{"id":"https://openalex.org/W2053551490","doi":"https://doi.org/10.1002/bip.10263","title":"Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants","display_name":"Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants","publication_year":2002,"publication_date":"2002-11-25","ids":{"openalex":"https://openalex.org/W2053551490","doi":"https://doi.org/10.1002/bip.10263","mag":"2053551490","pmid":"https://pubmed.ncbi.nlm.nih.gov/12579576"},"language":"en","primary_location":{"id":"doi:10.1002/bip.10263","doi":"https://doi.org/10.1002/bip.10263","is_oa":false,"landing_page_url":"https://doi.org/10.1002/bip.10263","pdf_url":null,"source":{"id":"https://openalex.org/S56808608","display_name":"Biopolymers","issn_l":"0006-3525","issn":["0006-3525","1097-0282"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biopolymers","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/A5032689264","display_name":"Haribabu Arthanari","orcid":"https://orcid.org/0000-0002-7281-1289","observed_orcids":["https://orcid.org/0000-0002-7281-1289"]},"institutions":[{"id":"https://openalex.org/I100538780","display_name":"Wesleyan University","ror":"https://ror.org/05h7xva58","country_code":"US","type":"education","lineage":["https://openalex.org/I100538780"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haribabu Arthanari","raw_affiliation_strings":["Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA","Department of Chemistry, and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA","institution_ids":["https://openalex.org/I100538780"]},{"raw_affiliation_string":"Department of Chemistry, and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459","institution_ids":["https://openalex.org/I100538780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046959420","display_name":"Kevin J. McConnell","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kevin J. McConnell","raw_affiliation_strings":["Agilix Corporation, P. O. Box 8175, New Haven, CT 06530"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Agilix Corporation, P. O. Box 8175, New Haven, CT 06530","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091129321","display_name":"Richard D. Beger","orcid":"https://orcid.org/0000-0003-4380-2356","observed_orcids":["https://orcid.org/0000-0003-4380-2356"]},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard Beger","raw_affiliation_strings":["Division of Chemistry, National Center for Toxicological Research U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079-9502"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Chemistry, National Center for Toxicological Research U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079-9502","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003090892","display_name":"Matthew Adam Young","orcid":"https://orcid.org/0000-0003-2921-3432","observed_orcids":["https://orcid.org/0000-0003-2921-3432"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew A. Young","raw_affiliation_strings":["Department of Molecular and Cell Biology, 401 BARKER MC 3202, University of California, Berkeley, CA 94720-3202"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Cell Biology, 401 BARKER MC 3202, University of California, Berkeley, CA 94720-3202","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108221991","display_name":"D. L. Beveridge","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I100538780","display_name":"Wesleyan University","ror":"https://ror.org/05h7xva58","country_code":"US","type":"education","lineage":["https://openalex.org/I100538780"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"D. L. Beveridge","raw_affiliation_strings":["Department of Chemistry, and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459","institution_ids":["https://openalex.org/I100538780"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110055913","display_name":"Philip H. Bolton","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I100538780","display_name":"Wesleyan University","ror":"https://ror.org/05h7xva58","country_code":"US","type":"education","lineage":["https://openalex.org/I100538780"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Philip H. Bolton","raw_affiliation_strings":["Department of Chemistry, and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459","institution_ids":["https://openalex.org/I100538780"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5108221991","https://openalex.org/A5110055913"],"corresponding_institution_ids":["https://openalex.org/I100538780"],"apc_list":{"value":4150,"currency":"USD","value_usd":4150},"apc_paid":null,"fwci":1.844,"has_fulltext":false,"cited_by_count":37,"citation_normalized_percentile":{"value":0.84608907,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"68","issue":"1","first_page":"3","last_page":"15"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.8895999789237976,"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":0.8895999789237976,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.09200000017881393,"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/T11809","display_name":"Advanced