{"id":"https://openalex.org/W4200225724","doi":"https://doi.org/10.3390/mps5010003","title":"A Proximity Ligation Method to Detect Proteins Bound to Single-Stranded DNA after DNA End Resection at DNA Double-Strand Breaks","display_name":"A Proximity Ligation Method to Detect Proteins Bound to Single-Stranded DNA after DNA End Resection at DNA Double-Strand Breaks","publication_year":2021,"publication_date":"2021-12-29","ids":{"openalex":"https://openalex.org/W4200225724","doi":"https://doi.org/10.3390/mps5010003","pmid":"https://pubmed.ncbi.nlm.nih.gov/35076555","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/8788478"},"language":"en","primary_location":{"id":"doi:10.3390/mps5010003","doi":"https://doi.org/10.3390/mps5010003","is_oa":true,"landing_page_url":"https://doi.org/10.3390/mps5010003","pdf_url":"https://www.mdpi.com/2409-9279/5/1/3/pdf?version=1640749964","source":{"id":"https://openalex.org/S4210221179","display_name":"Methods and Protocols","issn_l":"2409-9279","issn":["2409-9279"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-1","poland-20","russia-white-list-2"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods and Protocols","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2409-9279/5/1/3/pdf?version=1640749964","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044147790","display_name":"Faith C. Fowler","orcid":"https://orcid.org/0000-0002-7180-8141","observed_orcids":["https://orcid.org/0000-0002-7180-8141"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Faith C. Fowler","raw_affiliation_strings":["Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA","Department of Pharmacology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA"],"raw_orcid":"https://orcid.org/0000-0002-7180-8141","affiliations":[{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA","institution_ids":["https://openalex.org/I4387153466"]},{"raw_affiliation_string":"Department of Pharmacology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042369850","display_name":"Jessica K. Tyler","orcid":"https://orcid.org/0000-0001-9765-1659","observed_orcids":["https://orcid.org/0000-0001-9765-1659"]},"institutions":[{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jessica K. Tyler","raw_affiliation_strings":["Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA","institution_ids":["https://openalex.org/I4387153466"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5042369850"],"corresponding_institution_ids":["https://openalex.org/I4387153466"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1512},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1512},"fwci":0.0784,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.34465847,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"5","issue":"1","first_page":"3","last_page":"3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10123","display_name":"DNA Repair Mechanisms","score":0.9990000128746033,"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/T10123","display_name":"DNA Repair Mechanisms","score":0.9990000128746033,"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":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"}},{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","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/proximity-ligation-assay","display_name":"proximity ligation assay","score":0.949999988079071},{"id":"https://openalex.org/keywords/single-stranded-dna","display_name":"single-stranded DNA","score":0.984000027179718},{"id":"https://openalex.org/keywords/dna-double-strand-breaks","display_name":"DNA double-strand breaks","score":0.9079999923706055},{"id":"https://openalex.org/keywords/dna-end-resection","display_name":"DNA end resection","score":0.8349999785423279},{"id":"https://openalex.org/keywords/homologous-recombination","display_name":"homologous recombination","score":0.9700000286102295},{"id":"https://openalex.org/keywords/non-homologous-end-joining","display_name":"non-homologous end joining","score":0.968999981880188},{"id":"https://openalex.org/keywords/replication-protein-a","display_name":"replication protein A","score":0.9869999885559082},{"id":"https://openalex.org/keywords/single-stranded-dna-binding-protein","display_name":"single-stranded DNA binding protein","score":0.8220000267028809},{"id":"https://openalex.org/keywords/bromodeoxyuridine-incorporation","display_name":"bromodeoxyuridine incorporation","score":0.8740000128746033},{"id":"https://openalex.org/keywords/protein-dna-interactions","display_name":"protein-DNA interactions","score":0.6460000276565552},{"id":"https://openalex.org/keywords/dna-repair","display_name":"DNA repair","score":0.5249999761581421}],"concepts":[{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.6797980070114136},{"id":"https://openalex.org/C179437574","wikidata":"https://www.wikidata.org/wiki/Q15089798","display_name":"Ligation","level":2,"score":0.596813440322876},{"id":"https://openalex.org/C175114707","wikidata":"https://www.wikidata.org/wiki/Q408483","display_name":"DNA ligase","level":3,"score":0.5394959449768066},{"id":"https://openalex.org/C31254050","wikidata":"https://www.wikidata.org/wiki/Q22328799","display_name":"DNA clamp","level":5,"score":0.5322586894035339},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.4638175368309021},{"id":"https://openalex.org/C159110652","wikidata":"https://www.wikidata.org/wiki/Q17078201","display_name":"Resection","level":2,"score":0.41074612736701965},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3951818346977234},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3101499378681183},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2077455222606659},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.19816356897354126},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1594146192073822},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13115453720092773},{"id":"https://openalex.org/C141071460","wikidata":"https://www.wikidata.org/wiki/Q40821","display_name":"Surgery","level":1,"score":0.08610361814498901},{"id":"https://openalex.org/C156719811","wikidata":"https://www.wikidata.org/wiki/Q28774","display_name":"Reverse