{"corpus_id":10067129,"paper_sha":"d0f342b8b51ddd043c867be137e5fd7edafbadde","doi":"10.1093/nar/gkv367","arxiv_id":null,"pmid":25897116,"pmcid":"4538805","mag_id":2158128478,"dblp_id":null,"acl_id":null,"title":"Synthesis of 2′-Fluoro RNA by Syn5 RNA polymerase","year":2015,"publication_date":"2015-04-20","venue":"Nucleic Acids Research","journal":{"name":"Nucleic Acids Research","pages":"e94 - e94","volume":"43"},"journal_issn":null,"journal_title":null,"publication_types":["JournalArticle"],"pubmed_pub_types":["Journal Article","Research Support, Non-U.S. Gov't"],"s2_fields_of_study":["Biology","Medicine","Chemistry"],"reference_count":26,"citation_count":29,"influential_citation_count":2,"is_open_access":true,"arxiv_categories":null,"arxiv_license":null,"arxiv_journal_ref":null,"mesh_headings":[{"d":"DNA-Directed RNA Polymerases","mj":false,"qs":[{"q":"genetics","mj":false,"ui":"Q000235"},{"q":"metabolism","mj":true,"ui":"Q000378"}],"ui":"D012321"},{"d":"Deoxyribonucleotides","mj":false,"qs":[{"q":"metabolism","mj":false,"ui":"Q000378"}],"ui":"D003854"},{"d":"Fluorine","mj":false,"qs":[{"q":"chemistry","mj":false,"ui":"Q000737"}],"ui":"D005461"},{"d":"Manganese","mj":false,"ui":"D008345"},{"d":"Mutation","mj":false,"ui":"D009154"},{"d":"Podoviridae","mj":false,"qs":[{"q":"enzymology","mj":false,"ui":"Q000201"}],"ui":"D017902"},{"d":"RNA","mj":false,"qs":[{"q":"biosynthesis","mj":true,"ui":"Q000096"},{"q":"chemistry","mj":false,"ui":"Q000737"}],"ui":"D012313"},{"d":"RNA Stability","mj":false,"ui":"D020871"},{"d":"Transcription Initiation Site","mj":false,"ui":"D024363"},{"d":"Transcription, Genetic","mj":false,"ui":"D014158"}],"chemicals":[{"n":"Deoxyribonucleotides","ui":"D003854","reg":"0"},{"n":"Fluorine","ui":"D005461","reg":"284SYP0193"},{"n":"Manganese","ui":"D008345","reg":"42Z2K6ZL8P"},{"n":"RNA","ui":"D012313","reg":"63231-63-0"},{"n":"DNA-Directed RNA Polymerases","ui":"D012321","reg":"EC 2.7.7.6"}],"comments_corrections":null,"source_flags":5,"s2_open_access_pdf_url":"https://academic.oup.com/nar/article-pdf/43/14/e94/16659430/gkv367.pdf","s2_open_access_landing_url":"https://www.semanticscholar.org/paper/d0f342b8b51ddd043c867be137e5fd7edafbadde","s2_open_access_license":"CCBY","s2_open_access_status":"GOLD","pmc_open_access_pdf_url":null,"pmc_open_access_landing_url":null,"pmc_open_access_license":null,"pmc_open_access_status":null,"unpaywall_open_access_pdf_url":null,"unpaywall_open_access_landing_url":null,"unpaywall_open_access_license":null,"unpaywall_open_access_status":null,"abstract":"The substitution of 2′-fluoro for 2′-hydroxyl moieties in RNA substantially improves the stability of RNA. RNA stability is a major issue in RNA research and applications involving RNA. We report that the RNA polymerase from the marine cyanophage Syn5 has an intrinsic low discrimination against the incorporation of 2′-fluoro dNMPs during transcription elongation. The presence of both magnesium and manganese ions at high concentrations further reduce this discrimination without decreasing the efficiency of incorporation. We have constructed a Syn5 RNA polymerase in which tyrosine 564 is replaced with phenylalanine (Y564F) that further decreases the discrimination against 2′-fluoro-dNTPs during RNA synthesis. Sequence elements in DNA templates that affect the yield of RNA and incorporation of 2′-fluoro-dNMPs by Syn5 RNA polymerase have been identified.","claims":[{"public_id":"cl_8d0437ebcb2982f8e2c8372787f8da2f","status":"active","text":"High concentrations of magnesium and manganese ions further reduce discrimination against 2′-fluoro dNMPs without decreasing incorporation efficiency.","confidence":0.95,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_8d0437ebcb2982f8e2c8372787f8da2f"},{"public_id":"cl_7c69544b22c8af1606eb8f5bca965694","status":"active","text":"Specific DNA template sequence elements that affect RNA yield and incorporation of 2′-fluoro-dNMPs by Syn5 RNA polymerase have been identified.","confidence":0.93,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_7c69544b22c8af1606eb8f5bca965694"},{"public_id":"cl_a230998db9e1964b17cee30a06a778d2","status":"active","text":"Syn5 RNA polymerase shows intrinsically low discrimination against incorporation of 2′-fluoro dNMPs during transcription elongation.","confidence":0.98,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_a230998db9e1964b17cee30a06a778d2"},{"public_id":"cl_52bbfb27c668754443bcb5d17068fd49","status":"active","text":"The Y564F substitution in Syn5 RNA polymerase further decreases discrimination against 2′-fluoro-dNTPs during RNA synthesis.","confidence":0.97,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_52bbfb27c668754443bcb5d17068fd49"}],"concepts":[{"public_id":"co_128d959155668ecfdf484a7e2c0e5fe2","status":"active","name":"2′-fluoro dNMPs","description":"2′-fluoro-modified nucleotide monophosphates incorporated during