The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain
We report here an in-depth characterization of the aptamer domain of the transcriptional adenine-sensing riboswitch (pbuE) by NMR and fluorescence spectroscopy. By NMR studies, the structure of two aptamer sequences with different lengths of the helix P1, the central element involved in riboswitch c...
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| Veröffentlicht in: | RNA biology 2014-05, Vol.11 (5), p.655-666 |
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| container_title | RNA biology |
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| creator | Nozinovic, Senada Reining, Anke Kim, Yong-Boum Noeske, Jonas Schlepckow, Kai Wöhnert, Jens Schwalbe, Harald |
| description | We report here an in-depth characterization of the aptamer domain of the transcriptional adenine-sensing riboswitch (pbuE) by NMR and fluorescence spectroscopy. By NMR studies, the structure of two aptamer sequences with different lengths of the helix P1, the central element involved in riboswitch conformational switching, was characterized. Hydrogen-bond interactions could be mapped at nucleotide resolution providing information about secondary and tertiary structure, structure homogeneity and dynamics. Our study reveals that the elongation of helix P1 has pronounced effects not only on the local but on the global structure of the apo aptamer domain. The structural differences induced by stabilizing helix P1 were found to be linked to changes of the ligand binding affinity as revealed from analysis of kinetic and thermodynamic data obtained from stopped-flow fluorescence studies. The results provide new insight into the sequence-dependent fine tuning of the structure and function of purine-sensing riboswitches. |
| doi_str_mv | 10.4161/rna.29439 |
| format | Article |
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By NMR studies, the structure of two aptamer sequences with different lengths of the helix P1, the central element involved in riboswitch conformational switching, was characterized. Hydrogen-bond interactions could be mapped at nucleotide resolution providing information about secondary and tertiary structure, structure homogeneity and dynamics. Our study reveals that the elongation of helix P1 has pronounced effects not only on the local but on the global structure of the apo aptamer domain. The structural differences induced by stabilizing helix P1 were found to be linked to changes of the ligand binding affinity as revealed from analysis of kinetic and thermodynamic data obtained from stopped-flow fluorescence studies. The results provide new insight into the sequence-dependent fine tuning of the structure and function of purine-sensing riboswitches.</description><identifier>ISSN: 1547-6286</identifier><identifier>ISSN: 1555-8584</identifier><identifier>EISSN: 1555-8584</identifier><identifier>DOI: 10.4161/rna.29439</identifier><identifier>PMID: 24921630</identifier><language>eng</language><publisher>United States: Taylor & Francis</publisher><subject>adenine ; Adenine - metabolism ; Aptamers, Nucleotide - metabolism ; Base Pairing ; binding capacity ; fluorescence ; fluorescence emission spectroscopy ; hydrogen bonding ; Ligands ; Magnesium - metabolism ; Models, Molecular ; nuclear magnetic resonance spectroscopy ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; oligonucleotides ; Research Paper ; Riboswitch ; RNA Stability ; RNA, Bacterial - chemistry ; RNA, Bacterial - genetics ; RNA, Bacterial - metabolism ; Thermodynamics ; transcription (genetics)</subject><ispartof>RNA biology, 2014-05, Vol.11 (5), p.655-666</ispartof><rights>Copyright © 2014 Landes Bioscience 