Specificity of mammalian Y-box binding protein p50 in interaction with ss and ds DNA analyzed with generic oligonucleotide microchip.
Identifieur interne : 002483 ( PubMed/Curation ); précédent : 002482; suivant : 002484Specificity of mammalian Y-box binding protein p50 in interaction with ss and ds DNA analyzed with generic oligonucleotide microchip.
Auteurs : O A Zasedateleva [Russie] ; A S Krylov ; D V Prokopenko ; M A Skabkin ; L P Ovchinnikov ; A. Kolchinsky ; A D MirzabekovSource :
- Journal of molecular biology [ 0022-2836 ] ; 2002.
Descripteurs français
- KwdFr :
- ADN (métabolisme), ADN simple brin (métabolisme), Animaux, Mammifères, Oligonucléotides (), Oligonucléotides (métabolisme), Protéines de liaison à l'ARN (génétique), Protéines de liaison à l'ARN (métabolisme), Protéines de répression (génétique), Protéines de répression (métabolisme), Spécificité du substrat, Séquençage par oligonucléotides en batterie (), Température, Test de retard de migration électrophorétique, Traitement d'image par ordinateur.
- MESH :
- génétique : Protéines de liaison à l'ARN, Protéines de répression.
- métabolisme : ADN, ADN simple brin, Oligonucléotides, Protéines de liaison à l'ARN, Protéines de répression.
- Animaux, Mammifères, Oligonucléotides, Spécificité du substrat, Séquençage par oligonucléotides en batterie, Température, Test de retard de migration électrophorétique, Traitement d'image par ordinateur.
English descriptors
- KwdEn :
- Animals, DNA (metabolism), DNA, Single-Stranded (metabolism), Electrophoretic Mobility Shift Assay, Image Processing, Computer-Assisted, Mammals, Oligonucleotide Array Sequence Analysis (methods), Oligonucleotides (chemistry), Oligonucleotides (metabolism), RNA-Binding Proteins (genetics), RNA-Binding Proteins (metabolism), Repressor Proteins (genetics), Repressor Proteins (metabolism), Substrate Specificity, Temperature.
- MESH :
- chemical , chemistry : Oligonucleotides.
- chemical , genetics : RNA-Binding Proteins, Repressor Proteins.
- chemical , metabolism : DNA, DNA, Single-Stranded, Oligonucleotides, RNA-Binding Proteins, Repressor Proteins.
- methods : Oligonucleotide Array Sequence Analysis.
- Animals, Electrophoretic Mobility Shift Assay, Image Processing, Computer-Assisted, Mammals, Substrate Specificity, Temperature.
Abstract
p50 protein is a member of the Y-box binding transcription factor family and is a counterpart of YB-1 protein. The generic microchip was used to analyze the sequence specificity of p50 binding to single (ss) and double-stranded (ds) oligodeoxyribonucleotides. The generic microchip contained 4,096 single-stranded octadeoxyribonucleotides in which all possible core 6-mers (4(6)=4,096) were flanked at their 3' and 5'-ends with degenerated nucleotides. The oligonucleotides were chemically immobilized within polyacrylamide gel pads fixed on a glass slide. The binding of p50 to the generic microchip was shown to be the most specific to ss GGGG motif and then to ss CACC and CATC motifs. GC-rich ds oligonucleotides of the generic microchip, and particularly those containing GGTG/CACC, GATG/CATC, and GTGG/CCAC heterogeneous motifs, were most efficiently destabilized due to interaction with p50. Gel-shift electrophoresis has shown that the protein exhibits much higher binding specificity to 24-mer oligoA-TGGGGG-oligoA containing G-rich 6-mer, in comparison with 24-mer oligoA-AAATAT-oligoA carrying A,T-rich 6-mer in full correspondence with the data obtained with the microchip. Studies of DNA-binding proteins using gel-immobilized ss and ds DNA fragments provide a unique possibility to detect low-affinity complexes of these proteins with short sequence motifs and assess the role of these motifs in sequence-specific interactions with long recognition sites.
