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Folding of pyrimidine-enriched RNA fragments from the vicinity of the internal ribosomal entry site ofHepatitis A virus
Two RNA fragments from the region just upstream of the internal ribosome entry site of Hepatitis A virus (HAV) were studied, a 35mer (HAV-35), 5'U
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| Published in: | Nucleic acids research 1999-01, Vol.27 (2), p.665 |
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| container_title | Nucleic acids research |
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| creator | Hardin, Charles C Sneeden, Jessica L Lemon, Stanley M Brown, Bernard A Guenther, Richard H Hanna Sierzputowska-Gracz |
| description | Two RNA fragments from the region just upstream of the internal ribosome entry site of Hepatitis A virus (HAV) were studied, a 35mer (HAV-35), 5'U |
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Secondary structural predictions and nuclease digestion patterns obtained with genomic RNAs suggested that they link two stable Watson-Crick (WC) hairpins in the genomic RNA and do not form conventional WC secondary structure, but do fold to form a condensed, stacked `domain'. To obtain more information, folding of HAV-23 and -35 RNA fragments was characterized using 1H nuclear magnetic resonance, in H<2<O as a function of pH and temperature, circular dichroism as a function of NaCl concentration, pH and temperature, and square-wave voltammetry as afunction of pH. The results indicate that these oligo-nucleotides form intramolecular structures that contain transient U*U base pairs at pH 7 and moderate ionic strength (100 mM NaCl). This folded structure becomes destabilized and loses the U*U base pairs above and below neutral pH, especially at ionic strengths above 0.1. All of the cytidine protons exchange relatively rapidly with solvent protons (exchange lifetimes shorter than 1 ms), so the structure contains few if any C*C<H<<+< base pairs at neutral pH, but can apparently form them at pH values below 6. We present a series of possible models in which chain folding draws the strand termini closer together, possibly serving to pull the attached WC hairpin domains together and providing a functional advantage by nucleating reversible formation of a more viable RNA substrate.]]></description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>CODEN: NARHAD</identifier><language>eng</language><publisher>Oxford: Oxford Publishing Limited (England)</publisher><ispartof>Nucleic acids research, 1999-01, Vol.27 (2), p.665</ispartof><rights>Copyright Oxford University Press(England) Jan 15, 1999</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780</link.rule.ids></links><search><creatorcontrib>Hardin, Charles C</creatorcontrib><creatorcontrib>Sneeden, Jessica L</creatorcontrib><creatorcontrib>Lemon, Stanley M</creatorcontrib><creatorcontrib>Brown, Bernard A</creatorcontrib><creatorcontrib>Guenther, Richard H</creatorcontrib><creatorcontrib>Hanna Sierzputowska-Gracz</creatorcontrib><title>Folding of pyrimidine-enriched RNA fragments from the vicinity of the internal ribosomal entry site ofHepatitis A virus</title><title>Nucleic acids research</title><description><![CDATA[Two RNA fragments from the region just upstream of the internal ribosome entry site of Hepatitis A virus (HAV) were studied, a 35mer (HAV-35), 5'U<4<C<3<U<3<C<3<U<4<C<3<U<3<C<2<UAU<2<C<3<U<3<3<4<, and a 23mer (HAV-23), 5<4<U<4<C<3<U<3<C<3<U<4<C<3<U<3<3<4<. Secondary structural predictions and nuclease digestion patterns obtained with genomic RNAs suggested that they link two stable Watson-Crick (WC) hairpins in the genomic RNA and do not form conventional WC secondary structure, but do fold to form a condensed, stacked `domain'. To obtain more information, folding of HAV-23 and -35 RNA fragments was characterized using 1H nuclear magnetic resonance, in H<2<O as a function of pH and temperature, circular dichroism as a function of NaCl concentration, pH and temperature, and square-wave voltammetry as afunction of pH. The results indicate that these oligo-nucleotides form intramolecular structures that contain transient U*U base pairs at pH 7 and moderate ionic strength (100 mM NaCl). This folded structure becomes destabilized and loses the U*U base pairs above and below neutral pH, especially at ionic strengths above 0.1. All of the cytidine protons exchange relatively rapidly with solvent protons (exchange lifetimes shorter than 1 ms), so the structure contains few if any C*C<H<<+< base pairs at neutral pH, but can apparently form them at pH values below 6. We present a series of possible models in which chain folding draws the strand termini closer together, possibly serving to pull the attached WC hairpin domains together and providing a functional advantage by nucleating reversible formation of a more viable RNA substrate.]]