{"id":"https://openalex.org/W1972821677","doi":"https://doi.org/10.1080/07391102.1994.10508092","title":"Structure of Three-Way DNA Junctions. 2. Effects of Extra Bases and Mismatches","display_name":"Structure of Three-Way DNA Junctions. 2. Effects of Extra Bases and Mismatches","publication_year":1994,"publication_date":"1994-08-01","ids":{"openalex":"https://openalex.org/W1972821677","doi":"https://doi.org/10.1080/07391102.1994.10508092","mag":"1972821677","pmid":"https://pubmed.ncbi.nlm.nih.gov/7848563"},"language":"en","primary_location":{"id":"doi:10.1080/07391102.1994.10508092","doi":"https://doi.org/10.1080/07391102.1994.10508092","is_oa":false,"landing_page_url":"https://doi.org/10.1080/07391102.1994.10508092","pdf_url":null,"source":{"id":"https://openalex.org/S178711970","display_name":"Journal of Biomolecular Structure and Dynamics","issn_l":"0739-1102","issn":["0739-1102","1538-0254"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomolecular Structure and Dynamics","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/A5110809906","display_name":"Luda S. Shlyakhtenko","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Luda S. Shlyakhtenko","raw_affiliation_strings":["University of Nevada Reno","Department of Biochemistry , University of Nevada Reno , Reno , NY , 89557 , USA","Departments of Microbiology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Nevada Reno","institution_ids":["https://openalex.org/I134113660"]},{"raw_affiliation_string":"Department of Biochemistry , University of Nevada Reno , Reno , NY , 89557 , USA","institution_ids":["https://openalex.org/I134113660"]},{"raw_affiliation_string":"Departments of Microbiology","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036354240","display_name":"Ettore Appella","orcid":"https://orcid.org/0000-0003-0569-9722","observed_orcids":["https://orcid.org/0000-0003-0569-9722"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ettore Appella","raw_affiliation_strings":["National Cancer Institute","Laboratory of Cell Biology , National Cancer Institute , NIH, Bethesda , MD , 20892 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Cancer Institute","institution_ids":["https://openalex.org/I4210140884"]},{"raw_affiliation_string":"Laboratory of Cell Biology , National Cancer Institute , NIH, Bethesda , MD , 20892 , USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111380705","display_name":"Rodney E. Harrington","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rodney E. Harrington","raw_affiliation_strings":["University of Nevada Reno","Department of Biochemistry , University of Nevada Reno , Reno , NY , 89557 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Nevada Reno","institution_ids":["https://openalex.org/I134113660"]},{"raw_affiliation_string":"Department of Biochemistry , University of Nevada Reno , Reno , NY , 89557 , USA","institution_ids":["https://openalex.org/I134113660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049533479","display_name":"Igor V. Kutyavin","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210136386","display_name":"Microprobes (United States)","ror":"https://ror.org/03286xn88","country_code":"US","type":"company","lineage":["https://openalex.org/I4210136386"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Igor Kutyavin","raw_affiliation_strings":["MicroProbe Corp","MicroProbe Corp. , 1725 220th Street, SE#104, Bothell , WA , 98021 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MicroProbe Corp","institution_ids":["https://openalex.org/I4210136386"]},{"raw_affiliation_string":"MicroProbe Corp. , 1725 220th Street, SE#104, Bothell , WA , 98021 , USA","institution_ids":["https://openalex.org/I4210136386"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020066689","display_name":"Yuri L. Lyubchenko","orcid":"https://orcid.org/0000-0001-9721-8302","observed_orcids":["https://orcid.org/0000-0001-9721-8302"]},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuri L. Lyubchenko","raw_affiliation_strings":["Arizona State University","Departments of Microbiology","Physics , Arizona State University , Box 872701, Tempe , AZ , 85287-2701 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Arizona State University","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"Departments of Microbiology","institution_ids":[]},{"raw_affiliation_string":"Physics , Arizona State University , Box 872701, Tempe , AZ , 85287-2701 , USA","institution_ids":["https://openalex.org/I55732556"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6326,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.62784244,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"1","first_page":"131","last_page":"143"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9965999722480774,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9965999722480774,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.0017000000225380063,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.0003000000142492354,"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/three-way-dna-junctions","display_name":"DNA three-way junction","score":0.9860000014305115},{"id":"https://openalex.org/keywords/dna-hairpin","display_name":"DNA hairpins","score":0.675000011920929},{"id":"https://openalex.org/keywords/base-pair-mismatch","display_name":"mismatched base pairs","score":0.8199999928474426},{"id":"https://openalex.org/keywords/bulge","display_name":"bulge","score":0.7609999775886536},{"id":"https://openalex.org/keywords/dna-structure","display_name":"DNA structure","score":0.44999998807907104},{"id":"https://openalex.org/keywords/kink-angle","display_name":"kink angle","score":0.5339999794960022},{"id":"https://openalex.org/keywords/pyramid-structure","display_name":"pyramid structure","score":0.7739999890327454},{"id":"https://openalex.org/keywords/dna-flexibility","display_name":"DNA