{"id":"https://openalex.org/W2082854559","doi":"https://doi.org/10.1093/nar/23.16.3231","title":"The secondary structure and sequence optimization of an RNA ligase ribozyme","display_name":"The secondary structure and sequence optimization of an RNA ligase ribozyme","publication_year":1995,"publication_date":"1995-01-01","ids":{"openalex":"https://openalex.org/W2082854559","doi":"https://doi.org/10.1093/nar/23.16.3231","mag":"2082854559","pmid":"https://pubmed.ncbi.nlm.nih.gov/7667099","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/307182"},"language":"en","primary_location":{"id":"doi:10.1093/nar/23.16.3231","doi":"https://doi.org/10.1093/nar/23.16.3231","is_oa":false,"landing_page_url":"https://doi.org/10.1093/nar/23.16.3231","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://europepmc.org/pmc/articles/PMC307182","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072154156","display_name":"Eric H. Ekland","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210157710","display_name":"Whitehead Institute for Biomedical Research","ror":"https://ror.org/04vqm6w82","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210157710","https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric H. Ekland","raw_affiliation_strings":["Whitehead Institute for Biomedical Research, Cambridge, MA 02114, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Whitehead Institute for Biomedical Research, Cambridge, MA 02114, USA","institution_ids":["https://openalex.org/I4210157710"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087589263","display_name":"David P. Bartel","orcid":"https://orcid.org/0000-0002-3872-2856","observed_orcids":["https://orcid.org/0000-0002-3872-2856"]},"institutions":[{"id":"https://openalex.org/I4210157710","display_name":"Whitehead Institute for Biomedical Research","ror":"https://ror.org/04vqm6w82","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210157710","https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David P. Bartel","raw_affiliation_strings":["Whitehead Institute for Biomedical Research Cambridge, MA 02114, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Whitehead Institute for Biomedical Research Cambridge, MA 02114, USA","institution_ids":["https://openalex.org/I4210157710"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5087589263"],"corresponding_institution_ids":["https://openalex.org/I4210157710"],"apc_list":{"value":3992,"currency":"USD","value_usd":3992},"apc_paid":null,"fwci":2.3536,"has_fulltext":false,"cited_by_count":127,"citation_normalized_percentile":{"value":0.8970646,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"16","first_page":"3231","last_page":"3238"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9887999892234802,"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":0.9887999892234802,"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":0.004100000020116568,"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/T12610","display_name":"RNA regulation and disease","score":0.0008999999845400453,"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/in-vitro-selection","display_name":"in vitro selection","score":0.8489999771118164},{"id":"https://openalex.org/keywords/sequence-optimization","display_name":"sequence optimization","score":0.6790000200271606},{"id":"https://openalex.org/keywords/mutagenesis","display_name":"mutagenesis","score":0.5860000252723694}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8801277875900269},{"id":"https://openalex.org/C76346623","wikidata":"https://www.wikidata.org/wiki/Q205858","display_name":"Ribozyme","level":4,"score":0.860346794128418},{"id":"https://openalex.org/C175114707","wikidata":"https://www.wikidata.org/wiki/Q408483","display_name":"DNA ligase","level":3,"score":0.7407243847846985},{"id":"https://openalex.org/C2909068217","wikidata":"https://www.wikidata.org/wiki/Q7277177","display_name":"RNA ligase","level":4,"score":0.6173990964889526},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5907155275344849},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5610198974609375},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5185583233833313},{"id":"https://openalex.org/C1342335","wikidata":"https://www.wikidata.org/wiki/Q6545871","display_name":"Ligase ribozyme","level":5,"score":0.47876158356666565},{"id":"https://openalex.org/C66144319","wikidata":"https://www.wikidata.org/wiki/Q7907583","display_name":"VS ribozyme","level":5,"score":0.456053227186203},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.4205944836139679},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.4125613570213318},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.20635157823562622},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.20136836171150208},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16875487565994263}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003001","descriptor_name":"Cloning, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":false},{"descriptor_ui":"D011130","descriptor_name":"RNA