2014</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c453t-89478b64bcd03685adb3bfbcb6c63404d9bf6da36a5d4cfe11826cc350e650a13</citedby><cites>FETCH-LOGICAL-c453t-89478b64bcd03685adb3bfbcb6c63404d9bf6da36a5d4cfe11826cc350e650a13</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/PMC4152369/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152369/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24921630$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Nozinovic, Senada</creatorcontrib><creatorcontrib>Reining, Anke</creatorcontrib><creatorcontrib>Kim, Yong-Boum</creatorcontrib><creatorcontrib>Noeske, Jonas</creatorcontrib><creatorcontrib>Schlepckow, Kai</creatorcontrib><creatorcontrib>Wöhnert, Jens</creatorcontrib><creatorcontrib>Schwalbe, Harald</creatorcontrib><title>The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain</title><title>RNA biology</title><addtitle>RNA Biol</addtitle><description>We report here an in-depth characterization of the aptamer domain of the transcriptional adenine-sensing riboswitch (pbuE) by NMR and fluorescence spectroscopy. By NMR studies, the structure of two aptamer sequences with different lengths of the helix P1, the central element involved in riboswitch conformational switching, was characterized. Hydrogen-bond interactions could be mapped at nucleotide resolution providing information about secondary and tertiary structure, structure homogeneity and dynamics. Our study reveals that the elongation of helix P1 has pronounced effects not only on the local but on the global structure of the apo aptamer domain. The structural differences induced by stabilizing helix P1 were found to be linked to changes of the ligand binding affinity as revealed from analysis of kinetic and thermodynamic data obtained from stopped-flow fluorescence studies. The results provide new insight into the sequence-dependent fine tuning of the structure and function of purine-sensing riboswitches.</description><subject>adenine</subject><subject>Adenine - metabolism</subject><subject>Aptamers, Nucleotide - metabolism</subject><subject>Base Pairing</subject><subject>binding capacity</subject><subject>fluorescence</subject><subject>fluorescence emission spectroscopy</subject><subject>hydrogen bonding</subject><subject>Ligands</subject><subject>Magnesium - metabolism</subject><subject>Models, Molecular</subject><subject>nuclear magnetic resonance spectroscopy</subject><subject>Nuclear Magnetic Resonance, Biomolecular</subject><subject>Nucleic Acid Conformation</subject><subject>oligonucleotides</subject><subject>Research Paper</subject><subject>Riboswitch</subject><subject>RNA Stability</subject><subject>RNA, Bacterial - chemistry</subject><subject>RNA, Bacterial - genetics</subject><subject>RNA, Bacterial - metabolism</subject><subject>Thermodynamics</subject><subject>transcription (genetics)</subject><issn>1547-6286</issn><issn>1555-8584</issn><issn>1555-8584</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>0YH</sourceid><sourceid>EIF</sourceid><recordid>eNqFkbtuFDEUhkcIREKg4AWQS1JM8D0zDRKKuEmRoAi1dXzbNZqxB9ubsHkD3hoPGyIQBdWx5c__8fHXdc8JPuNEklc5whkdORsfdMdECNEPYuAP1zU_7yUd5FH3pJSvGDM5jOJxd0T5SIlk-Lj7cbV1KMxLyhWicSh5tHVT-I4-E1Qq6DCFukc-5bbLO1N3GSa0ZNenvIEYbqGGFBFEi6awWYsO0Ya4QeB9iOvdllhbD7AuhuhQDjqVm1DNFsFSYXYZ2TRDiE-7Rx6m4p7d1ZPuy7u3Vxcf-stP7z9evLnsDRes9sPIzwctuTZ2HUeA1Ux7bbQ0knHM7ai9tMAkCMuNd4QMVBrDBHZSYCDspHt9yF12enbWuFjbTGrJYYa8VwmC-vskhq3apGvFiaBMji3g5V1ATt92rlQ1h2LcNEF0aVcU5RzL9r8D_i_aZBFMKRtoQ08PqMmplOz8_YsIVqtl1SyrX5Yb--LPEe7J31obwA9AiE3dDDcpT1ZV2E8p-9xEh6LYv7k_AdjVuN4</recordid><startdate>20140501</startdate><enddate>20140501</enddate><creator>Nozinovic, Senada</creator><creator>Reining, Anke</creator><creator>Kim, Yong-Boum</creator><creator>Noeske, Jonas</creator><creator>Schlepckow, Kai</creator><creator>Wöhnert, Jens</creator><creator>Schwalbe, Harald</creator><general>Taylor & Francis</general><general>Landes