Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA
Identifieur interne : 001575 ( Istex/Corpus ); précédent : 001574; suivant : 001576Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA
Auteurs : P. Maruthi Mohan ; R. PadmanabhanSource :
- Gene [ 0378-1119 ] ; 1991.
English descriptors
- Teeft :
Abstract
Abstract: The 3'-terminal sequences of flavivirus genomes within approx. 100 nucleotides (nt) have been suggested to have a highly conserved secondary structure, as based on the known nt sequence data and free-energy calculations using computer programs. To test the existence of a secondary structure in solution, we devised a strategy to generate truncated RNA molecules from about 0.3–1.4 kb in length, having the same polarity and nt sequence as dengue virus type 2 (DEN-2) RNA (New Guinea-C strain). When these labeled RNA molecules were digested by RNase A, and analyzed by denaturing polyacrylamide-gel electrophoresis, three resistant fragments of 16, 20 and 23 nt in length were reproducibly obtained. To examine whether these RNase A-resistant (RNaseR) fragments emerged from a stable secondary structure formed in solution consisting of 3'-terminal sequences, hybridization of the RNaseR fragments to four chemically synthesized oligodeoxyribonucleotides (oligos), complementary to nt 1–24, 25–48, 49–72, and 73–96 from the 3' terminus of DEN-2 RNA, followed by RNase H digestion were carried out. Oligos complementary to nt 25–48 and 49–72 from the 3' end of DEN-2 RNA were sufficient to render all three RNaseR fragments susceptible to RNase H digestion. These data indicate that a stable secondary structure is formed in solution involving nt 18–67 from the 3' terminus. The potential use of these unique transcripts to identify the viral and/or host proteins which might interact at the 3' terminus of DEN-2 RNA during initiation of replication is discussed.
Url:
DOI: 10.1016/0378-1119(91)90433-C
Links to Exploration step
ISTEX:1B390769465343ADD7601B585787C5C63C5896C9Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title>Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA</title><author><name sortKey="Mohan, P Maruthi" sort="Mohan, P Maruthi" uniqKey="Mohan P" first="P. Maruthi" last="Mohan">P. Maruthi Mohan</name><affiliation><mods:affiliation>Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103 U.S.A.</mods:affiliation></affiliation></author><author><name sortKey="Padmanabhan, R" sort="Padmanabhan, R" uniqKey="Padmanabhan R" first="R." last="Padmanabhan">R. Padmanabhan</name><affiliation><mods:affiliation>Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103 U.S.A.</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:1B390769465343ADD7601B585787C5C63C5896C9</idno><date when="1991" year="1991">1991</date><idno type="doi">10.1016/0378-1119(91)90433-C</idno><idno type="url">https://api.istex.fr/ark:/67375/6H6-ZV12H3NM-L/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">001575</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">001575</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a">Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA</title><author><name sortKey="Mohan, P Maruthi" sort="Mohan, P Maruthi" uniqKey="Mohan P" first="P. Maruthi" last="Mohan">P. Maruthi Mohan</name><affiliation><mods:affiliation>Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103 U.S.A.</mods:affiliation></affiliation></author><author><name sortKey="Padmanabhan, R" sort="Padmanabhan, R" uniqKey="Padmanabhan R" first="R." last="Padmanabhan">R. Padmanabhan</name><affiliation><mods:affiliation>Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103 U.S.A.</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Gene</title><title level="j" type="abbrev">GENE</title><idno type="ISSN">0378-1119</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1991">1991</date><biblScope unit="volume">108</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="185">185</biblScope><biblScope unit="page" to="191">191</biblScope></imprint><idno type="ISSN">0378-1119</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0378-1119</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Cdna</term><term>Cleavage sites</term><term>Clone</term><term>Coli</term><term>Dengue</term><term>Digestion</term><term>Encephalitis</term><term>Flavivirus</term><term>Fragment</term><term>Genome</term><term>Hahn</term><term>Nucleotide</term><term>Oligo</term><term>Oligos</term><term>Polymerase</term><term>Rnase</term><term>Rnaser</term><term>Rnaser fragments</term><term>Same conditions</term><term>Same polarity</term><term>Secondary structure</term><term>Terminus</term><term>Transcript</term><term>Vaccine strain</term><term>Virology</term><term>Wengler</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: The 3'-terminal sequences of flavivirus genomes within approx. 