Ligase (ATP)","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011130","descriptor_name":"RNA Ligase (ATP)","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011130","descriptor_name":"RNA Ligase (ATP)","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/23.16.3231","doi":"https://doi.org/10.1093/nar/23.16.3231","is_oa":false,"landing_page_url":"https://doi.org/10.1093/nar/23.16.3231","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:293494","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC307182","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:307182","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/307182","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmid:7667099","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/7667099","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":"Nucleic acids research","raw_type":"Comparative Study"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.415.430","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.415.430","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bartellab.wi.mit.edu/publication_reprints/Ekland_NuclAcidRes95.pdf","raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:europepmc.org:293494","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC307182","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306159","display_name":"W. M. Keck Foundation","ror":"https://ror.org/000dswa46"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W52968187","https://openalex.org/W1481423171","https://openalex.org/W1975497731","https://openalex.org/W1978202265","https://openalex.org/W1980461160","https://openalex.org/W2000738377","https://openalex.org/W2009396937","https://openalex.org/W2012268010","https://openalex.org/W2022777131","https://openalex.org/W2035783320","https://openalex.org/W2036358440","https://openalex.org/W2051188149","https://openalex.org/W2072448837","https://openalex.org/W2079321730","https://openalex.org/W2095397952","https://openalex.org/W2098021908","https://openalex.org/W2098393725","https://openalex.org/W2142393243"],"related_works":["https://openalex.org/W2116074616","https://openalex.org/W2097739415","https://openalex.org/W2170105047","https://openalex.org/W226152574","https://openalex.org/W1984212913","https://openalex.org/W2102564025","https://openalex.org/W2098393725","https://openalex.org/W2004821539","https://openalex.org/W2068559091","https://openalex.org/W2098021908"],"abstract_inverted_index":{"In":[0],"vitro":[1,100],"selection":[2,101,122],"can":[3],"generate":[4],"functional":[5],"sequence":[6,106],"variants":[7,62,91],"of":[8,37,45,60,63,82,92,121,136,169,177,186,194],"an":[9,64,98],"RNA":[10,65],"structural":[11],"motif":[12],"that":[13,80,103,140,171],"are":[14],"useful":[15],"for":[16,173],"comparative":[17],"analysis.":[18],"The":[19],"technique":[20],"is":[21,29],"particularly":[22],"valuable":[23],"in":[24,99],"cases":[25],"where":[26],"natural":[27],"variation":[28],"unavailable":[30],"or":[31],"non-existent.":[32],"We":[33],"report":[34],"the":[35,83,105,113,131,137,146,167,174,178,195],"extension":[36],"this":[38,93],"approach":[39],"to":[40,112,126],"a":[41,46,54,149],"new":[42],"extreme--the":[43],"identification":[44],"112":[47],"nt":[48,56],"ribozyme":[49,67],"secondary":[50,153],"structure":[51,154],"imbedded":[52],"within":[53],"186":[55,84],"RNA.":[57],"A":[58],"pool":[59,94],"10(14)":[61],"ligase":[66,147,180,197],"was":[68],"generated":[69],"using":[70,97],"combinatorial":[71,76],"chemical":[72],"synthesis":[73],"coupled":[74],"with":[75,143,155],"enzymatic":[77],"ligation":[78,114],"such":[79],"172":[81],"relevant":[85],"positions":[86,109],"were":[87,95,189],"partially":[88],"mutagenized.":[89],"Active":[90],"enriched":[96],"scheme":[102],"retains":[104],"variability":[107],"at":[108],"very":[110],"close":[111],"junction.":[115],"Ligases":[116],"isolated":[117],"after":[118],"four":[119],"rounds":[120],"catalyzed":[123],"self-ligation":[124],"up":[125],"700":[127],"times":[128],"faster":[129],"than":[130,192],"starting":[132],"sequence.":[133],"Comparative":[134,163],"analysis":[135,164],"isolates":[138],"indicated":[139],"when":[141],"complexed":[142],"substrate":[144],"RNAs":[145],"forms":[148],"nested,":[150],"double":[151],"pseudo-knot":[152],"seven":[156],"stems":[157],"and":[158],"several":[159],"important":[160],"joining":[161],"segments.":[162],"also":[165],"suggested":[166],"identity":[168],"mutations":[170],"account":[172],"increased":[175],"activity":[176],"selected":[179],"variants;":[181],"designed":[182],"constructs":[183],"incorporating":[184],"combinations":[185],"these":[187],"changes":[188],"more":[190],"active":[191],"any":[193],"individual":[196],"isolates.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