DOI: 10.1016/s0022-2836(02)00937-3
PubMed: 12421560
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Kolchinsky</name></author><author><name sortKey="Mirzabekov, A D" sort="Mirzabekov, A D" uniqKey="Mirzabekov A" first="A D" last="Mirzabekov">A D Mirzabekov</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2002">2002</date><idno type="RBID">pubmed:12421560</idno><idno type="pmid">12421560</idno><idno type="doi">10.1016/s0022-2836(02)00937-3</idno><idno type="wicri:Area/PubMed/Corpus">002483</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002483</idno><idno type="wicri:Area/PubMed/Curation">002483</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002483</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Specificity of mammalian Y-box binding protein p50 in interaction with ss and ds DNA analyzed with generic oligonucleotide microchip.</title><author><name sortKey="Zasedateleva, O A" sort="Zasedateleva, O A" uniqKey="Zasedateleva O" first="O A" last="Zasedateleva">O A Zasedateleva</name><affiliation wicri:level="1"><nlm:affiliation>Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russian Federation.</nlm:affiliation><country xml:lang="fr">Russie</country><wicri:regionArea>Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow</wicri:regionArea></affiliation></author><author><name sortKey="Krylov, A S" sort="Krylov, A S" uniqKey="Krylov A" first="A S" last="Krylov">A S Krylov</name></author><author><name sortKey="Prokopenko, D V" sort="Prokopenko, D V" uniqKey="Prokopenko D" first="D V" last="Prokopenko">D V Prokopenko</name></author><author><name sortKey="Skabkin, M A" sort="Skabkin, M A" uniqKey="Skabkin M" first="M A" last="Skabkin">M A Skabkin</name></author><author><name sortKey="Ovchinnikov, L P" sort="Ovchinnikov, L P" uniqKey="Ovchinnikov L" first="L P" last="Ovchinnikov">L P Ovchinnikov</name></author><author><name sortKey="Kolchinsky, A" sort="Kolchinsky, A" uniqKey="Kolchinsky A" first="A" last="Kolchinsky">A. Kolchinsky</name></author><author><name sortKey="Mirzabekov, A D" sort="Mirzabekov, A D" uniqKey="Mirzabekov A" first="A D" last="Mirzabekov">A D Mirzabekov</name></author></analytic><series><title level="j">Journal of molecular biology</title><idno type="ISSN">0022-2836</idno><imprint><date when="2002" type="published">2002</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>DNA (metabolism)</term><term>DNA, Single-Stranded (metabolism)</term><term>Electrophoretic Mobility Shift Assay</term><term>Image Processing, Computer-Assisted</term><term>Mammals</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Oligonucleotides (chemistry)</term><term>Oligonucleotides (metabolism)</term><term>RNA-Binding Proteins (genetics)</term><term>RNA-Binding Proteins (metabolism)</term><term>Repressor Proteins (genetics)</term><term>Repressor Proteins (metabolism)</term><term>Substrate Specificity</term><term>Temperature</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN (métabolisme)</term><term>ADN simple brin (métabolisme)</term><term>Animaux</term><term>Mammifères</term><term>Oligonucléotides ()</term><term>Oligonucléotides (métabolisme)</term><term>Protéines de liaison à l'ARN (génétique)</term><term>Protéines de liaison à l'ARN (métabolisme)</term><term>Protéines de répression (génétique)</term><term>Protéines de répression (métabolisme)</term><term>Spécificité du substrat</term><term>Séquençage par oligonucléotides en batterie ()</term><term>Température</term><term>Test de retard de migration électrophorétique</term><term>Traitement d'image par ordinateur</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Oligonucleotides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA-Binding Proteins</term><term>Repressor Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA</term><term>DNA, Single-Stranded</term><term>Oligonucleotides</term><term>RNA-Binding Proteins</term><term>Repressor Proteins</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Protéines de liaison à l'ARN</term><term>Protéines de répression</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term><term>ADN simple brin</term><term>Oligonucléotides</term><term>Protéines de liaison à l'ARN</term><term>Protéines de répression</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Electrophoretic Mobility Shift Assay</term><term>Image Processing, Computer-Assisted</term><term>Mammals</term><term>Substrate Specificity</term><term>Temperature</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Mammifères</term><term>Oligonucléotides</term><term>Spécificité du substrat</term><term>Séquençage par oligonucléotides en batterie</term><term>Température</term><term>Test de retard de migration électrophorétique</term><term>Traitement d'image par ordinateur</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">p50 protein is a member of the Y-box binding transcription factor family and is a counterpart of YB-1 protein. The generic microchip was used to analyze the sequence specificity of p50 binding to single (ss) and double-stranded (ds) oligodeoxyribonucleotides. The generic microchip contained 4,096 single-stranded octadeoxyribonucleotides in which all possible core 6-mers (4(6)=4,096) were flanked at their 3' and 5'-ends with degenerated nucleotides. The oligonucleotides were chemically