Triplex formation by oligonucleotides containing 5-(1-propynyl)-2'-deoxyuridine: decreased magnesium dependence and improved intracellular gene targeting.
Identifieur interne : 002647 ( PubMed/Curation ); précédent : 002646; suivant : 002648Triplex formation by oligonucleotides containing 5-(1-propynyl)-2'-deoxyuridine: decreased magnesium dependence and improved intracellular gene targeting.
Auteurs : L. Lacroix [États-Unis] ; J. Lacoste ; J F Reddoch ; J L Mergny ; D D Levy ; M M Seidman ; M D Matteucci ; P M GlazerSource :
- Biochemistry [ 0006-2960 ] ; 1999.
Descripteurs français
- KwdFr :
- ADN (), ADN (génétique), ADN (métabolisme), ARN de transfert (génétique), Animaux, Cellules COS, Ciblage de gène, Données de séquences moléculaires, Dénaturation d'acide nucléique, Désoxyuridine (), Désoxyuridine (analogues et dérivés), Désoxyuridine (métabolisme), Gènes rapporteurs, Gènes suppresseurs, Liquide intracellulaire (métabolisme), Magnésium (métabolisme), Mutagenèse dirigée, Oligonucléotides (), Oligonucléotides (génétique), Oligonucléotides (métabolisme), Sites de fixation, Séquence nucléotidique, Vecteurs génétiques, Virus simien 40 (génétique).
- MESH :
- analogues et dérivés : Désoxyuridine.
- génétique : ADN, ARN de transfert, Oligonucléotides, Virus simien 40.
- métabolisme : ADN, Désoxyuridine, Liquide intracellulaire, Magnésium, Oligonucléotides.
- ADN, Animaux, Cellules COS, Ciblage de gène, Données de séquences moléculaires, Dénaturation d'acide nucléique, Désoxyuridine, Gènes rapporteurs, Gènes suppresseurs, Mutagenèse dirigée, Oligonucléotides, Sites de fixation, Séquence nucléotidique, Vecteurs génétiques.
English descriptors
- KwdEn :
- Animals, Base Sequence, Binding Sites, COS Cells, DNA (chemistry), DNA (genetics), DNA (metabolism), Deoxyuridine (analogs & derivatives), Deoxyuridine (chemistry), Deoxyuridine (metabolism), Gene Targeting, Genes, Reporter, Genes, Suppressor, Genetic Vectors, Intracellular Fluid (metabolism), Magnesium (metabolism), Molecular Sequence Data, Mutagenesis, Site-Directed, Nucleic Acid Denaturation, Oligonucleotides (chemistry), Oligonucleotides (genetics), Oligonucleotides (metabolism), RNA, Transfer (genetics), Simian virus 40 (genetics).
- MESH :
- chemical , analogs & derivatives : Deoxyuridine.
- chemical , chemistry : DNA, Deoxyuridine, Oligonucleotides.
- chemical , genetics : DNA, Oligonucleotides, RNA, Transfer.
- chemical , metabolism : DNA, Deoxyuridine, Magnesium, Oligonucleotides.
- genetics : Simian virus 40.
- metabolism : Intracellular Fluid.
- Animals, Base Sequence, Binding Sites, COS Cells, Gene Targeting, Genes, Reporter, Genes, Suppressor, Genetic Vectors, Molecular Sequence Data, Mutagenesis, Site-Directed, Nucleic Acid Denaturation.
