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Specificity of Mammalian Y-box Binding Protein p50 in Interaction with ss and ds DNA Analyzed with Generic Oligonucleotide Microchip
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 4096 sin...
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| Published in: | Journal of molecular biology 2002-11, Vol.324 (1), p.73-87 |
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| Main Authors: | , , , , , , |
| Format: | Article |
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| cited_by | cdi_FETCH-LOGICAL-c392t-98fb0f868641c212a4af369fc1e534e30529dfb163c21a2664852c6b4dc027e3 |
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| cites | cdi_FETCH-LOGICAL-c392t-98fb0f868641c212a4af369fc1e534e30529dfb163c21a2664852c6b4dc027e3 |
| container_end_page | 87 |
| container_issue | 1 |
| container_start_page | 73 |
| container_title | Journal of molecular biology |
| container_volume | 324 |
| creator | Zasedateleva, O.A Krylov, A.S Prokopenko, D.V Skabkin, M.A Ovchinnikov, L.P Kolchinsky, A Mirzabekov, A.D |
| description | 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 4096 single-stranded octadeoxyribonucleotides in which all possible core 6-mers (4
6=4096) 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_str_mv | 10.1016/S0022-2836(02)00937-3 |
| format | article |
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6=4096) 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.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1016/S0022-2836(02)00937-3</identifier><identifier>PMID: 12421560</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Animals ; biochip ; DNA ; DNA - metabolism ; DNA, Single-Stranded - metabolism ; Electrophoretic Mobility Shift Assay ; Image Processing, Computer-Assisted ; interaction ; Mammals ; Oligonucleotide Array Sequence Analysis - methods ; Oligonucleotides - chemistry ; Oligonucleotides - metabolism ; p50 ; Repressor Proteins - genetics ; Repressor Proteins - metabolism ; RNA-Binding Proteins - genetics ; RNA-Binding Proteins - metabolism ; Substrate Specificity ; Temperature ; Y-box</subject><ispartof>Journal of molecular biology, 2002-11, Vol.324 (1), p.73-87</ispartof><rights>2002 Elsevier Science Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c392t-98fb0f868641c212a4af369fc1e534e30529dfb163c21a2664852c6b4dc027e3</citedby><cites>FETCH-LOGICAL-c392t-98fb0f868641c212a4af369fc1e534e30529dfb163c21a2664852c6b4dc027e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,786,790,27957,27958</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/12421560$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zasedateleva, O.A</creatorcontrib><creatorcontrib>Krylov, A.S</creatorcontrib><creatorcontrib>Prokopenko, D.V</creatorcontrib><creatorcontrib>Skabkin, M.A</creatorcontrib><creatorcontrib>Ovchinnikov, L.P</creatorcontrib><creatorcontrib>Kolchinsky, A</creatorcontrib><creatorcontrib>Mirzabekov, A.D</creatorcontrib><title>Specificity of Mammalian Y-box Binding Protein p50 in Interaction with ss and ds DNA Analyzed with Generic Oligonucleotide Microchip</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>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 4096 single-stranded octadeoxyribonucleotides in which all possible core 6-mers (4
6=4096) 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.</description><subject>Animals</subject><subject>biochip</subject><subject>DNA</subject><subject>DNA - metabolism</subject><subject>DNA, Single-Stranded - metabolism</subject><subject>Electrophoretic Mobility Shift Assay</subject><subject>Image Processing, Computer-Assisted</subject><subject>interaction</subject><subject>Mammals</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>Oligonucleotides - chemistry</subject><subject>Oligonucleotides - metabolism</subject><subject>p50</subject><subject>Repressor Proteins - genetics</subject><subject>Repressor Proteins - metabolism</subject><subject>RNA-Binding Proteins - genetics</subject><subject>RNA-Binding Proteins - metabolism</subject><subject>Substrate