{"id":"https://openalex.org/W1994402652","doi":"https://doi.org/10.1021/nn900303g","title":"Mapping the Position of DNA Polymerase-Bound DNA Templates in a Nanopore at 5 \u00c5 Resolution","display_name":"Mapping the Position of DNA Polymerase-Bound DNA Templates in a Nanopore at 5 \u00c5 Resolution","publication_year":2009,"publication_date":"2009-06-02","ids":{"openalex":"https://openalex.org/W1994402652","doi":"https://doi.org/10.1021/nn900303g","mag":"1994402652","pmid":"https://pubmed.ncbi.nlm.nih.gov/19489560"},"language":"en","primary_location":{"id":"doi:10.1021/nn900303g","doi":"https://doi.org/10.1021/nn900303g","is_oa":false,"landing_page_url":"https://doi.org/10.1021/nn900303g","pdf_url":null,"source":{"id":"https://openalex.org/S145476921","display_name":"ACS Nano","issn_l":"1936-0851","issn":["1936-0851","1936-086X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"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":"ACS Nano","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"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/A5084612781","display_name":"Brett Gyarfas","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brett Gyarfas","raw_affiliation_strings":["Department of Computer Engineering","Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085453498","display_name":"Felix Olasagasti","orcid":"https://orcid.org/0000-0002-2714-3568","observed_orcids":["https://orcid.org/0000-0002-2714-3568"]},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Felix Olasagasti","raw_affiliation_strings":["Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053753721","display_name":"Seico Benner","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Seico Benner","raw_affiliation_strings":["Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083172087","display_name":"Daniel R. Garalde","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Daniel Garalde","raw_affiliation_strings":["Department of Computer Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110043724","display_name":"Kate R. Lieberman","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kate R. Lieberman","raw_affiliation_strings":["Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012942178","display_name":"Mark A. Akeson","orcid":"https://orcid.org/0000-0001-9392-8075","observed_orcids":["https://orcid.org/0000-0001-9392-8075"]},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark Akeson","raw_affiliation_strings":["Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064","institution_ids":["https://openalex.org/I185103710"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5012942178"],"corresponding_institution_ids":["https://openalex.org/I185103710"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":3.8402,"has_fulltext":false,"cited_by_count":56,"citation_normalized_percentile":{"value":0.9306641,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"3","issue":"6","first_page":"1457","last_page":"1466"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10923","display_name":"Force Microscopy Techniques and Applications","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical 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"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-polymerase","display_name":"DNA polymerase","score":0.9789999723434448},{"id":"https://openalex.org/keywords/alpha-hemolysin-nanopore","display_name":"\u03b1-hemolysin nanopore","score":0.9269999861717224},{"id":"https://openalex.org/keywords/klenow-fragment","display_name":"Klenow fragment","score":0.7720000147819519},{"id":"https://openalex.org/keywords/escherichia-coli-dna-polymerase-i","display_name":"Escherichia coli DNA polymerase I","score":0.9570000171661377},{"id":"https://openalex.org/keywords/dna-replication","display_name":"DNA replication","score":0.4490000009536743},{"id":"https://openalex.org/keywords/primer-extension","display_name":"primer extension","score":0.7739999890327454}],"concepts":[{"id":"https://openalex.org/C2756471","wikidata":"https://www.wikidata.org/wiki/Q206286","display_name":"DNA polymerase","level":3,"score":0.6720856428146362},{"id":"https://openalex.org/C150777479","wikidata":"https://www.wikidata.org/wiki/Q176783","display_name":"AP site","level":4,"score":0.6636406183242798},{"id":"https://openalex.org/C31254050","wikidata":"https://www.wikidata.org/wiki/Q22328799","display_name":"DNA clamp","level":5,"score":0.6496851444244385},{"id":"https://openalex.org/C164965036","wikidata":"https://www.wikidata.org/wiki/Q2529148","display_name":"DNA polymerase I","level":5,"score":0.6158367395401001},{"id":"https://openalex.org/C88354546","wikidata":"https://www.wikidata.org/wiki/Q3502973","display_name":"DNA polymerase II","level":5,"score":0.6113044619560242},{"id":"https://openalex.org/C82381507","wikidata":"https://www.wikidata.org/wiki/Q416878","display_name":"Polymerase","level":3,"score":0.5379972457885742},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5053558945655823},{"id":"https://openalex.org/C73573662","wikidata":"https://www.wikidata.org/wiki/Q130996","display_name":"DNA replication","level":3,"score":0.4760196805000305},{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.4521106779575348},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4176103174686432},{"id":"https://openalex.org/C194830204","wikidata":"https://www.wikidata.org/wiki/Q106940703","display_name":"Primase","level":5,"score":0.41297605633735657},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3787904977798462},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3672780394554138},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3490105867385864},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.3382658362388611},{"id":"https://openalex.org/C134935766","wikidata":"https://www.wikidata.org/wiki/Q210538","display_name":"DNA