Occurrence and classification of T-shaped interactions between nucleobases in RNA structures
Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and...
Gespeichert in:
| Veröffentlicht in: | RNA (Cambridge) 2023-08, Vol.29 (8), p.1215-1229 |
|---|---|
| Hauptverfasser: | , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 1229 |
|---|---|
| container_issue | 8 |
| container_start_page | 1215 |
| container_title | RNA (Cambridge) |
| container_volume | 29 |
| creator | Ali, Zakir Kukhta, Teagan Jhunjhunwala, Ayush Trant, John F Sharma, Purshotam |
| description | Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid-protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3261 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date data set of ≤3.5 Å resolution crystal structures deposited in the Protein Data Bank. |
| doi_str_mv | 10.1261/rna.079486.122 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10351890</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2814530244</sourcerecordid><originalsourceid>FETCH-LOGICAL-c2892-de4dc26ad2425fc66cd58bfda5e852fbe2c8f98333578d252f2636189400a23</originalsourceid><addsrcrecordid>eNpdkc9LHDEUx0Ox1HXr1aMEvHiZbX5vcpJFbBWkQutRCJnkjY7MJmsyU-l_3yxrF9vTy_u-z_uSxxehE0oWlCn6JUe3IEsjtKo9-4BmVCjTGELoQX1zKRvNNTtER6U8V5HX8Sd0yJdUa2HYDD3ceT_lDNEDdjFgP7hS-q73buxTxKnD9015chsIuI8jZOe3esEtjK8AEcfJD5BaV6BUAP_4vsJlzJMfpwzlM_rYuaHA8Vudo59fr-4vr5vbu283l6vbxjNtWBNABM-UC0ww2XmlfJC67YKToCXrWmBed0ZzzuVSB1Ylprii2ghCHONzdLFz3UztGoKHOGY32E3u1y7_tsn19t9J7J_sY_plKeGyupDqcP7mkNPLBGW06754GAYXIU3FMk2F5IQJUdGz_9DnNNUQhi3FjaHKLHmlFjvK51RKhm7_G0rsNjdbV-wut9pvbzh9f8Me_xsU_wO_mZUC</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2839916973</pqid></control><display><type>article</type><title>Occurrence and classification of T-shaped interactions between nucleobases in RNA structures</title><source>MEDLINE</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><source>Alma/SFX Local Collection</source><creator>Ali, Zakir ; Kukhta, Teagan ; Jhunjhunwala, Ayush ; Trant, John F ; Sharma, Purshotam</creator><creatorcontrib>Ali, Zakir ; Kukhta, Teagan ; Jhunjhunwala, Ayush ; Trant, John F ; Sharma, Purshotam</creatorcontrib><description>Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid-protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3261 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date data set of ≤3.5 Å resolution crystal structures deposited in the Protein Data Bank.</description><identifier>ISSN: 1355-8382</identifier><identifier>ISSN: 1469-9001</identifier><identifier>EISSN: 1469-9001</identifier><identifier>DOI: 10.1261/rna.079486.122</identifier><identifier>PMID: 37188492</identifier><language>eng</language><publisher>United States: Cold Spring Harbor Laboratory Press</publisher><subject>Bases (nucleic acids) ; DNA - chemistry ; Nucleic Acids ; Nucleotides ; Nucleotides - chemistry ; Ribonucleic acid ; RNA ; RNA - chemistry</subject><ispartof>RNA (Cambridge), 2023-08, Vol.29 (8), p.1215-1229</ispartof><rights>2023 Ali et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.</rights><rights>Copyright Cold Spring Harbor Laboratory Press Aug 2023</rights><rights>2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c2892-de4dc26ad2425fc66cd58bfda5e852fbe2c8f98333578d252f2636189400a23</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10351890/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10351890/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37188492$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ali, Zakir</creatorcontrib><creatorcontrib>Kukhta, Teagan</creatorcontrib><creatorcontrib>Jhunjhunwala, Ayush</creatorcontrib><creatorcontrib>Trant, John F</creatorcontrib><creatorcontrib>Sharma, Purshotam</creatorcontrib><title>Occurrence and classification of T-shaped interactions between nucleobases in RNA structures</title><title>RNA (Cambridge)</title><addtitle>RNA</addtitle><description>Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid-protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3261 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date data set of ≤3.5 Å resolution crystal structures deposited in the Protein Data Bank.