100 nucleotides (nt) have been suggested to have a highly conserved secondary structure, as based on the known nt sequence data and free-energy calculations using computer programs. To test the existence of a secondary structure in solution, we devised a strategy to generate truncated RNA molecules from about 0.3–1.4 kb in length, having the same polarity and nt sequence as dengue virus type 2 (DEN-2) RNA (New Guinea-C strain). When these labeled RNA molecules were digested by RNase A, and analyzed by denaturing polyacrylamide-gel electrophoresis, three resistant fragments of 16, 20 and 23 nt in length were reproducibly obtained. To examine whether these RNase A-resistant (RNaseR) fragments emerged from a stable secondary structure formed in solution consisting of 3'-terminal sequences, hybridization of the RNaseR fragments to four chemically synthesized oligodeoxyribonucleotides (oligos), complementary to nt 1–24, 25–48, 49–72, and 73–96 from the 3' terminus of DEN-2 RNA, followed by RNase H digestion were carried out. Oligos complementary to nt 25–48 and 49–72 from the 3' end of DEN-2 RNA were sufficient to render all three RNaseR fragments susceptible to RNase H digestion. These data indicate that a stable secondary structure is formed in solution involving nt 18–67 from the 3' terminus. The potential use of these unique transcripts to identify the viral and/or host proteins which might interact at the 3' terminus of DEN-2 RNA during initiation of replication is discussed.</div></front></TEI><istex><corpusName>elsevier</corpusName><keywords><teeft><json:string>rnase</json:string><json:string>rnaser</json:string><json:string>digestion</json:string><json:string>oligo</json:string><json:string>flavivirus</json:string><json:string>rnaser fragments</json:string><json:string>oligos</json:string><json:string>genome</json:string><json:string>virology</json:string><json:string>hahn</json:string><json:string>polymerase</json:string><json:string>dengue</json:string><json:string>wengler</json:string><json:string>cdna</json:string><json:string>clone</json:string><json:string>coli</json:string><json:string>secondary structure</json:string><json:string>same polarity</json:string><json:string>cleavage sites</json:string><json:string>fragment</json:string><json:string>encephalitis</json:string><json:string>transcript</json:string><json:string>vaccine strain</json:string><json:string>same conditions</json:string><json:string>nucleotide</json:string><json:string>terminus</json:string></teeft></keywords><author><json:item><name>P.Maruthi Mohan</name><affiliations><json:string>Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103 U.S.A.</json:string></affiliations></json:item><json:item><name>R. Padmanabhan</name><affiliations><json:string>Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103 U.S.A.</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Recombinant DNA</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>flavivirus</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>in vitro transcription</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>polymerase chain reaction</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>RNase A cleavage sites</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>RNase H mapping</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>bp : base pair(s)</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>cDNA : DNA complementary to viral RNA</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>DEN-2 : dengue virus type 2</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>dNTP : deoxynucleoside triphosphates</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>ds : double strand(ed)</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>DTT : dithiothreitol</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>JE : Japanese encephalitis virus</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>kb : kilobase(s) or 1000 bp</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>MVE : Murray valley encephalitis virus</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>NGS-C : New Guinea strain