repair","level":3,"score":0.20628896355628967},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.15228605270385742},{"id":"https://openalex.org/C156719811","wikidata":"https://www.wikidata.org/wiki/Q28774","display_name":"Reverse transcriptase","level":4,"score":0.10725241899490356},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06067743897438049},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004259","descriptor_name":"DNA-Directed DNA Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013698","descriptor_name":"Templates, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049329","descriptor_name":"Nanostructures","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/nn900303g","doi":"https://doi.org/10.1021/nn900303g","is_oa":false,"landing_page_url":"https://doi.org/10.1021/nn900303g","pdf_url":null,"source":{"id":"https://openalex.org/S145476921","display_name":"ACS Nano","issn_l":"1936-0851","issn":["1936-0851","1936-086X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"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":"ACS Nano","raw_type":"journal-article"},{"id":"pmid:19489560","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19489560","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":"ACS nano","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G6906972668","display_name":"UCSC Center for Genomic Science and Minority Outreach Program","funder_award_id":"P41HG002371","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337367","display_name":"Division of Materials Research","ror":"https://ror.org/01pc7k308"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1481296411","https://openalex.org/W1493170168","https://openalex.org/W1520835950","https://openalex.org/W1546917481","https://openalex.org/W1592730805","https://openalex.org/W1968034613","https://openalex.org/W1971212710","https://openalex.org/W1986594702","https://openalex.org/W1990083018","https://openalex.org/W1991853276","https://openalex.org/W1994660369","https://openalex.org/W1999052302","https://openalex.org/W2018872766","https://openalex.org/W2030683115","https://openalex.org/W2056386145","https://openalex.org/W2069352337","https://openalex.org/W2070764974","https://openalex.org/W2078442842","https://openalex.org/W2089898350","https://openalex.org/W2095898308","https://openalex.org/W2111400509","https://openalex.org/W2113231874","https://openalex.org/W2124729483","https://openalex.org/W2125021618","https://openalex.org/W2127407003","https://openalex.org/W2138270253","https://openalex.org/W2149410625","https://openalex.org/W2163043365"],"related_works":["https://openalex.org/W2015375243","https://openalex.org/W1994660369","https://openalex.org/W2070764974","https://openalex.org/W2335692051","https://openalex.org/W2056386145","https://openalex.org/W7097086600","https://openalex.org/W2934056906","https://openalex.org/W1976275264","https://openalex.org/W2078884016","https://openalex.org/W4280525998"],"abstract_inverted_index":{"DNA":[0,8,13,45,61,69,160,168,245,266],"polymerases":[1],"are":[2,178],"molecular":[3],"motors":[4],"that":[5,108,211,257],"catalyze":[6],"template-dependent":[7],"replication,":[9],"advancing":[10],"along":[11],"template":[12,189],"by":[14,111,183],"one":[15],"nucleotide":[16],"with":[17,208,233,239,261],"each":[18],"catalytic":[19],"cycle.":[20],"Nanopore-based":[21],"measurements":[22],"have":[23],"emerged":[24],"as":[25,120],"a":[26,86,98,121,148,186,194,203,240],"single":[27,149],"molecule":[28],"technique":[29],"for":[30,91],"the":[31,37,42,55,116,124,127,135,139,143,156,159,163,167,171,174,191,223,230,252,262,275],"study":[32],"of":[33,44,49,58,72,88,100,104,123,126,138,173,193,196,205,225,243,259],"these":[34],"enzymes.":[35,249],"Using":[36],"alpha-hemolysin":[38],"nanopore,":[39],"we":[40],"determined":[41],"position":[43],"templates":[46,101,254],"bearing":[47,102],"inserts":[48],"abasic":[50,106,128,164,188,253],"(1',2'-dideoxy)":[51],"residues,":[52],"bound":[53],"to":[54,66,214,255],"Klenow":[56],"fragment":[57],"Escherichia":[59],"coli":[60],"polymerase":[62,74],"I":[63],"(KF)":[64],"or":[65],"bacteriophage":[67],"T7":[68,265],"polymerase.":[70],"Hundreds":[71],"individual":[73],"complexes":[75,207,260],"were":[76,109],"analyzed":[77],"at":[78],"5":[79,113],"A":[80,114],"precision":[81],"within":[82],"minutes.":[83],"We":[84,250],"generated":[85],"map":[87,146,152,220,231,271],"current":[89,219],"amplitudes":[90,210],"DNA-KF-deoxynucleoside":[92],"triphosphate":[93],"(dNTP)":[94],"ternary":[95,206],"complexes,":[96],"using":[97,185],"series":[99],"blocks":[103],"three":[105,187],"residues":[107],"displaced":[110],"approximately":[112],"in":[115,134,170,190,202,222],"nanopore":[117],"lumen.":[118],"Plotted":[119],"function":[122],"distance":[125],"insert":[129],"from":[130,274],"n":[131],"=":[132],"0":[133],"active":[136,176],"site":[137,177],"enzyme":[140],"held":[141],"atop":[142],"pore,":[144],"this":[145,215],"has":[147],"peak.":[150],"The":[151],"is":[153],"similar":[154],"when":[155],"primer":[157],"length,":[158],"sequences":[161,169],"flanking":[162],"insert,":[165],"and":[166,198,246],"vicinity":[172],"KF":[175,184,263,276],"varied.":[179],"Primer":[180],"extension":[181],"catalyzed":[182],"presence":[192,224],"mixture":[195],"dNTPs":[197],"2',3'-dideoxynucleoside":[199],"triphosphates":[200],"resulted":[201],"ladder":[204],"discrete":[209],"closely":[212],"corresponded":[213],"map.":[216,277],"An":[217],"ionic":[218],"measured":[221],"0.15":[226],"M":[227,235],"KCl":[228],"mirrored":[229],"obtained":[232],"0.3":[234],"KCl,":[236],"permitting":[237],"experiments":[238],"broader":[241],"range":[242],"mesophilic":[244],"RNA":[247],"processing":[248],"used":[251],"show":[256],"capture":[258],"homologue,":[264],"polymerase,":[267],"yields":[268],"an":[269],"amplitude":[270],"nearly":[272],"indistinguishable":[273]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":12}],"updated_date":"2026-11-05T12:25:35.769452","created_date":"2016-06-24T00:00:00"}