immobilized within polyacrylamide gel pads fixed on a glass slide. The binding of p50 to the generic microchip was shown to be the most specific to ss GGGG motif and then to ss CACC and CATC motifs. GC-rich ds oligonucleotides of the generic microchip, and particularly those containing GGTG/CACC, GATG/CATC, and GTGG/CCAC heterogeneous motifs, were most efficiently destabilized due to interaction with p50. Gel-shift electrophoresis has shown that the protein exhibits much higher binding specificity to 24-mer oligoA-TGGGGG-oligoA containing G-rich 6-mer, in comparison with 24-mer oligoA-AAATAT-oligoA carrying A,T-rich 6-mer in full correspondence with the data obtained with the microchip. Studies of DNA-binding proteins using gel-immobilized ss and ds DNA fragments provide a unique possibility to detect low-affinity complexes of these proteins with short sequence motifs and assess the role of these motifs in sequence-specific interactions with long recognition sites.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">12421560</PMID><DateCompleted><Year>2002</Year><Month>12</Month><Day>19</Day></DateCompleted><DateRevised><Year>2019</Year><Month>07</Month><Day>10</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0022-2836</ISSN><JournalIssue CitedMedium="Print"><Volume>324</Volume><Issue>1</Issue><PubDate><Year>2002</Year><Month>Nov</Month><Day>15</Day></PubDate></JournalIssue><Title>Journal of molecular biology</Title><ISOAbbreviation>J. Mol. Biol.</ISOAbbreviation></Journal><ArticleTitle>Specificity of mammalian Y-box binding protein p50 in interaction with ss and ds DNA analyzed with generic oligonucleotide microchip.</ArticleTitle><Pagination><MedlinePgn>73-87</MedlinePgn></Pagination><Abstract><AbstractText>p50 protein is a member of the Y-box binding transcription factor family and is a counterpart of YB-1 protein. The generic microchip was used to analyze the sequence specificity of p50 binding to single (ss) and double-stranded (ds) oligodeoxyribonucleotides. The generic microchip contained 4,096 single-stranded octadeoxyribonucleotides in which all possible core 6-mers (4(6)=4,096) were flanked at their 3' and 5'-ends with degenerated nucleotides. The oligonucleotides were chemically immobilized within polyacrylamide gel pads fixed on a glass slide. The binding of p50 to the generic microchip was shown to be the most specific to ss GGGG motif and then to ss CACC and CATC motifs. GC-rich ds oligonucleotides of the generic microchip, and particularly those containing GGTG/CACC, GATG/CATC, and GTGG/CCAC heterogeneous motifs, were most efficiently destabilized due to interaction with p50. Gel-shift electrophoresis has shown that the protein exhibits much higher binding specificity to 24-mer oligoA-TGGGGG-oligoA containing G-rich 6-mer, in comparison with 24-mer oligoA-AAATAT-oligoA carrying A,T-rich 6-mer in full correspondence with the data obtained with the microchip. Studies of DNA-binding proteins using gel-immobilized ss and ds DNA fragments provide a unique possibility to detect low-affinity complexes of these proteins with short sequence motifs and assess the role of these motifs in sequence-specific interactions with long recognition sites.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zasedateleva</LastName><ForeName>O A</ForeName><Initials>OA</Initials><AffiliationInfo><Affiliation>Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russian Federation.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Krylov</LastName><ForeName>A S</ForeName><Initials>AS</Initials></Author><Author ValidYN="Y"><LastName>Prokopenko</LastName><ForeName>D V</ForeName><Initials>DV</Initials></Author><Author ValidYN="Y"><LastName>Skabkin</LastName><ForeName>M A</ForeName><Initials>MA</Initials></Author><Author ValidYN="Y"><LastName>Ovchinnikov</LastName><ForeName>L P</ForeName><Initials>LP</Initials></Author><Author ValidYN="Y"><LastName>Kolchinsky</LastName><ForeName>A</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Mirzabekov</LastName><ForeName>A D</ForeName><Initials>AD</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>England</Country><MedlineTA>J Mol Biol</MedlineTA><NlmUniqueID>2985088R</NlmUniqueID><ISSNLinking>0022-2836</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004277">DNA, Single-Stranded</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance 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MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012097" MajorTopicYN="N">Repressor Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013379" MajorTopicYN="N">Substrate Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013696" MajorTopicYN="N">Temperature</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2002</Year><Month>11</Month><Day>8</Day><Hour>4</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2002</Year><Month>12</Month><Day>20</Day><Hour>4</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2002</Year><Month>11</Month><Day>8</Day><Hour>4</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">12421560</ArticleId><ArticleId IdType="pii">S0022283602009373</ArticleId><ArticleId IdType="doi">10.1016/s0022-2836(02)00937-3</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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