Characterization of the ATF/CREB Site and Its Complex with GCN4
We have studied DNA minicircles containing the ATF/CREB binding site for GCN4 by using a combination of cyclization kinetics experiments and Monte Carlo simulations. Cyclization rates were determined with and without GCN4 for DNA constructs containing the ATF/CREB site separated from a phased A-trac...
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| Veröffentlicht in: | Proceedings of the National Academy of Sciences - PNAS 1998-02, Vol.95 (4), p.1410-1415 |
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| creator | Hockings, Susan C. Kahn, Jason D. Crothers, Donald M. |
| description | We have studied DNA minicircles containing the ATF/CREB binding site for GCN4 by using a combination of cyclization kinetics experiments and Monte Carlo simulations. Cyclization rates were determined with and without GCN4 for DNA constructs containing the ATF/CREB site separated from a phased A-tract multimer bend by a variable length phasing adaptor. The cyclization results show that GCN4 binding does not significantly change the conformation of the ATF/CREB site, which is intrinsically slightly bent toward the major groove. Monte Carlo simulations quantative the ATF/CREB site structure as an 8 degrees bend toward the major groove in a coordinate frame near the center of the site. The ATF/CREB site is underwound by 53 degrees relative to the related AP-1 site DNA. The effect of GCN4 binding can be modeled either as a decrease in the local flexibility, corresponding to an estimated 60% increase in the persistence length for the 10-bp binding site, or possibly as a small decrease (1 degrees) in intrinsic bend angle. Our results agree with recent electrophoretic and crystallographic studies and demonstrate that cyclization and simulation can characterize subtle changes in DNA structure and flexibility. |
| doi_str_mv | 10.1073/pnas.95.4.1410 |
| format | Article |
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Cyclization rates were determined with and without GCN4 for DNA constructs containing the ATF/CREB site separated from a phased A-tract multimer bend by a variable length phasing adaptor. The cyclization results show that GCN4 binding does not significantly change the conformation of the ATF/CREB site, which is intrinsically slightly bent toward the major groove. Monte Carlo simulations quantative the ATF/CREB site structure as an 8 degrees bend toward the major groove in a coordinate frame near the center of the site. The ATF/CREB site is underwound by 53 degrees relative to the related AP-1 site DNA. The effect of GCN4 binding can be modeled either as a decrease in the local flexibility, corresponding to an estimated 60% increase in the persistence length for the 10-bp binding site, or possibly as a small decrease (1 degrees) in intrinsic bend angle. 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Cyclization rates were determined with and without GCN4 for DNA constructs containing the ATF/CREB site separated from a phased A-tract multimer bend by a variable length phasing adaptor. The cyclization results show that GCN4 binding does not significantly change the conformation of the ATF/CREB site, which is intrinsically slightly bent toward the major groove. Monte Carlo simulations quantative the ATF/CREB site structure as an 8 degrees bend toward the major groove in a coordinate frame near the center of the site. The ATF/CREB site is underwound by 53 degrees relative to the related AP-1 site DNA. The effect of GCN4 binding can be modeled either as a decrease in the local flexibility, corresponding to an estimated 60% increase in the persistence length for the 10-bp binding site, or possibly as a small decrease (1 degrees) in intrinsic bend angle. 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Kahn, Jason D. ; Crothers, Donald M.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c513t-ed7945f5009245fa4884622561a9e3be17072b43424dd2f1086ef2a782003afa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1998</creationdate><topic>Bending</topic><topic>Binding Sites</topic><topic>Biochemistry</topic><topic>Biological Sciences</topic><topic>Cell-Free System</topic><topic>Cyclic AMP Response Element-Binding Protein - chemistry</topic><topic>Deoxyribonucleic acid</topic><topic>Deoxyribonucleoproteins - chemistry</topic><topic>DNA</topic><topic>DNA, Circular - chemistry</topic><topic>DNA-Binding Proteins - chemistry</topic><topic>Electrophoresis, Agar Gel</topic><topic>Fungal Proteins - chemistry</topic><topic>Gels</topic><topic>Kinetics</topic><topic>Molecules</topic><topic>Monte Carlo Method</topic><topic>Monte Carlo methods</topic><topic>Motion</topic><topic>Nucleic Acid Conformation</topic><topic>Polymerase chain reaction</topic><topic>Protein Kinases - chemistry</topic><topic>Proteins</topic><topic>Saccharomyces cerevisiae Proteins</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hockings, Susan C.</creatorcontrib><creatorcontrib>Kahn, Jason D.</creatorcontrib><creatorcontrib>Crothers, Donald M.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hockings, Susan C.</au><au>Kahn, Jason D.</au><au>Crothers, Donald M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Characterization of the ATF/CREB Site and Its Complex with GCN4</atitle><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle><addtitle>Proc Natl Acad Sci U S A</addtitle><date>1998-02-17</date><risdate>1998</risdate><volume>95</volume><issue>4</issue><spage>1410</spage><epage>1415</epage><pages>1410-1415</pages><issn>0027-8424</issn><eissn>1091-6490</eissn><abstract>We have studied DNA minicircles containing the ATF/CREB binding site for GCN4 by using a combination of cyclization kinetics experiments and Monte Carlo simulations. Cyclization rates were determined with and without GCN4 for DNA constructs containing the ATF/CREB site separated from a phased A-tract multimer bend by a variable length phasing adaptor. The cyclization results show that GCN4 binding does not significantly change the conformation of the ATF/CREB site, which is intrinsically slightly bent toward the major groove. Monte Carlo simulations quantative the ATF/CREB site structure as an 8 degrees bend toward the major groove in a coordinate frame near the center of the site. The ATF/CREB site is underwound by 53 degrees relative to the related AP-1 site DNA. The effect of GCN4 binding can be modeled either as a decrease in the local flexibility, corresponding to an estimated 60% increase in the persistence length for the 10-bp binding site, or possibly as a small decrease (1 degrees) in intrinsic bend angle. 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| subjects | Bending Binding Sites Biochemistry Biological Sciences Cell-Free System Cyclic AMP Response Element-Binding Protein - chemistry Deoxyribonucleic acid Deoxyribonucleoproteins - chemistry DNA DNA, Circular - chemistry DNA-Binding Proteins - chemistry Electrophoresis, Agar Gel Fungal Proteins - chemistry Gels Kinetics Molecules Monte Carlo Method Monte Carlo methods Motion Nucleic Acid Conformation Polymerase chain reaction Protein Kinases - chemistry Proteins Saccharomyces cerevisiae Proteins |
| title | Characterization of the ATF/CREB Site and Its Complex with GCN4 |
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