Specificity</subject><subject>Temperature</subject><subject>Y-box</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2002</creationdate><recordtype>article</recordtype><recordid>eNqFkUtv1DAQgC1ERZfCTwD5hOCQ4kfidU5oKdBWailSe-FkOfa4HZTYqZ0FljM_vGl3Bcee5jDfPD9CXnF2yBlX7y8ZE6ISWqq3TLxjrJXLSj4hC850W2kl9VOy-Ifsk-el_GCMNbLWz8g-F7XgjWIL8vdyBIcBHU4bmgI9t8Nge7SRfq-69Jt-xOgxXtNvOU2AkY4No3M4jRNk6yZMkf7C6YaWQm301Bf66euKrqLtN3_Ab3PHECGjoxc9Xqe4dj2kCT3Qc3Q5uRscX5C9YPsCL3fxgFx9-Xx1dFKdXRyfHq3OKidbMVWtDh0LWmlVcye4sLUNUrXBcZjvAska0frQcSXnrBVK1boRTnW1d0wsQR6QN9u2Y063ayiTGbA46HsbIa2LWQq1FFLUj4J83kBI2cxgswXnQ0rJEMyYcbB5Yzgz95rMgyZz78AwYR40GTnXvd4NWHcD-P9VOy8z8GELwPyOnwjZFIcQHXjM4CbjEz4y4g5t8KGS</recordid><startdate>20021115</startdate><enddate>20021115</enddate><creator>Zasedateleva, O.A</creator><creator>Krylov, A.S</creator><creator>Prokopenko, D.V</creator><creator>Skabkin, M.A</creator><creator>Ovchinnikov, L.P</creator><creator>Kolchinsky, A</creator><creator>Mirzabekov, A.D</creator><general>Elsevier Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TM</scope><scope>7X8</scope></search><sort><creationdate>20021115</creationdate><title>Specificity of Mammalian Y-box Binding Protein p50 in Interaction with ss and ds DNA Analyzed with Generic Oligonucleotide Microchip</title><author>Zasedateleva, O.A ; Krylov, A.S ; Prokopenko, D.V ; Skabkin, M.A ; Ovchinnikov, L.P ; Kolchinsky, A ; Mirzabekov, A.D</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c392t-98fb0f868641c212a4af369fc1e534e30529dfb163c21a2664852c6b4dc027e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2002</creationdate><topic>Animals</topic><topic>biochip</topic><topic>DNA</topic><topic>DNA - metabolism</topic><topic>DNA, Single-Stranded - metabolism</topic><topic>Electrophoretic Mobility Shift Assay</topic><topic>Image Processing, Computer-Assisted</topic><topic>interaction</topic><topic>Mammals</topic><topic>Oligonucleotide Array Sequence Analysis - methods</topic><topic>Oligonucleotides - chemistry</topic><topic>Oligonucleotides - metabolism</topic><topic>p50</topic><topic>Repressor Proteins - genetics</topic><topic>Repressor Proteins - metabolism</topic><topic>RNA-Binding Proteins - genetics</topic><topic>RNA-Binding Proteins - metabolism</topic><topic>Substrate Specificity</topic><topic>Temperature</topic><topic>Y-box</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zasedateleva, O.A</creatorcontrib><creatorcontrib>Krylov, A.S</creatorcontrib><creatorcontrib>Prokopenko, D.V</creatorcontrib><creatorcontrib>Skabkin, M.A</creatorcontrib><creatorcontrib>Ovchinnikov, L.P</creatorcontrib><creatorcontrib>Kolchinsky, A</creatorcontrib><creatorcontrib>Mirzabekov, A.D</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zasedateleva, O.A</au><au>Krylov, A.S</au><au>Prokopenko, D.V</au><au>Skabkin, M.A</au><au>Ovchinnikov, L.P</au><au>Kolchinsky, A</au><au>Mirzabekov, A.D</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Specificity of Mammalian Y-box Binding Protein p50 in Interaction with ss and ds DNA Analyzed with Generic Oligonucleotide Microchip</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>2002-11-15</date><risdate>2002</risdate><volume>324</volume><issue>1</issue><spage>73</spage><epage>87</epage><pages>73-87</pages><issn>0022-2836</issn><eissn>1089-8638</eissn><notes>ObjectType-Article-2</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-1</notes><notes>content type line 23</notes><notes>ObjectType-Article-1</notes><notes>ObjectType-Feature-2</notes><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 4096 single-stranded octadeoxyribonucleotides in which all possible core 6-mers (4
6=4096) 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.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>12421560</pmid><doi>10.1016/S0022-2836(02)00937-3</doi><tpages>15</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0022-2836 |
| ispartof | Journal of molecular biology, 2002-11, Vol.324 (1), p.73-87 |
| issn | 0022-2836 1089-8638 |
| language | eng |
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| source | Elsevier |
| subjects | Animals biochip DNA DNA - metabolism DNA, Single-Stranded - metabolism Electrophoretic Mobility Shift Assay Image Processing, Computer-Assisted interaction Mammals Oligonucleotide Array Sequence Analysis - methods Oligonucleotides - chemistry Oligonucleotides - metabolism p50 Repressor Proteins - genetics Repressor Proteins - metabolism RNA-Binding Proteins - genetics RNA-Binding Proteins - metabolism Substrate Specificity Temperature Y-box |
| title | Specificity of Mammalian Y-box Binding Protein p50 in Interaction with ss and ds DNA Analyzed with Generic Oligonucleotide Microchip |
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