NMR Techniques and Applications","score":0.00419999985024333,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-solution-structure","display_name":"DNA solution structure","score":0.7850000262260437},{"id":"https://openalex.org/keywords/oligonucleotide-duplexes","display_name":"oligonucleotide duplexes","score":0.8320000171661377},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"dihedral angle","score":0.8899999856948853},{"id":"https://openalex.org/keywords/spin-spin-coupling-constants","display_name":"spin-spin coupling constants","score":0.9829999804496765},{"id":"https://openalex.org/keywords/amber-force-field","display_name":"AMBER force field","score":0.8989999890327454},{"id":"https://openalex.org/keywords/dipolar-coupling","display_name":"dipolar coupling","score":0.6330000162124634},{"id":"https://openalex.org/keywords/nucleic-acid-conformation","display_name":"nucleic acid conformation","score":0.5640000104904175}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.8638674020767212},{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.6460701823234558},{"id":"https://openalex.org/C19549132","wikidata":"https://www.wikidata.org/wiki/Q11141463","display_name":"Two-dimensional nuclear magnetic resonance spectroscopy","level":2,"score":0.6290416121482849},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6041556000709534},{"id":"https://openalex.org/C66974803","wikidata":"https://www.wikidata.org/wiki/Q10359898","display_name":"Nuclear magnetic resonance spectroscopy","level":2,"score":0.6040344834327698},{"id":"https://openalex.org/C140463767","wikidata":"https://www.wikidata.org/wiki/Q4391036","display_name":"J-coupling","level":3,"score":0.5650659799575806},{"id":"https://openalex.org/C122707536","wikidata":"https://www.wikidata.org/wiki/Q7068137","display_name":"Nuclear magnetic resonance spectroscopy of nucleic acids","level":5,"score":0.533928394317627},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.4996664524078369},{"id":"https://openalex.org/C119851462","wikidata":"https://www.wikidata.org/wiki/Q901095","display_name":"Nuclear Overhauser effect","level":3,"score":0.4326731264591217},{"id":"https://openalex.org/C67787023","wikidata":"https://www.wikidata.org/wiki/Q6954755","display_name":"NMR spectra database","level":3,"score":0.42792263627052307},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.42303991317749023},{"id":"https://openalex.org/C100705429","wikidata":"https://www.wikidata.org/wiki/Q5037892","display_name":"Carbon-13 NMR satellite","level":4,"score":0.4106544852256775},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.38895389437675476},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3097301721572876},{"id":"https://openalex.org/C4839761","wikidata":"https://www.wikidata.org/wiki/Q212111","display_name":"Spectral line","level":2,"score":0.2695232927799225},{"id":"https://openalex.org/C116447816","wikidata":"https://www.wikidata.org/wiki/Q3415253","display_name":"Fluorine-19 NMR","level":3,"score":0.26263880729675293},{"id":"https://openalex.org/C205860874","wikidata":"https://www.wikidata.org/wiki/Q7835448","display_name":"Transverse relaxation-optimized spectroscopy","level":4,"score":0.2518683075904846},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.24422675371170044},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.11066344380378723},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0879141092300415},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08698692917823792},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0556463897228241}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003460","descriptor_name":"Crystallization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":true},{"descriptor_ui":"D012996","descriptor_name":"Solutions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019906","descriptor_name":"Nuclear Magnetic Resonance, Biomolecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1002/bip.10263","doi":"https://doi.org/10.1002/bip.10263","is_oa":false,"landing_page_url":"https://doi.org/10.1002/bip.10263","pdf_url":null,"source":{"id":"https://openalex.org/S56808608","display_name":"Biopolymers","issn_l":"0006-3525","issn":["0006-3525","1097-0282"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biopolymers","raw_type":"journal-article"},{"id":"pmid:12579576","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12579576","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":"Biopolymers","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.306.7628","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.306.7628","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://dbeveridge.blogs.wesleyan.edu/outgoing/dbeveridge.blogs.wesleyan.edu/files/2011/07/Arthanari-Biopolymers-68-1.