Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer
Abstract The ability of the cytidine analog Çmf to act as a position specific reporter of RNA-dynamics was spectroscopically evaluated. Çmf-labeled single- and double-stranded RNAs differ in their fluorescence lifetimes, quantum yields and anisotropies. These observables were also influenced by the...
Gespeichert in:
| Veröffentlicht in: | Nucleic acids research 2019-01, Vol.47 (1), p.15-28 |
|---|---|
| Hauptverfasser: | , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 28 |
|---|---|
| container_issue | 1 |
| container_start_page | 15 |
| container_title | Nucleic acids research |
| container_volume | 47 |
| creator | Gustmann, Henrik Segler, Anna-Lena J Gophane, Dnyaneshwar B Reuss, Andreas J Grünewald, Christian Braun, Markus Weigand, Julia E Sigurdsson, Snorri Th Wachtveitl, Josef |
| description | Abstract
The ability of the cytidine analog Çmf to act as a position specific reporter of RNA-dynamics was spectroscopically evaluated. Çmf-labeled single- and double-stranded RNAs differ in their fluorescence lifetimes, quantum yields and anisotropies. These observables were also influenced by the nucleobases flanking Çmf. This conformation and position specificity allowed to investigate the binding dynamics and mechanism of neomycin to its aptamer N1 by independently incorporating Çmf at four different positions within the aptamer. Remarkably fast binding kinetics of neomycin binding was observed with stopped-flow measurements, which could be satisfactorily explained with a two-step binding. Conformational selection was identified as the dominant mechanism. |
| doi_str_mv | 10.1093/nar/gky1110 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6326822</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/nar/gky1110</oup_id><sourcerecordid>2136552582</sourcerecordid><originalsourceid>FETCH-LOGICAL-c412t-f19b2150fb3e7569516d4eb4e93983c871f1135c2f0b1eeade6b687bfef79bf03</originalsourceid><addsrcrecordid>eNp9kU1v1DAQhi0EotvCiTvyCVWqQj127E0uSFXFl1S1UoGzZSfjrUsSB9sp2n9fr3ap4MJpDvPomY-XkDfA3gNrxflk4vnm5xYA2DOyAqF4VbeKPycrJpisgNXNETlO6Z4xqEHWL8mRYLXiXKkVuf-W49LlJSLdLL7HnrphCRFTh1OHdDAWBz9taMQHNEOihubfoUoZZ2r91O9aI3Z3ZvJppMHRCcO47fxEc6A-J3p7fUHNnM2I8RV54YoCXx_qCfnx6eP3yy_V1c3nr5cXV1VXA8-Vg9ZykMxZgWupWgmqr9HW2Iq2EV2zBgcgZMcds4BoelRWNWvr0K1b65g4IR_23nmxI_blkBzNoOfoRxO3Ohiv_-1M_k5vwoNWgquG8yI4PQhi-LVgynr05R_DYMp1S9K8_FhKLpsderZHuxhSiuiexgDTu3R0SUcf0in02783e2L_xFGAd3sgLPN_TY8NLJuf</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2136552582</pqid></control><display><type>article</type><title>Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Access via Oxford University Press (Open Access Collection)</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Gustmann, Henrik ; Segler, Anna-Lena J ; Gophane, Dnyaneshwar B ; Reuss, Andreas J ; Grünewald, Christian ; Braun, Markus ; Weigand, Julia E ; Sigurdsson, Snorri Th ; Wachtveitl, Josef</creator><creatorcontrib>Gustmann, Henrik ; Segler, Anna-Lena J ; Gophane, Dnyaneshwar B ; Reuss, Andreas J ; Grünewald, Christian ; Braun, Markus ; Weigand, Julia E ; Sigurdsson, Snorri Th ; Wachtveitl, Josef</creatorcontrib><description>Abstract
The ability of the cytidine analog Çmf to act as a position specific reporter of RNA-dynamics was spectroscopically evaluated. Çmf-labeled single- and double-stranded RNAs differ in their fluorescence lifetimes, quantum yields and anisotropies. These observables were also influenced by the nucleobases flanking Çmf. This conformation and position specificity allowed to investigate the binding dynamics and mechanism of neomycin to its aptamer N1 by independently incorporating Çmf at four different positions within the aptamer. Remarkably fast binding kinetics of neomycin binding was observed with stopped-flow measurements, which could be satisfactorily explained with a two-step binding. Conformational selection was identified as the dominant mechanism.