C</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>nt : nucleotide(s)</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>oligo : oligodeoxyribonucleotide</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>ORF : open reading frame</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>PCR : polymerase chain reaction</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>PolIk : Klenow (large) fragment of E. coli DNA polymerase I</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>r : resistance/resistant</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>RNaseR : resistant to RNase A digestion</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>ss : single strand(ed)</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>SSC : 0.15 M NaCl/0.015 M Na3 · citrate pH 7.6</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Taq polymerase : DNA polymerase isolated from Thermus aquaticus YT1</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>TBE : tick-borne encephalitis</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>WN : West Nile virus</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>YF : yellow fever virus</value></json:item></subject><arkIstex>ark:/67375/6H6-ZV12H3NM-L</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>Full-length article</json:string></originalGenre><abstract>Abstract: The 3'-terminal sequences of flavivirus genomes within approx. 100 nucleotides (nt) have been suggested to have a highly conserved secondary structure, as based on the known nt sequence data and free-energy calculations using computer programs. To test the existence of a secondary structure in solution, we devised a strategy to generate truncated RNA molecules from about 0.3–1.4 kb in length, having the same polarity and nt sequence as dengue virus type 2 (DEN-2) RNA (New Guinea-C strain). When these labeled RNA molecules were digested by RNase A, and analyzed by denaturing polyacrylamide-gel electrophoresis, three resistant fragments of 16, 20 and 23 nt in length were reproducibly obtained. To examine whether these RNase A-resistant (RNaseR) fragments emerged from a stable secondary structure formed in solution consisting of 3'-terminal sequences, hybridization of the RNaseR fragments to four chemically synthesized oligodeoxyribonucleotides (oligos), complementary to nt 1–24, 25–48, 49–72, and 73–96 from the 3' terminus of DEN-2 RNA, followed by RNase H digestion were carried out. Oligos complementary to nt 25–48 and 49–72 from the 3' end of DEN-2 RNA were sufficient to render all three RNaseR fragments susceptible to RNase H digestion. These data indicate that a stable secondary structure is formed in solution involving nt 18–67 from the 3' terminus. The potential use of these unique transcripts to identify the viral and/or host proteins which might interact at the 3' terminus of DEN-2 RNA during initiation of replication is discussed.</abstract><qualityIndicators><score>8.561</score><pdfWordCount>3693</pdfWordCount><pdfCharCount>25388</pdfCharCount><pdfVersion>1.2</pdfVersion><pdfPageCount>7</pdfPageCount><pdfPageSize>612 x 792 pts (letter)</pdfPageSize><refBibsNative>true</refBibsNative><abstractWordCount>239</abstractWordCount><abstractCharCount>1573</abstractCharCount><keywordCount>29</keywordCount></qualityIndicators><title>Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA</title><pmid><json:string>1660836</json:string></pmid><pii><json:string>0378-1119(91)90433-C</json:string></pii><genre><json:string>research-article</json:string></genre><serie><title>Proc. Natl. Acad. Sci. USA</title><language><json:string>unknown</json:string></language><volume>74</volume><pages><first>5463</first><last>5467</last></pages></serie><host><title>Gene</title><language><json:string>unknown</json:string></language><publicationDate>1991</publicationDate><issn><json:string>0378-1119</json:string></issn><pii><json:string>S0378-1119(00)X0425-8</json:string></pii><volume>108</volume><issue>2</issue><pages><first>185</first><last>191</last></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date><json:string>1339</json:string><json:string>1991</json:string></date><geogName></geogName><orgName><json:string>Prime, Inc.