></description><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1999</creationdate><recordtype>article</recordtype><recordid>eNqNjMsKwjAQRYMoWB__MLgvJH2ILkUUVy7EvdQ6tVPapGZSpX9vCn6Aq3svnHNHIlDxOgqT7Toai0DGMg2VTDZTMWOupFSJSpNAfI6mfpB-gimg7S015BeGqC3lJT7gct5BYbNng9qxb6YBVyK8KSdNrh-0YZN2aHVWg6W7YdP45gXbA5NDD52wzRw5Yth513a8EJMiqxmXv5yL1fFw3Z_C1ppXh-xulemGR75FUqabKFYy_gv6AtEsTmI</recordid><startdate>19990115</startdate><enddate>19990115</enddate><creator>Hardin, Charles C</creator><creator>Sneeden, Jessica L</creator><creator>Lemon, Stanley M</creator><creator>Brown, Bernard A</creator><creator>Guenther, Richard H</creator><creator>Hanna Sierzputowska-Gracz</creator><general>Oxford Publishing Limited (England)</general><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>19990115</creationdate><title>Folding of pyrimidine-enriched RNA fragments from the vicinity of the internal ribosomal entry site ofHepatitis A virus</title><author>Hardin, Charles C ; Sneeden, Jessica L ; Lemon, Stanley M ; Brown, Bernard A ; Guenther, Richard H ; Hanna Sierzputowska-Gracz</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-proquest_journals_2005823103</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1999</creationdate><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hardin, Charles C</creatorcontrib><creatorcontrib>Sneeden, Jessica L</creatorcontrib><creatorcontrib>Lemon, Stanley M</creatorcontrib><creatorcontrib>Brown, Bernard A</creatorcontrib><creatorcontrib>Guenther, Richard H</creatorcontrib><creatorcontrib>Hanna Sierzputowska-Gracz</creatorcontrib><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hardin, Charles C</au><au>Sneeden, Jessica L</au><au>Lemon, Stanley M</au><au>Brown, Bernard A</au><au>Guenther, Richard H</au><au>Hanna Sierzputowska-Gracz</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Folding of pyrimidine-enriched RNA fragments from the vicinity of the internal ribosomal entry site ofHepatitis A virus</atitle><jtitle>Nucleic acids research</jtitle><date>1999-01-15</date><risdate>1999</risdate><volume>27</volume><issue>2</issue><spage>665</spage><pages>665-</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><coden>NARHAD</coden><abstract><![CDATA[Two RNA fragments from the region just upstream of the internal ribosome entry site of Hepatitis A virus (HAV) were studied, a 35mer (HAV-35), 5'U<4<C<3<U<3<C<3<U<4<C<3<U<3<C<2<UAU<2<C<3<U<3<3<4<, and a 23mer (HAV-23), 5<4<U<4<C<3<U<3<C<3<U<4<C<3<U<3<3<4<. Secondary structural predictions and nuclease digestion patterns obtained with genomic RNAs suggested that they link two stable Watson-Crick (WC) hairpins in the genomic RNA and do not form conventional WC secondary structure, but do fold to form a condensed, stacked `domain'. To obtain more information, folding of HAV-23 and -35 RNA fragments was characterized using 1H nuclear magnetic resonance, in H<2<O as a function of pH and temperature, circular dichroism as a function of NaCl concentration, pH and temperature, and square-wave voltammetry as afunction of pH. The results indicate that these oligo-nucleotides form intramolecular structures that contain transient U*U base pairs at pH 7 and moderate ionic strength (100 mM NaCl). This folded structure becomes destabilized and loses the U*U base pairs above and below neutral pH, especially at ionic strengths above 0.1. All of the cytidine protons exchange relatively rapidly with solvent protons (exchange lifetimes shorter than 1 ms), so the structure contains few if any C*C<H<<+< base pairs at neutral pH, but can apparently form them at pH values below 6. We present a series of possible models in which chain folding draws the strand termini closer together, possibly serving to pull the attached WC hairpin domains together and providing a functional advantage by nucleating reversible formation of a more viable RNA substrate.]]></abstract><cop>Oxford</cop><pub>Oxford Publishing Limited (England)</pub></addata></record> |
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| ispartof | Nucleic acids research, 1999-01, Vol.27 (2), p.665 |
| issn | 0305-1048 1362-4962 |
| language | eng |
| recordid | cdi_proquest_journals_200582310 |
| source | Oxford Open; PubMed Central |
| title | Folding of pyrimidine-enriched RNA fragments from the vicinity of the internal ribosomal entry site ofHepatitis A virus |
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