Specificity of mammalian Y-box binding protein p50 in interaction with ss and ds DNA analyzed with generic oligonucleotide microchip.
Identifieur interne : 003312 ( Main/Exploration ); précédent : 003311; suivant : 003313Specificity 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
Affiliations:
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Le document en format XML
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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></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><affiliations><list><country><li>Russie</li></country><region><li>District fédéral central</li></region><settlement><li>Moscou</li></settlement></list><tree><noCountry><name sortKey="Kolchinsky, A" sort="Kolchinsky, A" uniqKey="Kolchinsky A" first="A" last="Kolchinsky">A. Kolchinsky</name><name sortKey="Krylov, A S" sort="Krylov, A S" uniqKey="Krylov A" first="A S" last="Krylov">A S Krylov</name><name sortKey="Mirzabekov, A D" sort="Mirzabekov, A D" uniqKey="Mirzabekov A" first="A D" last="Mirzabekov">A D Mirzabekov</name><name sortKey="Ovchinnikov, L P" sort="Ovchinnikov, L P" uniqKey="Ovchinnikov L" first="L P" last="Ovchinnikov">L P Ovchinnikov</name><name sortKey="Prokopenko, D V" sort="Prokopenko, D V" uniqKey="Prokopenko D" first="D V" last="Prokopenko">D V Prokopenko</name><name sortKey="Skabkin, M A" sort="Skabkin, M A" uniqKey="Skabkin M" first="M A" last="Skabkin">M A Skabkin</name></noCountry><country name="Russie"><region name="District fédéral central"><name sortKey="Zasedateleva, O A" sort="Zasedateleva, O A" uniqKey="Zasedateleva O" first="O A" last="Zasedateleva">O A Zasedateleva</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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