flexibility","score":0.5289999842643738},{"id":"https://openalex.org/keywords/cyclization","display_name":"cyclization","score":0.4830000102519989}],"concepts":[{"id":"https://openalex.org/C14103023","wikidata":"https://www.wikidata.org/wiki/Q11681459","display_name":"Pairing","level":3,"score":0.7737236618995667},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.6693928837776184},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.6509413123130798},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5539509057998657},{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.5464164614677429},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.5327455997467041},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.49707940220832825},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.4759383201599121},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.465782105922699},{"id":"https://openalex.org/C10767094","wikidata":"https://www.wikidata.org/wiki/Q854155","display_name":"Bulge","level":3,"score":0.46479931473731995},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.43903791904449463},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.4215964674949646},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4159257411956787},{"id":"https://openalex.org/C41999313","wikidata":"https://www.wikidata.org/wiki/Q489328","display_name":"Molecular physics","level":1,"score":0.4054659903049469},{"id":"https://openalex.org/C26873012","wikidata":"https://www.wikidata.org/wiki/Q214781","display_name":"Condensed matter physics","level":1,"score":0.24328500032424927},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19429117441177368},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17578789591789246},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.11861521005630493},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07871371507644653},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C98444146","wikidata":"https://www.wikidata.org/wiki/Q318","display_name":"Galaxy","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0},{"id":"https://openalex.org/C54101563","wikidata":"https://www.wikidata.org/wiki/Q124131","display_name":"Superconductivity","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004249","descriptor_name":"DNA Damage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004270","descriptor_name":"DNA, Circular","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1080/07391102.1994.10508092","doi":"https://doi.org/10.1080/07391102.1994.10508092","is_oa":false,"landing_page_url":"https://doi.org/10.1080/07391102.1994.10508092","pdf_url":null,"source":{"id":"https://openalex.org/S178711970","display_name":"Journal of Biomolecular Structure and Dynamics","issn_l":"0739-1102","issn":["0739-1102","1538-0254"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomolecular Structure and Dynamics","raw_type":"journal-article"},{"id":"pmid:7848563","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/7848563","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":"Journal of biomolecular structure & dynamics","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320337345","display_name":"Office of Naval Research","ror":"https://ror.org/00rk2pe57"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W81487621","https://openalex.org/W1597782075","https://openalex.org/W1973427350","https://openalex.org/W1981949351","https://openalex.org/W1994171119","https://openalex.org/W2004659412","https://openalex.org/W2013614046","https://openalex.org/W2016253703","https://openalex.org/W2019204592","https://openalex.org/W2019638764","https://openalex.org/W2019878495","https://openalex.org/W2050774163","https://openalex.org/W2058288282","https://openalex.org/W2084182950","https://openalex.org/W2085685468","https://openalex.org/W2088046080","https://openalex.org/W2134925793"],"related_works":["https://openalex.org/W2047926781","https://openalex.org/W2085685468","https://openalex.org/W4243281706","https://openalex.org/W1997506759","https://openalex.org/W1981949351","https://openalex.org/W1975692864","https://openalex.org/W4416340590","https://openalex.org/W2058288282","https://openalex.org/W2004659412","https://openalex.org/W2069158902"],"abstract_inverted_index":{"The":[0,74,115,127],"structure":[1,188],"of":[2,23,68,71,92,112,132,172,179,194],"three-way":[3,38,94,143],"DNA":[4,144],"junctions,":[5],"containing":[6,32,161],"two":[7,165],"linear":[8,102],"double":[9],"helices":[10],"(arms)":[11],"and":[12,42,60,88,135,164],"a":[13,16,24,150],"hairpin":[14,124],"as":[15],"third":[17,196],"arm,":[18],"was":[19,63],"studied":[20],"by":[21],"means":[22],"cyclization":[25],"technique.":[26],"In":[27],"addition":[28],"to":[29,139,191],"branched":[30],"molecules":[31],"perfect":[33],"base-pairing":[34],"in":[35,79],"helical":[36],"parts,":[37],"junctions":[39],"with":[40,146,153],"mismatches":[41,97],"extra":[43],"non-complementary":[44],"nucleotides":[45,148],"(bulges)":[46],"at":[47,57,122],"junction":[48,125,145,181],"points":[49],"were":[50,55],"studied.":[51],"Molecules":[52],"thus":[53],"designed":[54],"ligated":[56],"identical":[58],"conditions":[59],"their":[61],"geometry":[62,152,178],"compared":[64],"through":[65],"the":[66,69,86,93,99,106,110,113,123,142,162,195],"analysis":[67,75],"efficiency":[70],"circle":[72],"formation.":[73],"showed":[76],"that":[77,141,175],"irregularities":[78],"base":[80],"pairing":[81],"listed":[82],"above":[83],"dramatically":[84],"change":[85],"static":[87],"dynamic":[89],"structural":[90],"characteristics":[91],"junctions.":[95],"All":[96],"facilitate":[98],"kink":[100],"between":[101,159],"arms,":[103],"but":[104],"quantitatively,":[105],"effect":[107,116],"depends":[108],"on":[109],"position":[111],"mismatch.":[114],"is":[117,182],"maximal":[118],"for":[119,129],"GG-mismatch":[120],"placed":[121],"point.":[126],"results":[128],"bulges":[130],"are":[131],"different":[133],"kind,":[134],"they":[136],"lead":[137],"us":[138],"conclude":[140],"unpaired":[147],"adopts":[149],"T-like":[151],"an":[154],"angle":[155],"around":[156],"90":[157],"degrees":[158],"arms":[160,167],"bulge":[163],"other":[166],"coaxially":[168],"stacked.":[169],"Broad":[170],"distribution":[171],"circles":[173],"indicates":[174],"this":[176],"T-form":[177],"bulge-containing":[180],"more":[183],"flexible":[184],"than":[185],"initial":[186],"pyramidal":[187],"predominantly":[189],"due":[190],"high":[192],"mobility":[193],"arm.":[197]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