transcriptase","level":4,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3390/mps5010003","doi":"https://doi.org/10.3390/mps5010003","is_oa":true,"landing_page_url":"https://doi.org/10.3390/mps5010003","pdf_url":"https://www.mdpi.com/2409-9279/5/1/3/pdf?version=1640749964","source":{"id":"https://openalex.org/S4210221179","display_name":"Methods and Protocols","issn_l":"2409-9279","issn":["2409-9279"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-1","poland-20","russia-white-list-2"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods and Protocols","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8788478","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8788478","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods Protoc","raw_type":"Text"},{"id":"pmid:35076555","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35076555","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":"Methods and protocols","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:8172da726f6d41c3b549cb3f9d8af0d8","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/8172da726f6d41c3b549cb3f9d8af0d8","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Methods and Protocols, Vol 5, Iss 1, p 3 (2021)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3390/mps5010003","doi":"https://doi.org/10.3390/mps5010003","is_oa":true,"landing_page_url":"https://doi.org/10.3390/mps5010003","pdf_url":"https://www.mdpi.com/2409-9279/5/1/3/pdf?version=1640749964","source":{"id":"https://openalex.org/S4210221179","display_name":"Methods and Protocols","issn_l":"2409-9279","issn":["2409-9279"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-1","poland-20","russia-white-list-2"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods and Protocols","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G4376717398","display_name":"Chromatin Assembly Structure and Function","funder_award_id":"R01GM064475","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4380169263","display_name":"Chromatin's Role in Repair of Radiation-induced Damage","funder_award_id":"R01CA095641","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G9000919613","display_name":"Novel pathways that regulate DNA double-strand break repair events in mammalian cells","funder_award_id":"R35GM139816","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4200225724.pdf","grobid_xml":"https://content.openalex.org/works/W4200225724.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W335095904","https://openalex.org/W1979385111","https://openalex.org/W1993026474","https://openalex.org/W1994363917","https://openalex.org/W2021870890","https://openalex.org/W2050164609","https://openalex.org/W2052547134","https://openalex.org/W2091364606","https://openalex.org/W2094020226","https://openalex.org/W2119346494","https://openalex.org/W2124837740","https://openalex.org/W2130628767","https://openalex.org/W2131646714","https://openalex.org/W2135469496","https://openalex.org/W2138076097","https://openalex.org/W2139442812","https://openalex.org/W2145200068","https://openalex.org/W2169741450","https://openalex.org/W2495544654","https://openalex.org/W2558818939","https://openalex.org/W2594599258","https://openalex.org/W2620322469","https://openalex.org/W2801246231","https://openalex.org/W2883825889"],"related_works":["https://openalex.org/W7125634164","https://openalex.org/W3004441806","https://openalex.org/W1978183360","https://openalex.org/W3080163075","https://openalex.org/W3214907681","https://openalex.org/W2793424148","https://openalex.org/W335095904","https://openalex.org/W2073378063","https://openalex.org/W6966395255","https://openalex.org/W4386093750"],"abstract_inverted_index":{"After":[0],"a":[1,57,80,100],"DNA":[2,18,30,39,43,92,137],"double-strand":[3],"break,":[4],"cells":[5],"utilize":[6],"either":[7],"non-homologous":[8],"end":[9],"joining":[10],"or":[11],"homologous":[12],"recombination":[13,21],"to":[14,49,73,89,95],"repair":[15],"the":[16,29,51,97,152],"broken":[17],"ends.":[19],"Homologous":[20],"requires":[22],"extensive":[23],"nucleolytic":[24],"processing":[25],"of":[26,28,36,53,63,99,102,154],"one":[27,130],"strands,":[31],"resulting":[32],"in":[33,93],"long":[34],"stretches":[35],"3'":[37],"single-strand":[38],"overhangs.":[40],"Typically,":[41],"single-stranded":[42,58,75,91,105],"is":[44,109,117],"measured":[45],"using":[46,145],"immunofluorescence":[47],"microscopy":[48,126,147],"image":[50],"foci":[52,65,113,124],"replication":[54,155],"protein":[55,101,156],"A,":[56],"DNA-binding":[59],"protein.":[60],"Microscopy":[61],"analysis":[62,114],"bromodeoxyuridine":[64,87,159],"under":[66],"nondenaturing":[67],"conditions":[68],"has":[69],"also":[70],"been":[71],"used":[72],"measure":[74,96],"DNA.":[76,106],"Here,":[77],"we":[78],"describe":[79],"proximity":[81],"ligation":[82],"assay":[83],"which":[84],"uses":[85,128],"genome-wide":[86],"incorporation":[88],"label":[90],"order":[94],"association":[98,153],"interest":[103],"with":[104],"This":[107],"method":[108],"advantageous":[110],"over":[111],"traditional":[112,123,146],"because":[115],"it":[116],"more":[118],"direct":[119],"and":[120,133,142,158],"specific":[121],"than":[122],"co-localization":[125],"methods,":[127],"only":[129],"color":[131],"channel,":[132],"can":[134],"reveal":[135],"protein-single-stranded":[136],"interactions":[138],"that":[139],"are":[140],"rare":[141],"potentially":[143],"undetectable":[144],"methods.":[148],"We":[149],"show":[150],"here":[151],"A":[157],"as":[160],"proof-of-concept.":[161]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-10-30T12:39:25.321706","created_date":"2021-12-31T00:00:00"}