Abstract
Oligonucleotides capable of sequence-specific triple helix formation have been proposed as DNA binding ligands useful for modulation of gene expression and for directed genome modification. However, the effectiveness of such triplex-forming oligonucleotides (TFOs) depends on their ability to bind to their target sites within cells, and this can be limited under physiologic conditions. In particular, triplex formation in the pyrimidine motif is favored by unphysiologically low pH and high magnesium concentrations. To address these limitations, a series of pyrimidine TFOs were tested for third-strand binding under a variety of conditions. Those containing 5-(1-propynyl)-2'-deoxyuridine (pdU) and 5-methyl-2'-deoxycytidine (5meC) showed superior binding characteristics at neutral pH and at low magnesium concentrations, as determined by gel mobility shift assays and thermal dissociation profiles. Over a range of Mg2+ concentrations, pdU-modified TFOs formed more stable triplexes than did TFOs containing 2'-deoxythymidine. At 1 mM Mg2+, a DeltaTm of 30 degreesC was observed for pdU- versus T-containing 15-mers (of generic sequence 5' TTTTCTTTTTTCTTTTCT 3') binding to the cognate A:T bp rich site, indicating that pdU-containing TFOs are capable of substantial binding even at physiologically low Mg2+ concentrations. In addition, the pdU-containing TFOs were superior in gene targeting experiments in mammalian cells, yielding 4-fold higher mutation frequencies in a shuttle vector-based mutagenesis assay designed to detect mutations induced by third-strand-directed psoralen adducts. These results suggest the utility of the pdU substitution in the pyrimidine motif for triplex-based gene targeting experiments.
DOI: 10.1021/bi982290q
PubMed: 10026270
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Lacoste</name></author><author><name sortKey="Reddoch, J F" sort="Reddoch, J F" uniqKey="Reddoch J" first="J F" last="Reddoch">J F Reddoch</name></author><author><name sortKey="Mergny, J L" sort="Mergny, J L" uniqKey="Mergny J" first="J L" last="Mergny">J L Mergny</name></author><author><name sortKey="Levy, D D" sort="Levy, D D" uniqKey="Levy D" first="D D" last="Levy">D D Levy</name></author><author><name sortKey="Seidman, M M" sort="Seidman, M M" uniqKey="Seidman M" first="M M" last="Seidman">M M Seidman</name></author><author><name sortKey="Matteucci, M D" sort="Matteucci, M D" uniqKey="Matteucci M" first="M D" last="Matteucci">M D Matteucci</name></author><author><name sortKey="Glazer, P M" sort="Glazer, P M" uniqKey="Glazer P" first="P M" last="Glazer">P M Glazer</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1999">1999</date><idno type="RBID">pubmed:10026270</idno><idno type="pmid">10026270</idno><idno type="doi">10.1021/bi982290q</idno><idno type="wicri:Area/PubMed/Corpus">002647</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002647</idno><idno type="wicri:Area/PubMed/Curation">002647</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002647</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Triplex formation by oligonucleotides containing 5-(1-propynyl)-2'-deoxyuridine: decreased magnesium dependence and improved intracellular gene targeting.</title><author><name sortKey="Lacroix, L" sort="Lacroix, L" uniqKey="Lacroix L" first="L" last="Lacroix">L. Lacroix</name><affiliation wicri:level="1"><nlm:affiliation>Department of Therapeutic Radiology and Genetics, Yale University, New Haven, Connecticut 06536, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Therapeutic Radiology and Genetics, Yale University, New Haven, Connecticut 06536</wicri:regionArea></affiliation></author><author><name sortKey="Lacoste, J" sort="Lacoste, J" uniqKey="Lacoste J" first="J" last="Lacoste">J. Lacoste</name></author><author><name sortKey="Reddoch, J F" sort="Reddoch, J F" uniqKey="Reddoch J" first="J F" last="Reddoch">J F Reddoch</name></author><author><name sortKey="Mergny, J L" sort="Mergny, J L" uniqKey="Mergny J" first="J L" last="Mergny">J L Mergny</name></author><author><name sortKey="Levy, D D" sort="Levy, D D" uniqKey="Levy D" first="D D" last="Levy">D D Levy</name></author><author><name sortKey="Seidman, M M" sort="Seidman, M M" uniqKey="Seidman M" first="M M" last="Seidman">M M Seidman</name></author><author><name sortKey="Matteucci, M D" sort="Matteucci, M D" uniqKey="Matteucci M" first="M D" last="Matteucci">M D Matteucci</name></author><author><name sortKey="Glazer, P M" sort="Glazer, P M" uniqKey="Glazer P" first="P M" last="Glazer">P M Glazer</name></author></analytic><series><title level="j">Biochemistry</title><idno type="ISSN">0006-2960</idno><imprint><date when="1999" type="published">1999</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Binding Sites</term><term>COS Cells</term><term>DNA (chemistry)</term><term>DNA (genetics)</term><term>DNA (metabolism)</term><term>Deoxyuridine (analogs & derivatives)</term><term>Deoxyuridine (chemistry)</term><term>Deoxyuridine (metabolism)</term><term>Gene Targeting</term><term>Genes, Reporter</term><term>Genes, Suppressor</term><term>Genetic Vectors</term><term>Intracellular Fluid (metabolism)</term><term>Magnesium (metabolism)</term><term>Molecular Sequence Data</term><term>Mutagenesis, Site-Directed</term><term>Nucleic Acid Denaturation</term><term>Oligonucleotides (chemistry)</term><term>Oligonucleotides (genetics)</term><term>Oligonucleotides (metabolism)</term><term>RNA, Transfer (genetics)</term><term>Simian virus 40 (genetics)</term></keywords><keywords scheme="KwdFr" 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scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>Deoxyuridine</term><term>Oligonucleotides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term><term>Oligonucleotides</term><term>RNA, Transfer</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA</term><term>Deoxyuridine</term><term>Magnesium</term><term>Oligonucleotides</term></keywords><keywords scheme="MESH" qualifier="analogues et dérivés" xml:lang="fr"><term>Désoxyuridine</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Simian virus 40</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term><term>ARN de transfert</term><term>Oligonucléotides</term><term>Virus simien 40</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Intracellular Fluid</term></keywords><keywords scheme="MESH" 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génétiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Oligonucleotides capable of sequence-specific triple helix formation have been proposed as DNA binding ligands useful for modulation of gene expression and for directed genome modification. However, the effectiveness of such triplex-forming oligonucleotides (TFOs) depends on their ability to bind to their target sites within cells, and this can be limited under physiologic conditions. In particular, triplex formation in the pyrimidine motif is favored by unphysiologically low pH and high magnesium concentrations. To address these limitations, a series of pyrimidine TFOs were tested for third-strand binding under a variety of conditions. Those containing 5-(1-propynyl)-2'-deoxyuridine (pdU) and 5-methyl-2'-deoxycytidine (5meC) showed superior binding characteristics at neutral pH and at low magnesium concentrations, as determined by gel mobility shift assays and thermal dissociation profiles. Over a range of Mg2+ concentrations, pdU-modified TFOs formed more stable triplexes than did TFOs containing 2'-deoxythymidine. At 1 mM Mg2+, a DeltaTm of 30 degreesC was observed for pdU- versus T-containing 15-mers (of generic sequence 5' TTTTCTTTTTTCTTTTCT 3') binding to the cognate A:T bp rich site, indicating that pdU-containing TFOs are capable of substantial binding even at physiologically low Mg2+ concentrations. In addition, the pdU-containing TFOs were superior in gene targeting experiments in mammalian cells, yielding 4-fold higher mutation frequencies in a shuttle vector-based mutagenesis assay designed to detect mutations induced by third-strand-directed psoralen adducts. These results suggest the utility of the pdU substitution in the pyrimidine motif for triplex-based gene targeting experiments.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">10026270</PMID><DateCompleted><Year>1999</Year><Month>03</Month><Day>04</Day></DateCompleted><DateRevised><Year>2013</Year><Month>11</Month><Day>21</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0006-2960</ISSN><JournalIssue CitedMedium="Print"><Volume>38</Volume><Issue>6</Issue><PubDate><Year>1999</Year><Month>Feb</Month><Day>09</Day></PubDate></JournalIssue><Title>Biochemistry</Title><ISOAbbreviation>Biochemistry</ISOAbbreviation></Journal><ArticleTitle>Triplex formation by oligonucleotides containing 5-(1-propynyl)-2'-deoxyuridine: decreased magnesium dependence and improved intracellular gene targeting.</ArticleTitle><Pagination><MedlinePgn>1893-901</MedlinePgn></Pagination><Abstract><AbstractText>Oligonucleotides capable of sequence-specific triple helix formation have been proposed as DNA binding ligands useful for modulation of gene expression and for directed genome modification. However, the effectiveness of such triplex-forming oligonucleotides (TFOs) depends on their ability to bind to their target sites within cells, and this can be limited under physiologic conditions. In particular, triplex formation in the pyrimidine motif is favored by unphysiologically low pH and high magnesium concentrations. To address these limitations, a series of pyrimidine TFOs were tested for third-strand binding under a variety of