{"id":"https://openalex.org/W1990276804","doi":"https://doi.org/10.1021/bi026539m","title":"RNA Polymerase Alters the Mobility of an A-Residue Crucial to Polymerase-Induced Melting of Promoter DNA","display_name":"RNA Polymerase Alters the Mobility of an A-Residue Crucial to Polymerase-Induced Melting of Promoter DNA","publication_year":2002,"publication_date":"2002-11-26","ids":{"openalex":"https://openalex.org/W1990276804","doi":"https://doi.org/10.1021/bi026539m","mag":"1990276804","pmid":"https://pubmed.ncbi.nlm.nih.gov/12484772"},"language":"en","primary_location":{"id":"doi:10.1021/bi026539m","doi":"https://doi.org/10.1021/bi026539m","is_oa":false,"landing_page_url":"https://doi.org/10.1021/bi026539m","pdf_url":null,"source":{"id":"https://openalex.org/S104038378","display_name":"Biochemistry","issn_l":"0006-2960","issn":["0006-2960","1520-4995","1943-295X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biochemistry","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010165450","display_name":"Laura M. Tsujikawa","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laura Tsujikawa","raw_affiliation_strings":["Departments of Biochemistry and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biochemistry and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028037107","display_name":"Michael G. Strainic","orcid":"https://orcid.org/0000-0003-2438-8540","observed_orcids":["https://orcid.org/0000-0003-2438-8540"]},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael G. Strainic","raw_affiliation_strings":["Departments of Biochemistry and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biochemistry and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070469801","display_name":"Heather M. Watrob","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heather Watrob","raw_affiliation_strings":["Departments of Biochemistry and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biochemistry and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016174754","display_name":"Mary D. Barkley","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mary D. Barkley","raw_affiliation_strings":["Departments of Biochemistry and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biochemistry and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108216980","display_name":"Pieter L. deHaseth","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pieter L. deHaseth","raw_affiliation_strings":["Departments of Biochemistry and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biochemistry and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106","institution_ids":["https://openalex.org/I58956616"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I58956616"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":1.3396,"has_fulltext":false,"cited_by_count":30,"citation_normalized_percentile":{"value":0.79091109,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":95},"biblio":{"volume":"41","issue":"51","first_page":"15334","last_page":"15341"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.44600000977516174,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.44600000977516174,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.36739999055862427,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.13210000097751617,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna-polymerase","display_name":"RNA polymerase","score":0.9700000286102295},{"id":"https://openalex.org/keywords/promoter-dna","display_name":"promoter DNA","score":0.8539999723434448},{"id":"https://openalex.org/keywords/2-aminopurine","display_name":"2-aminopurine","score":0.8650000095367432},{"id":"https://openalex.org/keywords/dna-strand-separation","display_name":"DNA strand separation","score":0.7409999966621399},{"id":"https://openalex.org/keywords/dna-melting","display_name":"DNA melting","score":0.5120000243186951},{"id":"https://openalex.org/keywords/fluorescence-anisotropy","display_name":"fluorescence anisotropy","score":0.6669999957084656},{"id":"https://openalex.org/keywords/dna-immobilization","display_name":"DNA immobilization","score":0.4970000088214874},{"id":"https://openalex.org/keywords/hydrophobic-pocket","display_name":"hydrophobic pocket","score":0.8410000205039978},{"id":"https://openalex.org/keywords/heparin-resistance","display_name":"heparin resistance","score":0.640999972820282},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.7749999761581421}],"concepts":[{"id":"https://openalex.org/C82381507","wikidata":"https://www.wikidata.org/wiki/Q416878","display_name":"Polymerase","level":3,"score":0.8052889108657837},{"id":"https://openalex.org/C2776449523","wikidata":"https://www.wikidata.org/wiki/Q272631","display_name":"RNA polymerase","level":4,"score":0.6477533578872681},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.554036021232605},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.5243052244186401},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5189804434776306},{"id":"https://openalex.org/C31254050","wikidata":"https://www.wikidata.org/wiki/Q22328799","display_name":"DNA clamp","level":5,"score":0.4980940818786621},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4893326163291931},{"id":"https://openalex.org/C41258723","wikidata":"https://www.wikidata.org/wiki/Q2919111","display_name":"RNA-dependent RNA