{"id":"https://openalex.org/W2912556945","doi":"https://doi.org/10.1021/acs.jcim.8b00815","title":"DNAzymes at Work: A DFT Computational Investigation on the Mechanism of 9DB1","display_name":"DNAzymes at Work: A DFT Computational Investigation on the Mechanism of 9DB1","publication_year":2019,"publication_date":"2019-01-31","ids":{"openalex":"https://openalex.org/W2912556945","doi":"https://doi.org/10.1021/acs.jcim.8b00815","mag":"2912556945","pmid":"https://pubmed.ncbi.nlm.nih.gov/30702292"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.8b00815","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00815","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"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/A5040693788","display_name":"Edoardo Jun Mattioli","orcid":"https://orcid.org/0000-0002-2598-497X"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Edoardo Jun Mattioli","raw_affiliation_strings":["Dipartimento di Chimica \u201cG. Ciamician\u201d, Alma Mater Studiorum - Universit\u00e0 di Bologna, V. F. Selmi 2, 40126 Bologna, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Chimica \u201cG. Ciamician\u201d, Alma Mater Studiorum - Universit\u00e0 di Bologna, V. F. Selmi 2, 40126 Bologna, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014137673","display_name":"Andr\u00e9a Bottoni","orcid":"https://orcid.org/0000-0003-2966-4065"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Andrea Bottoni","raw_affiliation_strings":["Dipartimento di Chimica \u201cG. Ciamician\u201d, Alma Mater Studiorum - Universit\u00e0 di Bologna, V. F. Selmi 2, 40126 Bologna, Italy"],"raw_orcid":"https://orcid.org/0000-0003-2966-4065","affiliations":[{"raw_affiliation_string":"Dipartimento di Chimica \u201cG. Ciamician\u201d, Alma Mater Studiorum - Universit\u00e0 di Bologna, V. F. Selmi 2, 40126 Bologna, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017487322","display_name":"Matteo Calvaresi","orcid":"https://orcid.org/0000-0002-9583-2146"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Matteo Calvaresi","raw_affiliation_strings":["Dipartimento di Chimica \u201cG. Ciamician\u201d, Alma Mater Studiorum - Universit\u00e0 di Bologna, V. F. Selmi 2, 40126 Bologna, Italy"],"raw_orcid":"https://orcid.org/0000-0002-9583-2146","affiliations":[{"raw_affiliation_string":"Dipartimento di Chimica \u201cG. Ciamician\u201d, Alma Mater Studiorum - Universit\u00e0 di Bologna, V. F. Selmi 2, 40126 Bologna, Italy","institution_ids":["https://openalex.org/I9360294"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014137673","https://openalex.org/A5017487322"],"corresponding_institution_ids":["https://openalex.org/I9360294"],"apc_list":null,"apc_paid":null,"fwci":0.6838,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.68206127,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"59","issue":"4","first_page":"1547","last_page":"1553"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9998999834060669,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9997000098228455,"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/chemistry","display_name":"Chemistry","score":0.8842630386352539},{"id":"https://openalex.org/keywords/nucleophile","display_name":"Nucleophile","score":0.7917090654373169},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.6322107315063477},{"id":"https://openalex.org/keywords/leaving-group","display_name":"Leaving group","score":0.5778876543045044},{"id":"https://openalex.org/keywords/ribose","display_name":"Ribose","score":0.5151047110557556},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.4970135986804962},{"id":"https://openalex.org/keywords/nucleotide","display_name":"Nucleotide","score":0.4719109833240509},{"id":"https://openalex.org/keywords/concerted-reaction","display_name":"Concerted reaction","score":0.4516443908214569},{"id":"https://openalex.org/keywords/phosphorane","display_name":"Phosphorane","score":0.43866753578186035},{"id":"https://openalex.org/keywords/nucleobase","display_name":"Nucleobase","score":0.43792724609375},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.23619124293327332},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.19100117683410645},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.17363882064819336},{"id":"https://openalex.org/keywords/catalysis","display_name":"Catalysis","score":0.1397538185119629},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.113006591796875},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.0889638364315033}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.8842630386352539},{"id":"https://openalex.org/C178907741","wikidata":"https://www.wikidata.org/wiki/Q745930","display_name":"Nucleophile","level":3,"score":0.7917090654373169},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.6322107315063477},{"id":"https://openalex.org/C160964918","wikidata":"https://www.wikidata.org/wiki/Q320141","display_name":"Leaving group","level":3,"score":0.5778876543045044},{"id":"https://openalex.org/C2779461342","wikidata":"https://www.wikidata.org/wiki/Q59817493","display_name":"Ribose","level":3,"score":0.5151047110557556},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.4970135986804962},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.4719109833240509},{"id":"https://openalex.org/C29135686","wikidata":"https://www.wikidata.org/wiki/Q2733609","display_name":"Concerted reaction","level":3,"score":0.4516443908214569},{"id":"https://openalex.org/C2780810681","wikidata":"https://www.wikidata.org/wiki/Q413172","display_name":"Phosphorane","level":2,"score":0.43866753578186035},{"id":"https://openalex.org/C61234307","wikidata":"https://www.wikidata.org/wiki/Q422960","display_name":"Nucleobase","level":3,"score":0.43792724609375},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.23619124293327332},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.19100117683410645},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.17363882064819336},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.1397538185119629},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.113006591796875},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0889638364315033},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000077318","descriptor_name":"Density