{"id":"https://openalex.org/W2080368679","doi":"https://doi.org/10.1021/bi010489o","title":"Thermodynamic Stabilities of Internal Loops with GU Closing Pairs in RNA","display_name":"Thermodynamic Stabilities of Internal Loops with GU Closing Pairs in RNA","publication_year":2001,"publication_date":"2001-08-30","ids":{"openalex":"https://openalex.org/W2080368679","doi":"https://doi.org/10.1021/bi010489o","mag":"2080368679","pmid":"https://pubmed.ncbi.nlm.nih.gov/11560499"},"language":"en","primary_location":{"id":"doi:10.1021/bi010489o","doi":"https://doi.org/10.1021/bi010489o","is_oa":false,"landing_page_url":"https://doi.org/10.1021/bi010489o","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","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/A5039675671","display_name":"Susan J. Schroeder","orcid":"https://orcid.org/0000-0003-4755-2294","observed_orcids":["https://orcid.org/0000-0003-4755-2294"]},"institutions":[{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Susan J. Schroeder","raw_affiliation_strings":["Department of Chemistry, RC Box 270216, University of Rochester, Rochester, New York 14627-0216","Department of Chemistry, RC Box 270216, University of Rochester, Rochester, New York 14627-0216, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, RC Box 270216, University of Rochester, Rochester, New York 14627-0216","institution_ids":["https://openalex.org/I5388228"]},{"raw_affiliation_string":"Department of Chemistry, RC Box 270216, University of Rochester, Rochester, New York 14627-0216, USA","institution_ids":["https://openalex.org/I5388228"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013801926","display_name":"Douglas H. Turner","orcid":"https://orcid.org/0000-0003-3853-8271","observed_orcids":["https://orcid.org/0000-0003-3853-8271"]},"institutions":[{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Douglas H. Turner","raw_affiliation_strings":["Department of Chemistry, RC Box 270216, University of Rochester, Rochester, New York 14627-0216"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, RC Box 270216, University of Rochester, Rochester, New York 14627-0216","institution_ids":["https://openalex.org/I5388228"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5013801926"],"corresponding_institution_ids":["https://openalex.org/I5388228"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":0.4655,"has_fulltext":false,"cited_by_count":41,"citation_normalized_percentile":{"value":0.6038238,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":"40","issue":"38","first_page":"11509","last_page":"11517"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9765999913215637,"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"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9765999913215637,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.023000000044703484,"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/T10604","display_name":"RNA Research and Splicing","score":9.999999747378752e-05,"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/thermodynamic-stability","display_name":"thermodynamic stability","score":0.8830000162124634},{"id":"https://openalex.org/keywords/rna-tertiary-structure","display_name":"RNA tertiary structure","score":0.6909999847412109},{"id":"https://openalex.org/keywords/group-i-introns","display_name":"group I introns","score":0.7630000114440918},{"id":"https://openalex.org/keywords/hydrogen-bonding","display_name":"hydrogen bonding","score":0.7200000286102295},{"id":"https://openalex.org/keywords/rna-folding","display_name":"RNA folding","score":0.3330000042915344}],"concepts":[{"id":"https://openalex.org/C2778775528","wikidata":"https://www.wikidata.org/wiki/Q5135432","display_name":"Closing (real estate)","level":2,"score":0.6893742084503174},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5812803506851196},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.5492945313453674},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.44326362013816833},{"id":"https://openalex.org/C66974803","wikidata":"https://www.wikidata.org/wiki/Q10359898","display_name":"Nuclear magnetic resonance spectroscopy","level":2,"score":0.4323121905326843},{"id":"https://openalex.org/C103319777","wikidata":"https://www.wikidata.org/wiki/Q1979695","display_name":"Proton