:xmlDeclaration><istex:document><article article-type="research-article" specific-use="acs2jats-2.0.3"><front><journal-meta><journal-id journal-id-type="acspubs">bi</journal-id><journal-id journal-id-type="coden">bichaw</journal-id><journal-title-group><journal-title>Biochemistry</journal-title><abbrev-journal-title>Biochemistry</abbrev-journal-title></journal-title-group><issn pub-type="ppub">0006-2960</issn><issn pub-type="epub">1520-4995</issn><publisher><publisher-name>American Chemical Society</publisher-name></publisher><self-uri>pubs.acs.org/biochemistry</self-uri></journal-meta><article-meta><article-id pub-id-type="doi">10.1021/bi052618x</article-id><article-categories><subj-group subj-group-type="document-type-name"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary
Structure: Application to the 3‘ End of <italic>Bombyx mori</italic> R2 RNA<xref rid="bi052618xAF2">†</xref></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Duan</surname><given-names>Shenghua</given-names></name><xref rid="bi052618xAF3">‡</xref></contrib><contrib contrib-type="author"><name><surname>Mathews</surname><given-names>David H.</given-names></name><xref rid="bi052618xAF4">§</xref><xref rid="bi052618xAF5">‖</xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Turner</surname><given-names>Douglas H.</given-names></name><xref rid="bi052618xAF1">*</xref><xref rid="bi052618xAF3">‡</xref><xref rid="bi052618xAF4">§</xref></contrib><aff>Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, and Center for Pediatric Biomedical
Research, Department of Pediatrics, and Department of Biochemistry and Biophysics, University of Rochester School of
Medicine and Dentistry, Rochester, New York, 14642
</aff></contrib-group><author-notes><fn id="bi052618xAF3"><label>‡</label><p>
Department of Chemistry.</p></fn><fn id="bi052618xAF4"><label>§</label><p>
Center for Pediatric Biomedical Research, Department of Pediatrics.
</p></fn><fn id="bi052618xAF5"><label>‖</label><p>
Department of Biochemistry and Biophysics, University of
Rochester School of Medicine and Dentistry.</p></fn><corresp id="bi052618xAF1">
To whom correspondence should be addressed. Telephone: (585)
275-3207. Fax: (585) 276-0205. E-mail: turner@chem.rochester.edu.
</corresp></author-notes><pub-date pub-type="epub"><day>21</day><month>07</month><year>2006</year></pub-date><pub-date pub-type="ppub"><day>15</day><month>08</month><year>2006</year></pub-date><volume>45</volume><issue>32</issue><fpage>9819</fpage><lpage>9832</lpage><supplementary-material xlink:href="bi052618xsi20060511_101020.pdf"></supplementary-material><history><date date-type="received"><day>22</day><month>12</month><year>2005</year></date><date date-type="rev-recd"><day>11</day><month>05</month><year>2006</year></date><date date-type="asap"><day>21</day><month>07</month><year>2006</year></date><date date-type="issue-pub"><day>15</day><month>08</month><year>2006</year></date></history><permissions><copyright-statement>Copyright © 2006 American Chemical Society</copyright-statement><copyright-year>2006</copyright-year><copyright-holder>American Chemical Society</copyright-holder></permissions><abstract><graphic content-type="abstract-graphic" xlink:href="bi052618xn00001.tif"></graphic><p>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 <italic>Bombyx mori</italic>. 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.
</p></abstract><custom-meta-group><custom-meta><meta-name>document-id-old-9</meta-name><meta-value>bi052618x</meta-value></custom-meta></custom-meta-group></article-meta><notes id="bi052618xAF2"><label>†</label><p>
This work was supported by NIH Grant GM22939 (to D.H.T.).</p></notes></front><body></body><back></back></article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo><title>Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary Structure: Application to the 3‘ End of Bombyx mori R2 RNA†</title></titleInfo><titleInfo contentType="CDATA"><title>Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary Structure: Application to the 3‘ End of Bombyx mori R2 RNA†</title></titleInfo><name type="personal"><namePart type="family">DUAN</namePart><namePart type="given">Shenghua</namePart><affiliation>Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, and Center for Pediatric BiomedicalResearch, Department of Pediatrics, and Department of Biochemistry and Biophysics, University of Rochester School ofMedicine and Dentistry, Rochester, New York, 14642</affiliation><affiliation> Department of Chemistry.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="family">MATHEWS</namePart><namePart type="given">David H.</namePart><affiliation>Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, and Center for Pediatric BiomedicalResearch, Department of Pediatrics, and Department of Biochemistry and Biophysics, University of Rochester School ofMedicine and Dentistry, Rochester, New York, 14642</affiliation><affiliation> Center for Pediatric Biomedical Research, Department of Pediatrics.</affiliation><affiliation> Department of Biochemistry and Biophysics, University ofRochester School of Medicine and Dentistry.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal" displayLabel="corresp"><namePart type="family">TURNER</namePart><namePart type="given">Douglas H.</namePart><affiliation>Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, and Center for Pediatric BiomedicalResearch, Department of Pediatrics, and Department of Biochemistry and Biophysics, University of Rochester School ofMedicine and Dentistry, Rochester, New York, 14642</affiliation><affiliation> Department of Chemistry.</affiliation><affiliation> Center for Pediatric Biomedical Research, Department of Pediatrics.</affiliation><affiliation> To whom correspondence should be addressed. Telephone: (585)275-3207. Fax: (585) 276-0205. E-mail: turner@chem.rochester.edu.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="research-article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>American Chemical Society</publisher><dateCreated encoding="w3cdtf">2006-07-21</dateCreated><dateIssued encoding="w3cdtf">2006-08-15</dateIssued><copyrightDate encoding="w3cdtf">2006</copyrightDate></originInfo><note type="footnote" ID="bi052618xAF2"> This work was supported by NIH Grant GM22939 (to D.H.T.).</note><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><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.</abstract><note type="footnote" ID="bi052618xAF2"> This work was supported by NIH Grant GM22939 (to D.H.T.).</note><relatedItem type="host"><titleInfo><title>Biochemistry</title></titleInfo><titleInfo type="abbreviated"><title>Biochemistry</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><identifier type="ISSN">0006-2960</identifier><identifier type="eISSN">1520-4995</identifier><identifier type="acspubs">bi</identifier><identifier type="coden">BICHAW</identifier><identifier type="uri">pubs.acs.org/biochemistry</identifier><part><date>2006</date><detail type="volume"><caption>vol.</caption><number>45</number></detail><detail type="issue"><caption>no.</caption><number>32</number></detail><extent unit="pages"><start>9819</start><end>9832</end></extent></part></relatedItem><identifier type="istex">961BE605853C8968681415ECE22FAFABE448C8CB</identifier><identifier type="ark">ark:/67375/TPS-CR0P76RD-4</identifier><identifier type="DOI">10.1021/bi052618x</identifier><accessCondition type="use and reproduction" contentType="restricted">Copyright © 2006 American Chemical Society</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-X5HBJWF8-J">acs</recordContentSource><recordOrigin>Converted from (version 1.2.10) to MODS version 3.6.</recordOrigin><recordCreationDate encoding="w3cdtf">2020-04-10</recordCreationDate></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/TPS-CR0P76RD-4/record.json</uri></json:item></metadata><annexes><json:item><extension>tiff</extension><original>true</original><mimetype>image/tiff</mimetype><uri>https://api.istex.fr/document/961BE605853C8968681415ECE22FAFABE448C8CB/annexes/tiff</uri></json:item><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/ark:/67375/TPS-CR0P76RD-4/annexes.pdf</uri></json:item></annexes><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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