Functional Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077318","descriptor_name":"Density Functional Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077318","descriptor_name":"Density Functional Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021881","descriptor_name":"DNA, Catalytic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021881","descriptor_name":"DNA, Catalytic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021881","descriptor_name":"DNA, Catalytic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021881","descriptor_name":"DNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D021881","descriptor_name":"DNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D021881","descriptor_name":"DNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055162","descriptor_name":"Biocatalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055162","descriptor_name":"Biocatalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055162","descriptor_name":"Biocatalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.8b00815","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00815","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:30702292","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30702292","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,"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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:cris.unibo.it:11585/717695","is_oa":false,"landing_page_url":"http://hdl.handle.net/11585/717695","pdf_url":null,"source":{"id":"https://openalex.org/S4306402579","display_name":"Archivio istituzionale della ricerca (Alma Mater Studiorum Universit\u00e0 di Bologna)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210117483","host_organization_name":"Istituto di Ematologia di Bologna","host_organization_lineage":["https://openalex.org/I4210117483"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Clean water and sanitation","id":"https://metadata.un.org/sdg/6","score":0.6299999952316284}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W851581899","https://openalex.org/W1848841113","https://openalex.org/W1966662663","https://openalex.org/W1976387129","https://openalex.org/W1980461160","https://openalex.org/W1981898202","https://openalex.org/W1986111808","https://openalex.org/W1992223332","https://openalex.org/W1993400962","https://openalex.org/W1993620005","https://openalex.org/W1997151511","https://openalex.org/W2002861696","https://openalex.org/W2007199645","https://openalex.org/W2011428226","https://openalex.org/W2012920894","https://openalex.org/W2017823783","https://openalex.org/W2017950385","https://openalex.org/W2019403558","https://openalex.org/W2020718085","https://openalex.org/W2022966592","https://openalex.org/W2026767484","https://openalex.org/W2027717778","https://openalex.org/W2030936891","https://openalex.org/W2045140923","https://openalex.org/W2049100574","https://openalex.org/W2061854641","https://openalex.org/W2062078686","https://openalex.org/W2068413101","https://openalex.org/W2069528284","https://openalex.org/W2069688986","https://openalex.org/W2073775872","https://openalex.org/W2077016030","https://openalex.org/W2078957174","https://openalex.org/W2087576664","https://openalex.org/W2111870773","https://openalex.org/W2112864600","https://openalex.org/W2117552063","https://openalex.org/W2130886644","https://openalex.org/W2147056217","https://openalex.org/W2150697053","https://openalex.org/W2153218150","https://openalex.org/W2164029323","https://openalex.org/W2238302853","https://openalex.org/W2299104338","https://openalex.org/W2313675767","https://openalex.org/W2409572969","https://openalex.org/W2415518253","https://openalex.org/W2497035521","https://openalex.org/W2625154988","https://openalex.org/W2791104128","https://openalex.org/W2793013270","https://openalex.org/W2800278200","https://openalex.org/W2810938282"],"related_works":["https://openalex.org/W2316599080","https://openalex.org/W2035149334","https://openalex.org/W2088659205","https://openalex.org/W2318959270","https://openalex.org/W1953904050","https://openalex.org/W2017383492","https://openalex.org/W2249779179","https://openalex.org/W1984370231","https://openalex.org/W2010635899","https://openalex.org/W4297020677"],"abstract_inverted_index":{"The":[0,44,64],"9DB1":[1],"DNAzyme":[2],"follows":[3],"an":[4,77,142],"addition\u2013elimination":[5],"(AN+DN)":[6],"two-step":[7],"mechanism,":[8],"involving":[9],"a":[10,34,92,105,129,133,149],"phosphorane":[11],"intermediate,":[12],"where":[13,116],"the":[14,23,41,54,59,72,82,85,88,97,100,109,117,123,137,145,157,166,169],"3\u2032-hydroxyl":[15,101],"group":[16,61],"(nucleophile)":[17],"of":[18,25,84,136,168],"one":[19],"RNA":[20,27],"fragment":[21],"attacks":[22],"5\u2032-triphosphate":[24],"another":[26],"fragment.":[28],"This":[29],"mechanism":[30],"does":[31],"not":[32,68],"involve":[33],"divalent":[35],"metal":[36],"cation":[37],"in":[38,71,80,122,144,154],"agreement":[39,155],"with":[40,96,141,156,171],"experimental":[42,158],"evidence.":[43,159],"process":[45],"is":[46,67,163],"assisted":[47],"by":[48,128,165],"two":[49],"proton":[50],"transfers":[51],"that":[52],"activate":[53],"nucleophile":[55,106],"(first":[56],"step)":[57],"and":[58,107,148,178],"leaving":[60],"(second":[62],"step).":[63],"dA13":[65,89,118],"nucleotide":[66],"directly":[69],"involved":[70,121],"reaction.":[73],"However,":[74],"it":[75],"plays":[76],"important":[78],"role":[79],"determining":[81],"regioselectivity":[83],"process:":[86],"since":[87],"phosphate":[90,119],"forms":[91],"strong":[93],"hydrogen":[94,124],"bond":[95],"2\u2032-hydroxyl,":[98],"only":[99],"can":[102],"behave":[103],"as":[104,175],"form":[108],"new":[110],"3\u2032-5\u2032":[111],"bond.":[112],"In":[113],"silico":[114],"mutagenesis,":[115],"oxygen":[120],"contact":[125],"was":[126],"replaced":[127],"sulfur":[130],"atom,":[131],"causes":[132],"significant":[134],"rearrangement":[135],"A50":[138],"ribose":[139],"position":[140],"increase":[143],"activation":[146],"barrier":[147],"consequent":[150],"lower":[151],"enzymatic":[152],"activity":[153],"A":[160],"similar":[161],"effect":[162],"determined":[164],"replacement":[167],"2\u2032-hydroxyl":[170],"different":[172],"groups":[173],"such":[174],"F,":[176],"H,":[177],"OMe.":[179]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}