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gky1110</identifier><identifier>PMID: 30462266</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Aptamers, Nucleotide - chemistry ; Aptamers, Nucleotide - genetics ; Binding Sites - genetics ; Chemical Biology and Nucleic Acid Chemistry ; Cytidine - analogs & derivatives ; Fluorescence ; Kinetics ; Neomycin - chemistry ; RNA, Double-Stranded - chemistry ; RNA, Double-Stranded - isolation & purification ; Spectrometry, Fluorescence ; Staining and Labeling - methods</subject><ispartof>Nucleic acids research, 2019-01, Vol.47 (1), p.15-28</ispartof><rights>The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c412t-f19b2150fb3e7569516d4eb4e93983c871f1135c2f0b1eeade6b687bfef79bf03</citedby><cites>FETCH-LOGICAL-c412t-f19b2150fb3e7569516d4eb4e93983c871f1135c2f0b1eeade6b687bfef79bf03</cites><orcidid>0000-0003-4247-1348 ; 0000-0002-8496-8240 ; 0000-0001-5150-627X ; 0000-0003-2492-1456</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326822/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326822/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,1605,27929,27930,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30462266$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gustmann, Henrik</creatorcontrib><creatorcontrib>Segler, Anna-Lena J</creatorcontrib><creatorcontrib>Gophane, Dnyaneshwar B</creatorcontrib><creatorcontrib>Reuss, Andreas J</creatorcontrib><creatorcontrib>Grünewald, Christian</creatorcontrib><creatorcontrib>Braun, Markus</creatorcontrib><creatorcontrib>Weigand, Julia E</creatorcontrib><creatorcontrib>Sigurdsson, Snorri Th</creatorcontrib><creatorcontrib>Wachtveitl, Josef</creatorcontrib><title>Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
The ability of the cytidine analog Çmf to act as a position specific reporter of RNA-dynamics was spectroscopically evaluated. Çmf-labeled single- and double-stranded RNAs differ in their fluorescence lifetimes, quantum yields and anisotropies. These observables were also influenced by the nucleobases flanking Çmf. This conformation and position specificity allowed to investigate the binding dynamics and mechanism of neomycin to its aptamer N1 by independently incorporating Çmf at four different positions within the aptamer. Remarkably fast binding kinetics of neomycin binding was observed with stopped-flow measurements, which could be satisfactorily explained with a two-step binding. Conformational selection was identified as the dominant mechanism.</description><subject>Aptamers, Nucleotide - chemistry</subject><subject>Aptamers, Nucleotide - genetics</subject><subject>Binding Sites - genetics</subject><subject>Chemical Biology and Nucleic Acid Chemistry</subject><subject>Cytidine - analogs & derivatives</subject><subject>Fluorescence</subject><subject>Kinetics</subject><subject>Neomycin - chemistry</subject><subject>RNA, Double-Stranded - chemistry</subject><subject>RNA, Double-Stranded - isolation & purification</subject><subject>Spectrometry, Fluorescence</subject><subject>Staining and Labeling - methods</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kU1v1DAQhi0EotvCiTvyCVWqQj127E0uSFXFl1S1UoGzZSfjrUsSB9sp2n9fr3ap4MJpDvPomY-XkDfA3gNrxflk4vnm5xYA2DOyAqF4VbeKPycrJpisgNXNETlO6Z4xqEHWL8mRYLXiXKkVuf-W49LlJSLdLL7HnrphCRFTh1OHdDAWBz9taMQHNEOihubfoUoZZ2r91O9aI3Z3ZvJppMHRCcO47fxEc6A-J3p7fUHNnM2I8RV54YoCXx_qCfnx6eP3yy_V1c3nr5cXV1VXA8-Vg9ZykMxZgWupWgmqr9HW2Iq2EV2zBgcgZMcds4BoelRWNWvr0K1b65g4IR_23nmxI_blkBzNoOfoRxO3Ohiv_-1M_k5vwoNWgquG8yI4PQhi-LVgynr05R_DYMp1S9K8_FhKLpsderZHuxhSiuiexgDTu3R0SUcf0in02783e2L_xFGAd3sgLPN_TY8NLJuf</recordid><startdate>20190110</startdate><enddate>20190110</enddate><creator>Gustmann, Henrik</creator><creator>Segler, Anna-Lena J</creator><creator>Gophane, Dnyaneshwar B</creator><creator>Reuss, Andreas J</creator><creator>Grünewald, Christian</creator><creator>Braun, Markus</creator><creator>Weigand, Julia E</creator><creator>Sigurdsson, Snorri Th</creator><creator>Wachtveitl, Josef</creator><general>Oxford University Press</general><scope>TOX</scope><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>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-4247-1348</orcidid><orcidid>https://orcid.org/0000-0002-8496-8240</orcidid><orcidid>https://orcid.org/0000-0001-5150-627X</orcidid><orcidid>https://orcid.org/0000-0003-2492-1456</orcidid></search><sort><creationdate>20190110</creationdate><title>Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer</title><author>Gustmann, Henrik ; Segler, Anna-Lena J ; Gophane, Dnyaneshwar B ; Reuss, Andreas J ; Grünewald, Christian ; Braun, Markus ; Weigand, Julia E ; Sigurdsson, Snorri Th ; Wachtveitl, Josef</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c412t-f19b2150fb3e7569516d4eb4e93983c871f1135c2f0b1eeade6b687bfef79bf03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Aptamers, Nucleotide - chemistry</topic><topic>Aptamers, Nucleotide - genetics</topic><topic>Binding Sites - genetics</topic><topic>Chemical Biology and Nucleic Acid Chemistry</topic><topic>Cytidine - analogs & derivatives</topic><topic>Fluorescence</topic><topic>Kinetics</topic><topic>Neomycin - chemistry</topic><topic>RNA, Double-Stranded - chemistry</topic><topic>RNA, Double-Stranded - isolation & purification</topic><topic>Spectrometry, Fluorescence</topic><topic>Staining and Labeling - methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gustmann, Henrik</creatorcontrib><creatorcontrib>Segler, Anna-Lena J</creatorcontrib><creatorcontrib>Gophane, Dnyaneshwar B</creatorcontrib><creatorcontrib>Reuss, Andreas J</creatorcontrib><creatorcontrib>Grünewald, Christian</creatorcontrib><creatorcontrib>Braun, Markus</creatorcontrib><creatorcontrib>Weigand, Julia E</creatorcontrib><creatorcontrib>Sigurdsson, Snorri Th</creatorcontrib><creatorcontrib>Wachtveitl, Josef</creatorcontrib><collection>Access via Oxford University Press (Open Access Collection)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gustmann, Henrik</au><au>Segler, Anna-Lena J</au><au>Gophane, Dnyaneshwar B</au><au>Reuss, Andreas J</au><au>Grünewald, Christian</au><au>Braun, Markus</au><au>Weigand, Julia E</au><au>Sigurdsson, Snorri Th</au><au>Wachtveitl, Josef</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2019-01-10</date><risdate>2019</risdate><volume>47</volume><issue>1</issue><spage>15</spage><epage>28</epage><pages>15-28</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
The ability of the cytidine analog Çmf to act as a position specific reporter of RNA-dynamics was spectroscopically evaluated. Çmf-labeled single- and double-stranded RNAs differ in their fluorescence lifetimes, quantum yields and anisotropies. These observables were also influenced by the nucleobases flanking Çmf. This conformation and position specificity allowed to investigate the binding dynamics and mechanism of neomycin to its aptamer N1 by independently incorporating Çmf at four different positions within the aptamer. Remarkably fast binding kinetics of neomycin binding was observed with stopped-flow measurements, which could be satisfactorily explained with a two-step binding. Conformational selection was identified as the dominant mechanism.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>30462266</pmid><doi>10.1093/nar/gky1110</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0003-4247-1348</orcidid><orcidid>https://orcid.org/0000-0002-8496-8240</orcidid><orcidid>https://orcid.org/0000-0001-5150-627X</orcidid><orcidid>https://orcid.org/0000-0003-2492-1456</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0305-1048 |
| ispartof | Nucleic acids research, 2019-01, Vol.47 (1), p.15-28 |
| issn | 0305-1048 1362-4962 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6326822 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Access via Oxford University Press (Open Access Collection); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Aptamers, Nucleotide - chemistry Aptamers, Nucleotide - genetics Binding Sites - genetics Chemical Biology and Nucleic Acid Chemistry Cytidine - analogs & derivatives Fluorescence Kinetics Neomycin - chemistry RNA, Double-Stranded - chemistry RNA, Double-Stranded - isolation & purification Spectrometry, Fluorescence Staining and Labeling - methods |
| title | Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-12T21%3A16%3A56IST&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=Structure%20guided%20fluorescence%20labeling%20reveals%20a%20two-step%20binding%20mechanism%20of%20neomycin%20to%20its%20RNA%20aptamer&rft.jtitle=Nucleic%20acids%20research&rft.au=Gustmann,%20Henrik&rft.date=2019-01-10&rft.volume=47&rft.issue=1&rft.spage=15&rft.epage=28&rft.pages=15-28&rft.issn=0305-1048&rft.eissn=1362-4962&rft_id=info:doi/10.1093/nar/gky1110&rft_dat=%3Cproquest_pubme%3E2136552582%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=2136552582&rft_id=info:pmid/30462266&rft_oup_id=10.1093/nar/gky1110&rfr_iscdi=true |