Selecting effective antisense reagents on combinatorial oligonucleotide arrays.
Identifieur interne : 002571 ( PubMed/Checkpoint ); précédent : 002570; suivant : 002572Selecting effective antisense reagents on combinatorial oligonucleotide arrays.
Auteurs : N. Milner [Royaume-Uni] ; K U Mir ; E M SouthernSource :
- Nature biotechnology [ 1087-0156 ] ; 1997.
Descripteurs français
- KwdFr :
- ARN messager (métabolisme), Animaux, Conformation d'acide nucléique, Données de séquences moléculaires, Exons, Globines (biosynthèse), Globines (génétique), Hétéroduplexes d'acides nucléiques (métabolisme), Lapins, Oligodésoxyribonucléotides (), Oligodésoxyribonucléotides (métabolisme), Oligodésoxyribonucléotides (synthèse chimique), Séquence nucléotidique, Transcription génétique.
- MESH :
- biosynthèse : Globines.
- génétique : Globines.
- métabolisme : ARN messager, Hétéroduplexes d'acides nucléiques, Oligodésoxyribonucléotides.
- synthèse chimique : Oligodésoxyribonucléotides.
- Animaux, Conformation d'acide nucléique, Données de séquences moléculaires, Exons, Lapins, Oligodésoxyribonucléotides, Séquence nucléotidique, Transcription génétique.
English descriptors
- KwdEn :
- Animals, Base Sequence, Exons, Globins (biosynthesis), Globins (genetics), Molecular Sequence Data, Nucleic Acid Conformation, Nucleic Acid Heteroduplexes (metabolism), Oligodeoxyribonucleotides (chemical synthesis), Oligodeoxyribonucleotides (chemistry), Oligodeoxyribonucleotides (metabolism), RNA, Messenger (metabolism), Rabbits, Transcription, Genetic.
- MESH :
- chemical , biosynthesis : Globins.
- chemical , chemical synthesis : Oligodeoxyribonucleotides.
- chemical , chemistry : Oligodeoxyribonucleotides.
- chemical , genetics : Globins.
- chemical , metabolism : Nucleic Acid Heteroduplexes, Oligodeoxyribonucleotides, RNA, Messenger.
- Animals, Base Sequence, Exons, Molecular Sequence Data, Nucleic Acid Conformation, Rabbits, Transcription, Genetic.
Abstract
An array of 1,938 oligodeoxynucleotides (ONs) ranging in length from monomers to 17-mers was fabricated on the surface of a glass plate and used to measure the potential of oligonucleotide for heteroduplex formation with rabbit beta-globin mRNA. The oligonucleotides were complementary to the first 122 bases of mRNA comprising the 5' UTR and bases 1 to 69 of the first exon. Surprisingly few oligonucleotides gave significant heteroduplex yield. Antisense activity, measured in a RNase H assay and by in vitro translation, correlated well with yield of heteroduplex on the array. These results help to explain the variable success that is commonly experienced in the choice of antisense oligonucleotides. For the optimal ON, the concentration required to inhibit translation by 50% was found to be five times less than for any other ON. We find no obvious features in the mRNA sequence or the predicted secondary structure that can explain the variation in heteroduplex yield. However, the arrays provide a simple empirical method of selecting effective antisense oligonucleotides for any RNA target of known sequence.
