Chemical Amination/Imination of Carbonothiolated Nucleosides During RNA Hydrolysis
Liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) has become the gold‐standard technique to study RNA and its various modifications. While most research on RNA nucleosides has been focused on their biological roles, discovery of new modifications remains of interest. With state‐of‐the‐art te...
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| Veröffentlicht in: | Angewandte Chemie International Edition 2021-02, Vol.60 (8), p.3961-3966 |
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| creator | Jora, Manasses Borland, Kayla Abernathy, Scott Zhao, Ruoxia Kelley, Melissa Kellner, Stefanie Addepalli, Balasubrahmanyam Limbach, Patrick A. |
| description | Liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) has become the gold‐standard technique to study RNA and its various modifications. While most research on RNA nucleosides has been focused on their biological roles, discovery of new modifications remains of interest. With state‐of‐the‐art technology, the presence of artifacts can confound the identification of new modifications. Here, we report the characterization of a non‐natural mcm5isoC ribonucleoside in S. cerevisiae total tRNA hydrolysate by higher‐energy collisional dissociation (HCD)‐based fingerprints and isotope labeling of RNA. Its discovery revealed a class of amino/imino ribonucleoside artifacts that are generated during RNA hydrolysis under ammonium‐buffered mild basic conditions. We then identified digestion conditions that can reduce or eliminate their formation. These finding and method enhancements will improve the accurate detection of new RNA modifications.
Discovery of amino/imino ribonucleoside artifacts that are generated during RNA hydrolysis under ammonium‐buffered mild basic conditions is described. The general approach for discovery uses higher‐energy collisional dissociation‐mass spectrometry (HCD‐MS) and isotope labeling of RNA. |
| doi_str_mv | 10.1002/anie.202010793 |
| format | Article |
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Discovery of amino/imino ribonucleoside artifacts that are generated during RNA hydrolysis under ammonium‐buffered mild basic conditions is described. The general approach for discovery uses higher‐energy collisional dissociation‐mass spectrometry (HCD‐MS) and isotope labeling of RNA.</description><edition>International ed. in English</edition><identifier>ISSN: 1433-7851</identifier><identifier>EISSN: 1521-3773</identifier><identifier>DOI: 10.1002/anie.202010793</identifier><identifier>PMID: 33125801</identifier><language>eng</language><publisher>Germany: Wiley Subscription Services, Inc</publisher><subject>Amination ; Ammonium ; Chromatography, High Pressure Liquid ; digestion artifact ; Energy of dissociation ; Hydrolysates ; Hydrolysis ; imination ; Isotope Labeling ; LC-MS/MS ; Liquid chromatography ; Mass spectrometry ; Mass spectroscopy ; nucleoside analysis ; Nucleosides ; Nucleosides - chemistry ; Ribonucleic acid ; RNA ; RNA - analysis ; RNA - metabolism ; RNA, Transfer - chemistry ; RNA, Transfer - metabolism ; Saccharomyces cerevisiae - genetics ; Saccharomyces cerevisiae - metabolism ; Sulfhydryl Compounds - chemistry ; Tandem Mass Spectrometry ; tRNA</subject><ispartof>Angewandte Chemie International Edition, 2021-02, Vol.60 (8), p.3961-3966</ispartof><rights>2020 Wiley‐VCH GmbH</rights><rights>2020 Wiley-VCH GmbH.</rights><rights>2021 Wiley‐VCH GmbH</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4103-efbd915461960f6ec74c2462efea8c35328c60894b300bd9bd9eb695c8a60cb3</citedby><cites>FETCH-LOGICAL-c4103-efbd915461960f6ec74c2462efea8c35328c60894b300bd9bd9eb695c8a60cb3</cites><orcidid>0000-0002-1999-1508 ; 0000-0003-1526-4546</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fanie.202010793$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fanie.202010793$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33125801$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Jora, Manasses</creatorcontrib><creatorcontrib>Borland, Kayla</creatorcontrib><creatorcontrib>Abernathy, Scott</creatorcontrib><creatorcontrib>Zhao, Ruoxia</creatorcontrib><creatorcontrib>Kelley, Melissa</creatorcontrib><creatorcontrib>Kellner, Stefanie</creatorcontrib><creatorcontrib>Addepalli, Balasubrahmanyam</creatorcontrib><creatorcontrib>Limbach, Patrick A.</creatorcontrib><title>Chemical Amination/Imination of Carbonothiolated Nucleosides During RNA Hydrolysis</title><title>Angewandte Chemie International Edition</title><addtitle>Angew Chem Int Ed Engl</addtitle><description>Liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) has become the gold‐standard technique to study RNA and its various modifications. While most research on RNA nucleosides has been focused on their biological roles, discovery of new modifications remains of interest. With state‐of‐the‐art technology, the presence of artifacts can confound the identification of new modifications. Here, we report the characterization of a non‐natural mcm5isoC ribonucleoside in S. cerevisiae total tRNA hydrolysate by higher‐energy collisional dissociation (HCD)‐based fingerprints and isotope labeling of RNA. Its discovery revealed a class of amino/imino ribonucleoside artifacts that are generated during RNA hydrolysis under ammonium‐buffered mild basic conditions. We then identified digestion conditions that can reduce or eliminate their formation. These finding and method enhancements will improve the accurate detection of new RNA modifications.