transcription elongation.","types":["nucleotide","substrate"],"aliases":["2′-fluoro deoxynucleotide monophosphates"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_128d959155668ecfdf484a7e2c0e5fe2"},{"public_id":"co_1d49ff181459a4aaabd0c5c060b64b67","status":"active","name":"DNA templates","description":"DNA sequences that direct RNA synthesis by the polymerase.","types":["material","template"],"aliases":["template DNA"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_1d49ff181459a4aaabd0c5c060b64b67"},{"public_id":"co_2360777ff96af730eea2d86d762dc5eb","status":"active","name":"transcription elongation","description":"The stage of transcription in which RNA polymerase extends the growing RNA chain.","types":["process"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_2360777ff96af730eea2d86d762dc5eb"},{"public_id":"co_3b1f98fd958a4464a832955c8f620fbb","status":"active","name":"Y564F","description":"A Syn5 RNA polymerase variant in which tyrosine at position 564 is replaced by phenylalanine.","types":["protein variant","mutant"],"aliases":["tyrosine 564 replaced with phenylalanine"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_3b1f98fd958a4464a832955c8f620fbb"},{"public_id":"co_43c2a3a810f957ebb63ed5a3df244603","status":"active","name":"RNA yield","description":"The amount of RNA produced in the transcription reaction.","types":["outcome","measurement"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_43c2a3a810f957ebb63ed5a3df244603"},{"public_id":"co_45e9a0a9e9109c3689b0d09a6f7dad24","status":"active","name":"Syn5 RNA polymerase","description":"An RNA polymerase from the marine cyanophage Syn5 used to synthesize RNA and modified RNA transcripts.","types":["enzyme","polymerase"],"aliases":["Syn5 polymerase"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_45e9a0a9e9109c3689b0d09a6f7dad24"},{"public_id":"co_4a6648c61ff4f822f2bfe46af5ab5e62","status":"active","name":"2′-fluoro RNA","description":"RNA containing 2′-fluoro substitutions in place of 2′-hydroxyl groups.","types":["nucleic acid","modified RNA"],"aliases":["2′-fluoro-substituted RNA"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_4a6648c61ff4f822f2bfe46af5ab5e62"},{"public_id":"co_529bfc05112d9d9e96648970a76cbccb","status":"active","name":"magnesium and manganese ions","description":"Divalent metal ions used in the transcription reaction to support polymerase activity.","types":["chemical factor","ion"],"aliases":["Mg2+ and Mn2+"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_529bfc05112d9d9e96648970a76cbccb"},{"public_id":"co_d44a80dc8017ca0ab967ee851ea212f7","status":"active","name":"2′-fluoro-dNTPs","description":"2′-fluoro-modified deoxynucleoside triphosphates used as transcription substrates.","types":["nucleotide","substrate"],"aliases":["2′-fluoro deoxynucleoside triphosphates"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_d44a80dc8017ca0ab967ee851ea212f7"},{"public_id":"co_f2b843e364c7ae4eea679a63351bd6e3","status":"active","name":"incorporation efficiency","description":"The effectiveness with which nucleotide substrates are added into the growing RNA product.","types":["measurement","performance metric"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_f2b843e364c7ae4eea679a63351bd6e3"}],"external_ids":{"DOI":"10.1093/nar/gkv367","ArXiv":null,"PubMed":25897116,"PubMedCentral":"4538805","MAG":2158128478,"DBLP":null,"ACL":null},"open_access":{"is_open_access":true,"pdf_url":"https://academic.oup.com/nar/article-pdf/43/14/e94/16659430/gkv367.pdf","landing_url":"https://www.semanticscholar.org/paper/d0f342b8b51ddd043c867be137e5fd7edafbadde","source":"semantic_scholar","pdf_url_source":"semantic_scholar_open_access_pdf","license":"CCBY","status":"GOLD","reason":null},"reference_availability":{"status":"available","references_indexed":true,"full_text_available":false,"full_text_source":null,"count_basis":"semantic_scholar_metadata","extraction_status":"not_applicable","reason":null},"source":{"provider":"episteme2","base_corpus":"semantic_scholar_dump","freshness_mode":"unknown","basis":["semantic_scholar_metadata","postgres_metadata"],"limits":["paper metadata is based on indexed upstream scholarly datasets","claims and concepts are available only for extracted papers","absence of claims or concepts means no extracted graph data is available in this response"],"status":"available","degraded":false,"degraded_reasons":[],"diagnostics":{"status":"available","degraded":false,"degraded_reasons":[],"metadata_status":"available","graph_status":"available","abstract_status":"available"},"source_flags":5},"paper_id":630596,"paper_uid":"7b9b2c61-4026-4b66-a1ba-5308d622e35a","canonical_identity":{"paper_id":630596,"paper_uid":"7b9b2c61-4026-4b66-a1ba-5308d622e35a","identity_status":"available","lookup_basis":"semantic_scholar_external_id","compatibility_path":"corpus_id"},"url":"https://sah.borca.ai/papers/10067129"}