DOI: 10.1038/nbt0697-537
PubMed: 9181575
Affiliations:
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Milner</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biochemistry, University of Oxford, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Biochemistry, University of Oxford</wicri:regionArea><placeName><settlement type="city">Oxford</settlement><region type="nation">Angleterre</region><region type="région" nuts="1">Oxfordshire</region></placeName><orgName type="university">Université d'Oxford</orgName></affiliation></author><author><name sortKey="Mir, K U" sort="Mir, K U" uniqKey="Mir K" first="K U" last="Mir">K U Mir</name></author><author><name sortKey="Southern, E M" sort="Southern, E M" uniqKey="Southern E" first="E M" last="Southern">E M Southern</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1997">1997</date><idno type="RBID">pubmed:9181575</idno><idno type="pmid">9181575</idno><idno type="doi">10.1038/nbt0697-537</idno><idno type="wicri:Area/PubMed/Corpus">002719</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002719</idno><idno type="wicri:Area/PubMed/Curation">002719</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002719</idno><idno type="wicri:Area/PubMed/Checkpoint">002571</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002571</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Selecting effective antisense reagents on combinatorial oligonucleotide arrays.</title><author><name sortKey="Milner, N" sort="Milner, N" uniqKey="Milner N" first="N" last="Milner">N. 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The oligonucleotides were complementary to the first 122 bases of mRNA comprising the 5' UTR and bases 1 to 69 of the first exon. Surprisingly few oligonucleotides gave significant heteroduplex yield. Antisense activity, measured in a RNase H assay and by in vitro translation, correlated well with yield of heteroduplex on the array. These results help to explain the variable success that is commonly experienced in the choice of antisense oligonucleotides. For the optimal ON, the concentration required to inhibit translation by 50% was found to be five times less than for any other ON. We find no obvious features in the mRNA sequence or the predicted secondary structure that can explain the variation in heteroduplex yield. However, the arrays provide a simple empirical method of selecting effective antisense oligonucleotides for any RNA target of known sequence.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">9181575</PMID><DateCompleted><Year>1997</Year><Month>08</Month><Day>19</Day></DateCompleted><DateRevised><Year>2006</Year><Month>11</Month><Day>15</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1087-0156</ISSN><JournalIssue CitedMedium="Print"><Volume>15</Volume><Issue>6</Issue><PubDate><Year>1997</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Nature biotechnology</Title><ISOAbbreviation>Nat. Biotechnol.</ISOAbbreviation></Journal><ArticleTitle>Selecting effective antisense reagents on combinatorial oligonucleotide arrays.</ArticleTitle><Pagination><MedlinePgn>537-41</MedlinePgn></Pagination><Abstract><AbstractText>An array of 1,938 oligodeoxynucleotides (ONs) ranging in length from monomers to 17-mers was fabricated on the surface of a glass plate and used to measure the potential of oligonucleotide for heteroduplex formation with rabbit beta-globin mRNA. The oligonucleotides were complementary to the first 122 bases of mRNA comprising the 5' UTR and bases 1 to 69 of the first exon. Surprisingly few oligonucleotides gave significant heteroduplex yield. Antisense activity, measured in a RNase H assay and by in vitro translation, correlated well with yield of heteroduplex on the array. These results help to explain the variable success that is commonly experienced in the choice of antisense oligonucleotides. For the optimal ON, the concentration required to inhibit translation by 50% was found to be five times less than for any other ON. We find no obvious features in the mRNA sequence or the predicted secondary structure that can explain the variation in heteroduplex yield. However, the arrays provide a simple empirical method of selecting effective antisense oligonucleotides for any RNA target of known sequence.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Milner</LastName><ForeName>N</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, University of Oxford, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mir</LastName><ForeName>K U</ForeName><Initials>KU</Initials></Author><Author ValidYN="Y"><LastName>Southern</LastName><ForeName>E M</ForeName><Initials>EM</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Nat Biotechnol</MedlineTA><NlmUniqueID>9604648</NlmUniqueID><ISSNLinking>1087-0156</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009692">Nucleic Acid Heteroduplexes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009838">Oligodeoxyribonucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance></Chemical><Chemical><RegistryNumber>9004-22-2</RegistryNumber><NameOfSubstance UI="D005914">Globins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="CommentIn"><RefSource>Nat Biotechnol. 1997 Jun;15(6):509</RefSource><PMID Version="1">9181566</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005091" MajorTopicYN="N">Exons</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005914" MajorTopicYN="N">Globins</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="Y">biosynthesis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009692" MajorTopicYN="N">Nucleic Acid Heteroduplexes</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009838" MajorTopicYN="N">Oligodeoxyribonucleotides</DescriptorName><QualifierName UI="Q000138" MajorTopicYN="Y">chemical synthesis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011817" MajorTopicYN="N">Rabbits</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014158" MajorTopicYN="N">Transcription, Genetic</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>1997</Year><Month>6</Month><Day>1</Day></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>1997</Year><Month>6</Month><Day>1</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>1997</Year><Month>6</Month><Day>1</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">9181575</ArticleId><ArticleId IdType="doi">10.1038/nbt0697-537</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Royaume-Uni</li></country><region><li>Angleterre</li><li>Oxfordshire</li></region><settlement><li>Oxford</li></settlement><orgName><li>Université d'Oxford</li></orgName></list><tree><noCountry><name sortKey="Mir, K U" sort="Mir, K U" uniqKey="Mir K" first="K U" last="Mir">K U Mir</name><name sortKey="Southern, E M" sort="Southern, E M" uniqKey="Southern E" first="E M" last="Southern">E M Southern</name></noCountry><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Milner, N" sort="Milner, N" uniqKey="Milner N" first="N" last="Milner">N. 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