Discovery of amino/imino ribonucleoside artifacts that are generated during RNA hydrolysis under ammonium‐buffered mild basic conditions is described. The general approach for discovery uses higher‐energy collisional dissociation‐mass spectrometry (HCD‐MS) and isotope labeling of RNA.</description><subject>Amination</subject><subject>Ammonium</subject><subject>Chromatography, High Pressure Liquid</subject><subject>digestion artifact</subject><subject>Energy of dissociation</subject><subject>Hydrolysates</subject><subject>Hydrolysis</subject><subject>imination</subject><subject>Isotope Labeling</subject><subject>LC-MS/MS</subject><subject>Liquid chromatography</subject><subject>Mass spectrometry</subject><subject>Mass spectroscopy</subject><subject>nucleoside analysis</subject><subject>Nucleosides</subject><subject>Nucleosides - chemistry</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA - analysis</subject><subject>RNA - metabolism</subject><subject>RNA, Transfer - chemistry</subject><subject>RNA, Transfer - metabolism</subject><subject>Saccharomyces cerevisiae - genetics</subject><subject>Saccharomyces cerevisiae - metabolism</subject><subject>Sulfhydryl Compounds - chemistry</subject><subject>Tandem Mass Spectrometry</subject><subject>tRNA</subject><issn>1433-7851</issn><issn>1521-3773</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqF0M1LwzAYBvAgipvTq0cpePHSLR9tmh7HnG4wJozdS5q-dRltM5MV6X9vxj4EL8ILeQ-_PLw8CD0SPCQY05FsNAwpppjgJGVXqE9iSkKWJOza7xFjYSJi0kN3zm29FwLzW9RjjNBYYNJHq8kGaq1kFYxr3ci9Ns1oft4CUwYTaXPTmP1Gm0ruoQiWrarAOF2AC15bq5vPYLUcB7OusKbqnHb36KaUlYOH0ztA67fpejILFx_v88l4EaqIYBZCmRcpiSNOUo5LDiqJFI04hRKkUCxmVCiORRrlDGNP_UDO01gJybHK2QC9HGN31ny14PZZrZ2CqpINmNZlNIp5RKjg1NPnP3RrWtv447wSIqZJQg5qeFTKGucslNnO6lraLiM4O5SdHcrOLmX7D0-n2Davobjwc7sepEfwrSvo_onLxsv59Df8B4k1isk</recordid><startdate>20210219</startdate><enddate>20210219</enddate><creator>Jora, Manasses</creator><creator>Borland, Kayla</creator><creator>Abernathy, Scott</creator><creator>Zhao, Ruoxia</creator><creator>Kelley, Melissa</creator><creator>Kellner, Stefanie</creator><creator>Addepalli, Balasubrahmanyam</creator><creator>Limbach, Patrick A.</creator><general>Wiley Subscription Services, Inc</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>K9.</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-1999-1508</orcidid><orcidid>https://orcid.org/0000-0003-1526-4546</orcidid></search><sort><creationdate>20210219</creationdate><title>Chemical Amination/Imination of Carbonothiolated Nucleosides During RNA Hydrolysis</title><author>Jora, Manasses ; Borland, Kayla ; Abernathy, Scott ; Zhao, Ruoxia ; Kelley, Melissa ; Kellner, Stefanie ; Addepalli, Balasubrahmanyam ; Limbach, Patrick A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4103-efbd915461960f6ec74c2462efea8c35328c60894b300bd9bd9eb695c8a60cb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Amination</topic><topic>Ammonium</topic><topic>Chromatography, High Pressure Liquid</topic><topic>digestion artifact</topic><topic>Energy of dissociation</topic><topic>Hydrolysates</topic><topic>Hydrolysis</topic><topic>imination</topic><topic>Isotope Labeling</topic><topic>LC-MS/MS</topic><topic>Liquid chromatography</topic><topic>Mass spectrometry</topic><topic>Mass spectroscopy</topic><topic>nucleoside analysis</topic><topic>Nucleosides</topic><topic>Nucleosides - chemistry</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA - analysis</topic><topic>RNA - metabolism</topic><topic>RNA, Transfer - chemistry</topic><topic>RNA, Transfer - metabolism</topic><topic>Saccharomyces cerevisiae - genetics</topic><topic>Saccharomyces cerevisiae - metabolism</topic><topic>Sulfhydryl Compounds - chemistry</topic><topic>Tandem Mass Spectrometry</topic><topic>tRNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Jora, Manasses</creatorcontrib><creatorcontrib>Borland, Kayla</creatorcontrib><creatorcontrib>Abernathy, Scott</creatorcontrib><creatorcontrib>Zhao, Ruoxia</creatorcontrib><creatorcontrib>Kelley, Melissa</creatorcontrib><creatorcontrib>Kellner, Stefanie</creatorcontrib><creatorcontrib>Addepalli, Balasubrahmanyam</creatorcontrib><creatorcontrib>Limbach, Patrick A.