Bioscience</general><scope>0YH</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>7S9</scope><scope>L.6</scope><scope>5PM</scope></search><sort><creationdate>20140501</creationdate><title>The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain</title><author>Nozinovic, Senada ; Reining, Anke ; Kim, Yong-Boum ; Noeske, Jonas ; Schlepckow, Kai ; Wöhnert, Jens ; Schwalbe, Harald</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c453t-89478b64bcd03685adb3bfbcb6c63404d9bf6da36a5d4cfe11826cc350e650a13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>adenine</topic><topic>Adenine - metabolism</topic><topic>Aptamers, Nucleotide - metabolism</topic><topic>Base Pairing</topic><topic>binding capacity</topic><topic>fluorescence</topic><topic>fluorescence emission spectroscopy</topic><topic>hydrogen bonding</topic><topic>Ligands</topic><topic>Magnesium - metabolism</topic><topic>Models, Molecular</topic><topic>nuclear magnetic resonance spectroscopy</topic><topic>Nuclear Magnetic Resonance, Biomolecular</topic><topic>Nucleic Acid Conformation</topic><topic>oligonucleotides</topic><topic>Research Paper</topic><topic>Riboswitch</topic><topic>RNA Stability</topic><topic>RNA, Bacterial - chemistry</topic><topic>RNA, Bacterial - genetics</topic><topic>RNA, Bacterial - metabolism</topic><topic>Thermodynamics</topic><topic>transcription (genetics)</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Nozinovic, Senada</creatorcontrib><creatorcontrib>Reining, Anke</creatorcontrib><creatorcontrib>Kim, Yong-Boum</creatorcontrib><creatorcontrib>Noeske, Jonas</creatorcontrib><creatorcontrib>Schlepckow, Kai</creatorcontrib><creatorcontrib>Wöhnert, Jens</creatorcontrib><creatorcontrib>Schwalbe, Harald</creatorcontrib><collection>Taylor & Francis Open Access</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>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>RNA biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nozinovic, Senada</au><au>Reining, Anke</au><au>Kim, Yong-Boum</au><au>Noeske, Jonas</au><au>Schlepckow, Kai</au><au>Wöhnert, Jens</au><au>Schwalbe, Harald</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain</atitle><jtitle>RNA biology</jtitle><addtitle>RNA Biol</addtitle><date>2014-05-01</date><risdate>2014</risdate><volume>11</volume><issue>5</issue><spage>655</spage><epage>666</epage><pages>655-666</pages><issn>1547-6286</issn><issn>1555-8584</issn><eissn>1555-8584</eissn><abstract>We report here an in-depth characterization of the aptamer domain of the transcriptional adenine-sensing riboswitch (pbuE) by NMR and fluorescence spectroscopy. By NMR studies, the structure of two aptamer sequences with different lengths of the helix P1, the central element involved in riboswitch conformational switching, was characterized. Hydrogen-bond interactions could be mapped at nucleotide resolution providing information about secondary and tertiary structure, structure homogeneity and dynamics. Our study reveals that the elongation of helix P1 has pronounced effects not only on the local but on the global structure of the apo aptamer domain. The structural differences induced by stabilizing helix P1 were found to be linked to changes of the ligand binding affinity as revealed from analysis of kinetic and thermodynamic data obtained from stopped-flow fluorescence studies. 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| subjects | adenine Adenine - metabolism Aptamers, Nucleotide - metabolism Base Pairing binding capacity fluorescence fluorescence emission spectroscopy hydrogen bonding Ligands Magnesium - metabolism Models, Molecular nuclear magnetic resonance spectroscopy Nuclear Magnetic Resonance, Biomolecular Nucleic Acid Conformation oligonucleotides Research Paper Riboswitch RNA Stability RNA, Bacterial - chemistry RNA, Bacterial - genetics RNA, Bacterial - metabolism Thermodynamics transcription (genetics) |
| title | The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain |
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