</json:string><json:string>University of Kansas Medical Center, Kansas City</json:string><json:string>Biochemistry Center</json:string><json:string>Department of the Army</json:string><json:string>New Guinea, Jamaica</json:string><json:string>Department of Biochemistry, Abbreviations</json:string><json:string>Biomedical Research Support Grant/Shared Instrumentation Facility</json:string></orgName><orgName_funder></orgName_funder><orgName_provider></orgName_provider><persName><json:string>O.OlS</json:string><json:string>R. Padmanabhan</json:string><json:string>Fred Sampson</json:string></persName><placeName><json:string>Nile</json:string><json:string>KS</json:string><json:string>Madison</json:string><json:string>India</json:string><json:string>Puerto Rico</json:string><json:string>Hyderabad</json:string><json:string>Kansas City</json:string><json:string>WI</json:string><json:string>Guinea</json:string><json:string>Chester</json:string></placeName><ref_url></ref_url><ref_bibl><json:string>Sanger et al., 1977</json:string><json:string>Mandl et al., 1991</json:string><json:string>Russell et al., 1980</json:string><json:string>Jamaica et al., 1988</json:string><json:string>Brinton et al., 1986</json:string><json:string>Hahn et al., 1988</json:string><json:string>Hahn et al. (1988)</json:string><json:string>Wengler et al., 1985</json:string><json:string>1986; Wengler and Castle, 1986</json:string><json:string>Grange et al., 1985</json:string><json:string>Duebel et al., 1986</json:string><json:string>Henikoff, 1984</json:string><json:string>Hahn et al., 1987</json:string><json:string>McAda et al., 1987</json:string><json:string>KpnI et al., 1982</json:string><json:string>Tinoco et al., 1973</json:string><json:string>Coia et al., 1988</json:string><json:string>Irie et al., 1989</json:string><json:string>Sumiyoshi et al., 1987</json:string><json:string>Deubel et al., 1988</json:string><json:string>Brinton et al. (1986)</json:string><json:string>Mandl et al., 1988</json:string><json:string>Yaegashi et al., 1986</json:string><json:string>Castle et al., 1985</json:string><json:string>Mackow et al., 1987</json:string><json:string>Takegami et al., 1986</json:string><json:string>Jay et al., 1974</json:string><json:string>Zhao et al., 1986</json:string><json:string>Westaway et al., 1985</json:string><json:string>Rice et al., 1985</json:string><json:string>Hahn et al. (1987)</json:string></ref_bibl><bibl></bibl></unitex></namedEntities><ark><json:string>ark:/67375/6H6-ZV12H3NM-L</json:string></ark><categories><wos><json:string>1 - science</json:string><json:string>2 - genetics & heredity</json:string></wos><scienceMetrix><json:string>1 - health sciences</json:string><json:string>2 - biomedical research</json:string><json:string>3 - developmental biology</json:string></scienceMetrix><scopus><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Genetics</json:string><json:string>1 - Health Sciences</json:string><json:string>2 - Medicine</json:string><json:string>3 - General Medicine</json:string></scopus><inist><json:string>1 - sciences appliquees, technologies et medecines</json:string><json:string>2 - sciences biologiques et medicales</json:string><json:string>3 - sciences biologiques fondamentales et appliquees. psychologie</json:string></inist></categories><publicationDate>1991</publicationDate><copyrightDate>1991</copyrightDate><doi><json:string>10.1016/0378-1119(91)90433-C</json:string></doi><id>1B390769465343ADD7601B585787C5C63C5896C9</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-ZV12H3NM-L/fulltext.pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-ZV12H3NM-L/bundle.zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/ark:/67375/6H6-ZV12H3NM-L/fulltext.tei"><teiHeader><fileDesc><titleStmt><title level="a">Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher scheme="https://scientific-publisher.data.istex.fr">ELSEVIER</publisher><availability><licence><p>elsevier</p></licence></availability><p scheme="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M"></p><date>1991</date></publicationStmt><notesStmt><note type="research-article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</note><note type="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note><note>Received by J.R. Putnak</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a">Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA</title><author xml:id="author-0000"><persName><forename type="first">P.Maruthi</forename><surname>Mohan</surname></persName><note type="biography">Present address: Department of Biochemistry, Osmania University, Hyderabad-500007 (A.P.) (India) Tel. (091) 842-868951 (Ext. 245); Fax (91) 842-869020.</note><affiliation>Present address: Department of Biochemistry, Osmania University, Hyderabad-500007 (A.P.) (India) Tel. (091) 842-868951 (Ext. 245); Fax (91) 842-869020.