</description><subject>Bases (nucleic acids)</subject><subject>DNA - chemistry</subject><subject>Nucleic Acids</subject><subject>Nucleotides</subject><subject>Nucleotides - chemistry</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA - chemistry</subject><issn>1355-8382</issn><issn>1469-9001</issn><issn>1469-9001</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpdkc9LHDEUx0Ox1HXr1aMEvHiZbX5vcpJFbBWkQutRCJnkjY7MJmsyU-l_3yxrF9vTy_u-z_uSxxehE0oWlCn6JUe3IEsjtKo9-4BmVCjTGELoQX1zKRvNNTtER6U8V5HX8Sd0yJdUa2HYDD3ceT_lDNEDdjFgP7hS-q73buxTxKnD9015chsIuI8jZOe3esEtjK8AEcfJD5BaV6BUAP_4vsJlzJMfpwzlM_rYuaHA8Vudo59fr-4vr5vbu283l6vbxjNtWBNABM-UC0ww2XmlfJC67YKToCXrWmBed0ZzzuVSB1Ylprii2ghCHONzdLFz3UztGoKHOGY32E3u1y7_tsn19t9J7J_sY_plKeGyupDqcP7mkNPLBGW06754GAYXIU3FMk2F5IQJUdGz_9DnNNUQhi3FjaHKLHmlFjvK51RKhm7_G0rsNjdbV-wut9pvbzh9f8Me_xsU_wO_mZUC</recordid><startdate>202308</startdate><enddate>202308</enddate><creator>Ali, Zakir</creator><creator>Kukhta, Teagan</creator><creator>Jhunjhunwala, Ayush</creator><creator>Trant, John F</creator><creator>Sharma, Purshotam</creator><general>Cold Spring Harbor Laboratory Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>202308</creationdate><title>Occurrence and classification of T-shaped interactions between nucleobases in RNA structures</title><author>Ali, Zakir ; Kukhta, Teagan ; Jhunjhunwala, Ayush ; Trant, John F ; Sharma, Purshotam</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c2892-de4dc26ad2425fc66cd58bfda5e852fbe2c8f98333578d252f2636189400a23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Bases (nucleic acids)</topic><topic>DNA - chemistry</topic><topic>Nucleic Acids</topic><topic>Nucleotides</topic><topic>Nucleotides - chemistry</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ali, Zakir</creatorcontrib><creatorcontrib>Kukhta, Teagan</creatorcontrib><creatorcontrib>Jhunjhunwala, Ayush</creatorcontrib><creatorcontrib>Trant, John F</creatorcontrib><creatorcontrib>Sharma, Purshotam</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>RNA (Cambridge)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ali, Zakir</au><au>Kukhta, Teagan</au><au>Jhunjhunwala, Ayush</au><au>Trant, John F</au><au>Sharma, Purshotam</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Occurrence and classification of T-shaped interactions between nucleobases in RNA structures</atitle><jtitle>RNA (Cambridge)</jtitle><addtitle>RNA</addtitle><date>2023-08</date><risdate>2023</risdate><volume>29</volume><issue>8</issue><spage>1215</spage><epage>1229</epage><pages>1215-1229</pages><issn>1355-8382</issn><issn>1469-9001</issn><eissn>1469-9001</eissn><abstract>Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid-protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3261 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date data set of ≤3.5 Å resolution crystal structures deposited in the Protein Data Bank.</abstract><cop>United States</cop><pub>Cold Spring Harbor Laboratory Press</pub><pmid>37188492</pmid><doi>10.1261/rna.079486.122</doi><tpages>15</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1355-8382 |
| ispartof | RNA (Cambridge), 2023-08, Vol.29 (8), p.1215-1229 |
| issn | 1355-8382 1469-9001 1469-9001 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10351890 |
| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Bases (nucleic acids) DNA - chemistry Nucleic Acids Nucleotides Nucleotides - chemistry Ribonucleic acid RNA RNA - chemistry |
| title | Occurrence and classification of T-shaped interactions between nucleobases in RNA structures |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-21T10%3A06%3A18IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Occurrence%20and%20classification%20of%20T-shaped%20interactions%20between%20nucleobases%20in%20RNA%20structures&rft.jtitle=RNA%20(Cambridge)&rft.au=Ali,%20Zakir&rft.date=2023-08&rft.volume=29&rft.issue=8&rft.spage=1215&rft.epage=1229&rft.pages=1215-1229&rft.issn=1355-8382&rft.eissn=1469-9001&rft_id=info:doi/10.1261/rna.079486.122&rft_dat=%3Cproquest_pubme%3E2814530244%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2839916973&rft_id=info:pmid/37188492&rfr_iscdi=true |