</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>ProQuest Health & Medical Complete (Alumni)</collection><collection>MEDLINE - Academic</collection><jtitle>Angewandte Chemie International Edition</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Jora, Manasses</au><au>Borland, Kayla</au><au>Abernathy, Scott</au><au>Zhao, Ruoxia</au><au>Kelley, Melissa</au><au>Kellner, Stefanie</au><au>Addepalli, Balasubrahmanyam</au><au>Limbach, Patrick A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Chemical Amination/Imination of Carbonothiolated Nucleosides During RNA Hydrolysis</atitle><jtitle>Angewandte Chemie International Edition</jtitle><addtitle>Angew Chem Int Ed Engl</addtitle><date>2021-02-19</date><risdate>2021</risdate><volume>60</volume><issue>8</issue><spage>3961</spage><epage>3966</epage><pages>3961-3966</pages><issn>1433-7851</issn><eissn>1521-3773</eissn><abstract>Liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) has become the gold‐standard technique to study RNA and its various modifications. While most research on RNA nucleosides has been focused on their biological roles, discovery of new modifications remains of interest. With state‐of‐the‐art technology, the presence of artifacts can confound the identification of new modifications. Here, we report the characterization of a non‐natural mcm5isoC ribonucleoside in S. cerevisiae total tRNA hydrolysate by higher‐energy collisional dissociation (HCD)‐based fingerprints and isotope labeling of RNA. Its discovery revealed a class of amino/imino ribonucleoside artifacts that are generated during RNA hydrolysis under ammonium‐buffered mild basic conditions. We then identified digestion conditions that can reduce or eliminate their formation. These finding and method enhancements will improve the accurate detection of new RNA modifications.
Discovery of amino/imino ribonucleoside artifacts that are generated during RNA hydrolysis under ammonium‐buffered mild basic conditions is described. The general approach for discovery uses higher‐energy collisional dissociation‐mass spectrometry (HCD‐MS) and isotope labeling of RNA.</abstract><cop>Germany</cop><pub>Wiley Subscription Services, Inc</pub><pmid>33125801</pmid><doi>10.1002/anie.202010793</doi><tpages>6</tpages><edition>International ed. in English</edition><orcidid>https://orcid.org/0000-0002-1999-1508</orcidid><orcidid>https://orcid.org/0000-0003-1526-4546</orcidid></addata></record> |
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| subjects | Amination Ammonium Chromatography, High Pressure Liquid digestion artifact Energy of dissociation Hydrolysates Hydrolysis imination Isotope Labeling LC-MS/MS Liquid chromatography Mass spectrometry Mass spectroscopy nucleoside analysis Nucleosides Nucleosides - chemistry Ribonucleic acid RNA RNA - analysis RNA - metabolism RNA, Transfer - chemistry RNA, Transfer - metabolism Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae - metabolism Sulfhydryl Compounds - chemistry Tandem Mass Spectrometry tRNA |
| title | Chemical Amination/Imination of Carbonothiolated Nucleosides During RNA Hydrolysis |
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