NMR","level":2,"score":0.4151785373687744},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006147","descriptor_name":"Guanine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009691","descriptor_name":"Nucleic Acid Denaturation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009843","descriptor_name":"Oligoribonucleotides","qualifier_ui":"Q000138","qualifier_name":"chemical synthesis","is_major_topic":false},{"descriptor_ui":"D009843","descriptor_name":"Oligoribonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014498","descriptor_name":"Uracil","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019906","descriptor_name":"Nuclear Magnetic Resonance, Biomolecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/bi010489o","doi":"https://doi.org/10.1021/bi010489o","is_oa":false,"landing_page_url":"https://doi.org/10.1021/bi010489o","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:11560499","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11560499","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":[],"sustainable_development_goals_aurora":[{"id":"https://metadata.un.org/sdg/7","score":0.699999988079071,"display_name":"Affordable and clean energy"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1563343907","display_name":null,"funder_award_id":"GM 22939","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6840855294","display_name":"Folding RNA: from Aids to the Human Genome","funder_award_id":"R01GM022939","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":21,"referenced_works":["https://openalex.org/W1525024558","https://openalex.org/W1965715702","https://openalex.org/W1985775264","https://openalex.org/W1990275895","https://openalex.org/W2009818318","https://openalex.org/W2016791718","https://openalex.org/W2019684102","https://openalex.org/W2040015982","https://openalex.org/W2053984304","https://openalex.org/W2054245944","https://openalex.org/W2060993373","https://openalex.org/W2064580019","https://openalex.org/W2087721492","https://openalex.org/W2123241418","https://openalex.org/W2124162379","https://openalex.org/W2144907241","https://openalex.org/W2154684482","https://openalex.org/W2159801888","https://openalex.org/W2400907483","https://openalex.org/W2763755907","https://openalex.org/W4298155443"],"related_works":["https://openalex.org/W2794076229","https://openalex.org/W2004116872","https://openalex.org/W1985296775","https://openalex.org/W2116156624","https://openalex.org/W2089243730","https://openalex.org/W2037329261","https://openalex.org/W3200923628","https://openalex.org/W2321025843","https://openalex.org/W2022187415","https://openalex.org/W2062562045"],"abstract_inverted_index":{"Many":[0],"internal":[1,32,53,77,106],"loops":[2,33,54,78,87,107,118],"that":[3,135],"form":[4,145],"tertiary":[5,47],"contacts":[6],"in":[7,24],"natural":[8],"RNAs":[9],"have":[10],"GU":[11,35,56,80,113,141],"closing":[12,36,57,81,90,114,121,142],"pairs;":[13],"examples":[14],"include":[15],"the":[16,41,100],"tetraloop":[17],"receptor":[18],"and":[19,46,68,130],"P1":[20],"helix":[21],"docking":[22],"site":[23],"group":[25],"I":[26],"introns.":[27],"Thus,":[28],"thermodynamic":[29,73],"parameters":[30],"of":[31,43,75,86,108],"with":[34,55,79,88,112,119],"pairs":[37,58,82,91,111,115,122,138,143],"can":[38],"contribute":[39],"to":[40,84,117,140],"prediction":[42],"both":[44],"secondary":[45],"structure.":[48],"Oligoribonucleotide":[49],"duplexes":[50],"containing":[51],"small":[52],"were":[59],"studied":[60],"by":[61,95],"optical":[62],"melting,":[63],"one-dimensional":[64,69],"imino":[65],"proton":[66,129],"NMR,":[67],"phosphorus":[70,131],"NMR.":[71],"The":[72],"stabilities":[74],"asymmetric":[76],"relative":[83,116],"those":[85],"GC":[89,120],"may":[92,144],"be":[93],"explained":[94],"hydrogen":[96],"bonds.":[97],"In":[98],"contrast,":[99],"free":[101],"energy":[102],"increments":[103],"for":[104],"symmetric":[105],"two":[109],"noncanonical":[110],"show":[123],"much":[124],"more":[125],"sequence":[126],"dependence.":[127],"Imino":[128],"NMR":[132],"spectra":[133],"suggest":[134],"some":[136],"GA":[137],"adjacent":[139],"an":[146],"overall":[147],"thermodynamically":[148],"stable":[149],"but":[150],"non-A-form":[151],"conformation.":[152]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