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G415480007","display_name":null,"funder_award_id":"NIH65871","funder_id":"https://openalex.org/F4320332505","funder_display_name":"U.S. Public Health Service"},{"id":"https://openalex.org/G8989170684","display_name":null,"funder_award_id":"NIH 37909","funder_id":"https://openalex.org/F4320332505","funder_display_name":"U.S. Public Health Service"}],"funders":[{"id":"https://openalex.org/F4320332505","display_name":"U.S. Public Health Service","ror":"https://ror.org/05xf94514"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W35158118","https://openalex.org/W53123824","https://openalex.org/W1539032650","https://openalex.org/W1589810575","https://openalex.org/W1969508348","https://openalex.org/W1969776708","https://openalex.org/W1971303996","https://openalex.org/W1971820073","https://openalex.org/W1974159142","https://openalex.org/W1975851628","https://openalex.org/W1978482484","https://openalex.org/W1984202875","https://openalex.org/W1988556506","https://openalex.org/W1988993336","https://openalex.org/W1993227183","https://openalex.org/W1997011390","https://openalex.org/W2002849149","https://openalex.org/W2004134464","https://openalex.org/W2006274376","https://openalex.org/W2006641720","https://openalex.org/W2012788169","https://openalex.org/W2014918715","https://openalex.org/W2015719553","https://openalex.org/W2023611498","https://openalex.org/W2028340208","https://openalex.org/W2031842331","https://openalex.org/W2034499275","https://openalex.org/W2042038534","https://openalex.org/W2045059035","https://openalex.org/W2050843661","https://openalex.org/W2052329232","https://openalex.org/W2054429712","https://openalex.org/W2056378638","https://openalex.org/W2057765314","https://openalex.org/W2058479011","https://openalex.org/W2062749418","https://openalex.org/W2065105763","https://openalex.org/W2065157739","https://openalex.org/W2067174909","https://openalex.org/W2069586757","https://openalex.org/W2071419803","https://openalex.org/W2073017905","https://openalex.org/W2079020386","https://openalex.org/W2083827956","https://openalex.org/W2085298685","https://openalex.org/W2086243700","https://openalex.org/W2094829564","https://openalex.org/W2102012791","https://openalex.org/W2110269314","https://openalex.org/W2122199548","https://openalex.org/W2138825634","https://openalex.org/W2143552926","https://openalex.org/W2158098325","https://openalex.org/W2165855161","https://openalex.org/W2313561635"],"related_works":["https://openalex.org/W7096194632","https://openalex.org/W1552683129","https://openalex.org/W2067006059","https://openalex.org/W7098427064","https://openalex.org/W4249399853","https://openalex.org/W2372778856","https://openalex.org/W2072840575","https://openalex.org/W2480246283","https://openalex.org/W2043605061","https://openalex.org/W1999162524"],"abstract_inverted_index":{"To":[0],"assess":[1],"the":[2,5,22,40,61,69,100,121,127,138,147,160,166,173,183,187,198,202,219],"accuracy":[3],"of":[4,10,21,25,36,63,133,163,172,197,218,222],"molecular":[6],"dynamics":[7],"(MD)":[8],"models":[9],"nucleic":[11],"acids,":[12],"a":[13,77,94,193,215],"detailed":[14,95],"comparison":[15,38,98,132],"between":[16,99],"MD-calculated":[17],"and":[18,54,96,102,114,124,150],"NMR-observed":[19],"indices":[20],"dynamical":[23],"structure":[24,62,162,221],"DNA":[26],"in":[27,65,90,142,186],"solution":[28,220],"has":[29,73],"been":[30,50,74,88],"carried":[31],"out.":[32],"The":[33,131,175,208],"specific":[34],"focus":[35],"our":[37],"is":[39,141,192,206],"oligonucleotide":[41],"duplex,":[42],"d(CGCGAATTCGCG)(2),":[43],"for":[44,60,84],"which":[45,191],"considerable":[46],"structural":[47],"data":[48,83],"have":[49,87],"obtained":[51,89],"from":[52,120],"crystallography":[53],"NMR":[55,82,129,148,176,225],"spectroscopy.":[56],"An":[57],"MD":[58,122,139,189,209],"model":[59,140],"d(CGCGAATTCGCG)(2)":[64,164,223],"solution,":[66],"based":[67,158],"on":[68,159],"AMBER":[70,188],"force":[71,204],"field,":[72],"extended":[75],"with":[76,126,146,154,214],"14":[78],"ns":[79],"trajectory.":[80],"New":[81],"this":[85],"sequence":[86],"order":[91],"to":[92,182],"allow":[93],"critical":[97],"calculated":[101],"observed":[103],"parameters.":[104],"Observable":[105],"two-dimensional":[106],"(2D)":[107],"nuclear":[108],"Overhauser":[109],"effect":[110],"spectroscopy":[111],"(NOESY)":[112],"volumes":[113],"scalar":[115],"coupling":[116,227],"constants":[117],"were":[118],"back-calculated":[119],"trajectory":[123],"compared":[125,213],"corresponding":[128],"data.":[130,228],"these":[134],"results":[135,210],"indicate":[136],"that":[137],"generally":[143],"good":[144],"agreement":[145],"data,":[149],"shows":[151],"closer":[152],"accord":[153],"experiment":[155],"than":[156],"back-calculations":[157],"crystal":[161],"or":[165,169],"canonical":[167],"A":[168],"B":[170],"forms":[171],"sequence.":[174],"parameters":[177],"are":[178,211],"not":[179],"particularly":[180],"sensitive":[181],"known":[184],"deficiency":[185],"model,":[190],"tendency":[194],"toward":[195],"undertwisting":[196],"double":[199],"helix":[200],"when":[201],"parm.94":[203],"field":[205],"used.":[207],"also":[212],"new":[216],"determination":[217],"using":[224],"dipolar":[226]},"counts_by_year":[{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":6}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}