conditions. Those containing 5-(1-propynyl)-2'-deoxyuridine (pdU) and 5-methyl-2'-deoxycytidine (5meC) showed superior binding characteristics at neutral pH and at low magnesium concentrations, as determined by gel mobility shift assays and thermal dissociation profiles. Over a range of Mg2+ concentrations, pdU-modified TFOs formed more stable triplexes than did TFOs containing 2'-deoxythymidine. At 1 mM Mg2+, a DeltaTm of 30 degreesC was observed for pdU- versus T-containing 15-mers (of generic sequence 5' TTTTCTTTTTTCTTTTCT 3') binding to the cognate A:T bp rich site, indicating that pdU-containing TFOs are capable of substantial binding even at physiologically low Mg2+ concentrations. In addition, the pdU-containing TFOs were superior in gene targeting experiments in mammalian cells, yielding 4-fold higher mutation frequencies in a shuttle vector-based mutagenesis assay designed to detect mutations induced by third-strand-directed psoralen adducts. These results suggest the utility of the pdU substitution in the pyrimidine motif for triplex-based gene targeting experiments.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lacroix</LastName><ForeName>L</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Department of Therapeutic Radiology and Genetics, Yale University, New Haven, Connecticut 06536, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lacoste</LastName><ForeName>J</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Reddoch</LastName><ForeName>J F</ForeName><Initials>JF</Initials></Author><Author ValidYN="Y"><LastName>Mergny</LastName><ForeName>J L</ForeName><Initials>JL</Initials></Author><Author ValidYN="Y"><LastName>Levy</LastName><ForeName>D D</ForeName><Initials>DD</Initials></Author><Author ValidYN="Y"><LastName>Seidman</LastName><ForeName>M M</ForeName><Initials>MM</Initials></Author><Author ValidYN="Y"><LastName>Matteucci</LastName><ForeName>M D</ForeName><Initials>MD</Initials></Author><Author ValidYN="Y"><LastName>Glazer</LastName><ForeName>P M</ForeName><Initials>PM</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>CA64186</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Biochemistry</MedlineTA><NlmUniqueID>0370623</NlmUniqueID><ISSNLinking>0006-2960</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009841">Oligonucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C096275">supF tRNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C051802">triplex DNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>65367-85-3</RegistryNumber><NameOfSubstance UI="C016081">propynyloxy-2'-deoxyuridine</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>9014-25-9</RegistryNumber><NameOfSubstance UI="D012343">RNA, Transfer</NameOfSubstance></Chemical><Chemical><RegistryNumber>I38ZP9992A</RegistryNumber><NameOfSubstance UI="D008274">Magnesium</NameOfSubstance></Chemical><Chemical><RegistryNumber>W78I7AY22C</RegistryNumber><NameOfSubstance UI="D003857">Deoxyuridine</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019556" MajorTopicYN="N">COS Cells</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003857" MajorTopicYN="N">Deoxyuridine</DescriptorName><QualifierName UI="Q000031" MajorTopicYN="Y">analogs & derivatives</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018390" MajorTopicYN="Y">Gene Targeting</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017930" MajorTopicYN="N">Genes, Reporter</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016153" MajorTopicYN="N">Genes, Suppressor</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005822" MajorTopicYN="N">Genetic Vectors</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007424" MajorTopicYN="N">Intracellular Fluid</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008274" MajorTopicYN="N">Magnesium</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016297" MajorTopicYN="N">Mutagenesis, Site-Directed</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009691" MajorTopicYN="N">Nucleic Acid Denaturation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009841" MajorTopicYN="N">Oligonucleotides</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012343" MajorTopicYN="N">RNA, Transfer</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013539" MajorTopicYN="N">Simian virus 40</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>1999</Year><Month>2</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>1999</Year><Month>2</Month><Day>23</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>1999</Year><Month>2</Month><Day>23</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">10026270</ArticleId><ArticleId IdType="doi">10.1021/bi982290q</ArticleId><ArticleId IdType="pii">bi982290q</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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