polymerase","level":4,"score":0.48079410195350647},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4612594544887543},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4585132598876953},{"id":"https://openalex.org/C119489563","wikidata":"https://www.wikidata.org/wiki/Q5140301","display_name":"Coding strand","level":4,"score":0.4147534668445587},{"id":"https://openalex.org/C2756471","wikidata":"https://www.wikidata.org/wiki/Q206286","display_name":"DNA polymerase","level":3,"score":0.4130784869194031},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3845961093902588},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37235206365585327},{"id":"https://openalex.org/C156719811","wikidata":"https://www.wikidata.org/wiki/Q28774","display_name":"Reverse transcriptase","level":4,"score":0.13874685764312744},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08995991945266724}],"mesh":[{"descriptor_ui":"D003850","descriptor_name":"Deoxyribonuclease I","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004277","descriptor_name":"DNA, Single-Stranded","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005454","descriptor_name":"Fluorescence Polarization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006358","descriptor_name":"Hot Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006493","descriptor_name":"Heparin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009692","descriptor_name":"Nucleic Acid Heteroduplexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012321","descriptor_name":"DNA-Directed RNA Polymerases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013050","descriptor_name":"Spectrometry, Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013698","descriptor_name":"Templates, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015075","descriptor_name":"2-Aminopurine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D018983","descriptor_name":"DNA Footprinting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/bi026539m","doi":"https://doi.org/10.1021/bi026539m","is_oa":false,"landing_page_url":"https://doi.org/10.1021/bi026539m","pdf_url":null,"source":{"id":"https://openalex.org/S104038378","display_name":"Biochemistry","issn_l":"0006-2960","issn":["0006-2960","1520-4995","1943-295X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biochemistry","raw_type":"journal-article"},{"id":"pmid:12484772","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12484772","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biochemistry","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G555299801","display_name":"BIOCHEMICAL EVALUATION OF RT-TEMPLATE-PRIMER/COMPLEXES","funder_award_id":"R01GM052263","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5590249401","display_name":"Structure-function relationships of promoter DNA","funder_award_id":"R01GM031808","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":2,"referenced_works":["https://openalex.org/W1512810258","https://openalex.org/W4237102582"],"related_works":["https://openalex.org/W2140017930","https://openalex.org/W2058285136","https://openalex.org/W1987735963","https://openalex.org/W204112833","https://openalex.org/W2033565485","https://openalex.org/W1971464225","https://openalex.org/W1884072035","https://openalex.org/W2109194296","https://openalex.org/W2123998895","https://openalex.org/W2034559720"],"abstract_inverted_index":{"Strand":[0],"separation":[1],"in":[2,61,78,111,129,144,169,177,189,209],"promoter":[3],"DNA":[4,46,105],"induced":[5],"by":[6],"Escherichia":[7],"coli":[8],"RNA":[9,39,80,117,148,171,195],"polymerase":[10,40,172],"is":[11,76,142,176],"likely":[12],"initiated":[13],"at":[14,19,57,72,94,165,204],"a":[15,62,190,210],"conserved":[16],"A":[17,93,133],"residue":[18,203],"position":[20,60,95],"-11":[21,43,59,96,166,205],"of":[22,31,38,88,91,104,116,123,136,147,152,161,183,213],"the":[23,29,36,42,51,58,66,69,86,102,112,121,126,130,137,145,162,181,202,214],"nontemplate":[24,70],"strand.":[25],"Here":[26],"we":[27],"describe":[28],"use":[30,122],"fluorescence":[32,131,139,153],"techniques":[33],"to":[34,106,187],"study":[35],"interaction":[37],"with":[41,180,194,201],"base.":[44],"Forked":[45],"templates":[47,124,185],"were":[48],"employed,":[49],"containing":[50,125],"fluorescent":[52],"base,":[53],"2-aminopurine":[54],"(2AP),":[55],"substituted":[56],"single-stranded":[63],"tail":[64],"comprising":[65],"nucleotides":[67],"on":[68,101],"strand":[71],"which":[73],"base":[74],"pairing":[75],"disrupted":[77],"an":[79,92,170],"polymerase-promoter":[81],"complex.":[82,173],"We":[83],"demonstrate":[84],"that":[85,158],"presence":[87,113,146],"2AP":[89,127,138,163],"instead":[90],"has":[97],"no":[98],"major":[99],"effect":[100],"accessibility":[103],"DNase":[107],"I":[108],"or":[109,114],"KMnO(4)":[110],"absence":[115],"polymerase,":[118],"thus":[119],"justifying":[120],"substitution":[128],"studies.":[132],"blue":[134],"shift":[135],"emission":[140],"maximum":[141],"observed":[143],"polymerase.":[149,196],"The":[150],"results":[151,198],"anisotropy":[154],"decay":[155],"studies":[156],"indicate":[157],"about":[159],"60%":[160],"residues":[164],"are":[167,199],"immobilized":[168],"This":[174],"value":[175],"good":[178],"agreement":[179],"fraction":[182],"2AP-substituted":[184],"determined":[186],"be":[188],"stable,":[191],"heparin-resistant":[192],"complex":[193],"These":[197],"consistent":[200],"being":[206],"tightly":[207],"bound":[208],"hydrophobic":[211],"pocket":[212],"enzyme.":[215]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2016-06-24T00:00:00"}