{"id":"https://openalex.org/W4200192541","doi":"https://doi.org/10.3791/51667-v","title":"Studying DNA Looping by Single-Molecule FRET","display_name":"Studying DNA Looping by Single-Molecule FRET","publication_year":2014,"publication_date":"2014-06-28","ids":{"openalex":"https://openalex.org/W4200192541","doi":"https://doi.org/10.3791/51667-v"},"language":"en","primary_location":{"id":"doi:10.3791/51667-v","doi":"https://doi.org/10.3791/51667-v","is_oa":false,"landing_page_url":"https://doi.org/10.3791/51667-v","pdf_url":null,"source":{"id":"https://openalex.org/S199738284","display_name":"Journal of Visualized Experiments","issn_l":"1940-087X","issn":["1940-087X","2834-8400"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1"],"host_organization":"https://openalex.org/P4310320416","host_organization_name":"MyJOVE","host_organization_lineage":["https://openalex.org/P4310320416"],"host_organization_lineage_names":["MyJOVE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Visualized Experiments","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref"],"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/A5058447016","display_name":"Tung T. Le","orcid":"https://orcid.org/0000-0002-5481-4080","observed_orcids":["https://orcid.org/0000-0002-5481-4080"]},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tung T. Le","raw_affiliation_strings":["School of Physics, Georgia Institute of Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physics, Georgia Institute of Technology","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067992520","display_name":"Harold D. Kim","orcid":"https://orcid.org/0000-0003-0878-2169","observed_orcids":["https://orcid.org/0000-0003-0878-2169"]},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Harold D. Kim","raw_affiliation_strings":["School of Physics, Georgia Institute of Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physics, Georgia Institute of Technology","institution_ids":["https://openalex.org/I130701444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I130701444"],"apc_list":null,"apc_paid":null,"fwci":0.2442,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.56170441,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":null,"issue":"88","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.6967999935150146,"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":0.6967999935150146,"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/T13187","display_name":"Diffusion and Search Dynamics","score":0.24690000712871552,"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":0.03739999979734421,"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/dna-looping","display_name":"DNA looping","score":0.8790000081062317},{"id":"https://openalex.org/keywords/single-molecule-fret","display_name":"single-molecule FRET","score":0.8659999966621399},{"id":"https://openalex.org/keywords/j-factor","display_name":"J-factor","score":0.703000009059906},{"id":"https://openalex.org/keywords/protein-dna-recognition","display_name":"protein-DNA recognition","score":0.6600000262260437},{"id":"https://openalex.org/keywords/dna-ligation","display_name":"DNA ligation","score":0.4320000112056732},{"id":"https://openalex.org/keywords/annealing-rate","display_name":"annealing rate","score":0.6510000228881836}],"concepts":[{"id":"https://openalex.org/C96305047","wikidata":"https://www.wikidata.org/wiki/Q367473","display_name":"F\u00f6rster resonance energy transfer","level":3,"score":0.8404890298843384},{"id":"https://openalex.org/C175114707","wikidata":"https://www.wikidata.org/wiki/Q408483","display_name":"DNA ligase","level":3,"score":0.8207945823669434},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.6498494744300842},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.6071505546569824},{"id":"https://openalex.org/C2781455991","wikidata":"https://www.wikidata.org/wiki/Q7523749","display_name":"Single-molecule FRET","level":4,"score":0.49172738194465637},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4865838289260864},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.41216713190078735},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30649644136428833},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.28554296493530273},{"id":"https://openalex.org/C91881484","wikidata":"https://www.wikidata.org/wiki/Q191807","display_name":"Fluorescence","level":2,"score":0.23150137066841125},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.20148375630378723},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.19759243726730347},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3791/51667-v","doi":"https://doi.org/10.3791/51667-v","is_oa":false,"landing_page_url":"https://doi.org/10.3791/51667-v","pdf_url":null,"source":{"id":"https://openalex.org/S199738284","display_name":"Journal of Visualized Experiments","issn_l":"1940-087X","issn":["1940-087X","2834-8400"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1"],"host_organization":"https://openalex.org/P4310320416","host_organization_name":"MyJOVE","host_organization_lineage":["https://openalex.org/P4310320416"],"host_organization_lineage_names":["MyJOVE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Visualized Experiments","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8700000047683716}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1986456770","https://openalex.org/W2029225224","https://openalex.org/W3092729883","https://openalex.org/W2554152821","https://openalex.org/W2762028981","https://openalex.org/W29063239","https://openalex.org/W1967654345","https://openalex.org/W2418246707","https://openalex.org/W4214637218","https://openalex.org/W1560296431"],"abstract_inverted_index":{"Bending":[0],"of":[1,22,44,172],"double-stranded":[2],"DNA":[3,17,36,66,102],"(dsDNA)":[4],"is":[5,137,166],"associated":[6],"with":[7,120,156],"many":[8,54],"important":[9],"biological":[10],"processes":[11],"such":[12,63,84],"as":[13,64,85,133],"DNA-protein":[14],"recognition":[15],"and":[16,73,124,143],"packaging":[18],"into":[19],"nucleosomes.":[20],"Thermodynamics":[21],"dsDNA":[23,61,94,111],"bending":[24],"has":[25],"been":[26],"studied":[27],"by":[28,53,99,105],"a":[29,45,116,121,125],"method":[30],"called":[31],"cyclization":[32],"which":[33],"relies":[34],"on":[35],"ligase":[37,74,98],"to":[38,60,92,168],"covalently":[39],"join":[40],"short":[41],"sticky":[42,71,150],"ends":[43],"dsDNA.":[46,174],"However,":[47],"ligation":[48],"efficiency":[49],"can":[50,75],"be":[51],"affected":[52],"factors":[55],"that":[56,162],"are":[57,113],"not":[58],"related":[59],"looping":[62,80,95,129,141],"the":[65,69,78,134,140,144,163,169,173],"structure":[67],"surrounding":[68],"joined":[70],"ends,":[72],"also":[76],"affect":[77],"apparent":[79],"rate":[81,142,146],"through":[82],"mechanisms":[83],"nonspecific":[86],"binding.":[87],"Here,":[88],"we":[89,160],"show":[90,161],"how":[91],"measure":[93],"kinetics":[96],"without":[97],"detecting":[100],"transient":[101],"loop":[103],"formation":[104],"FRET":[106,122],"(Fluorescence":[107],"Resonance":[108],"Energy":[109],"Transfer).":[110],"molecules":[112],"constructed":[114],"using":[115],"simple":[117],"PCR-based":[118],"protocol":[119],"pair":[123],"biotin":[126],"linker.":[127],"The":[128],"probability":[130],"density":[131],"known":[132],"J":[135,164],"factor":[136,165],"extracted":[138],"from":[139],"annealing":[145],"between":[147],"two":[148,154],"disconnected":[149],"ends.":[151],"By":[152],"testing":[153],"dsDNAs":[155],"different":[157],"intrinsic":[158,170],"curvatures,":[159],"sensitive":[167],"shape":[171]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-09-29T14:09:16.559479","created_date":"2025-10-10T00:00:00"}