</affiliation><affiliation>Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103 U.S.A.</affiliation></author><author xml:id="author-0001"><persName><forename type="first">R.</forename><surname>Padmanabhan</surname></persName><note type="correspondence"><p>Correspondence to: Dr. R. Padmanabhan, Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 39th and Rainbow Blvd., Kansas City, KS 66103 U.S.A. Tel. (913)588-7018; Fax (913)588-4903.</p></note><affiliation>Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103 U.S.A.</affiliation></author><idno type="istex">1B390769465343ADD7601B585787C5C63C5896C9</idno><idno type="ark">ark:/67375/6H6-ZV12H3NM-L</idno><idno type="DOI">10.1016/0378-1119(91)90433-C</idno><idno type="PII">0378-1119(91)90433-C</idno></analytic><monogr><title level="j">Gene</title><title level="j" type="abbrev">GENE</title><idno type="pISSN">0378-1119</idno><idno type="PII">S0378-1119(00)X0425-8</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1991"></date><biblScope unit="volume">108</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="185">185</biblScope><biblScope unit="page" to="191">191</biblScope></imprint></monogr></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>1991</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Abstract: The 3'-terminal sequences of flavivirus genomes within approx. 100 nucleotides (nt) have been suggested to have a highly conserved secondary structure, as based on the known nt sequence data and free-energy calculations using computer programs. To test the existence of a secondary structure in solution, we devised a strategy to generate truncated RNA molecules from about 0.3–1.4 kb in length, having the same polarity and nt sequence as dengue virus type 2 (DEN-2) RNA (New Guinea-C strain). When these labeled RNA molecules were digested by RNase A, and analyzed by denaturing polyacrylamide-gel electrophoresis, three resistant fragments of 16, 20 and 23 nt in length were reproducibly obtained. To examine whether these RNase A-resistant (RNaseR) fragments emerged from a stable secondary structure formed in solution consisting of 3'-terminal sequences, hybridization of the RNaseR fragments to four chemically synthesized oligodeoxyribonucleotides (oligos), complementary to nt 1–24, 25–48, 49–72, and 73–96 from the 3' terminus of DEN-2 RNA, followed by RNase H digestion were carried out. Oligos complementary to nt 25–48 and 49–72 from the 3' end of DEN-2 RNA were sufficient to render all three RNaseR fragments susceptible to RNase H digestion. These data indicate that a stable secondary structure is formed in solution involving nt 18–67 from the 3' terminus. The potential use of these unique transcripts to identify the viral and/or host proteins which might interact at the 3' terminus of DEN-2 RNA during initiation of replication is discussed.</p></abstract><textClass><keywords scheme="keyword"><list><head>Keywords</head><item><term>Recombinant DNA</term></item><item><term>flavivirus</term></item><item><term>in vitro transcription</term></item><item><term>polymerase chain reaction</term></item><item><term>RNase A cleavage sites</term></item><item><term>RNase H mapping</term></item></list></keywords></textClass><textClass><keywords scheme="keyword"><list><head>Abbreviations</head><item><term>bp</term><term>base pair(s)</term></item><item><term>cDNA</term><term>DNA complementary to viral RNA</term></item><item><term>DEN-2</term><term>dengue virus type 2</term></item><item><term>dNTP</term><term>deoxynucleoside triphosphates</term></item><item><term>ds</term><term>double strand(ed)</term></item><item><term>DTT</term><term>dithiothreitol</term></item><item><term>JE</term><term>Japanese encephalitis virus</term></item><item><term>kb</term><term>kilobase(s) or 1000 bp</term></item><item><term>MVE</term><term>Murray valley encephalitis virus</term></item><item><term>NGS-C</term><term>New Guinea strain C</term></item><item><term>nt</term><term>nucleotide(s)</term></item><item><term>oligo</term><term>oligodeoxyribonucleotide</term></item><item><term>ORF</term><term>open reading frame</term></item><item><term>PCR</term><term>polymerase chain reaction</term></item><item><term>PolIk</term><term>Klenow (large) fragment of E. coli DNA polymerase I</term></item><item><term>r</term><term>resistance/resistant</term></item><item><term>RNaseR</term><term>resistant to RNase A digestion</term></item><item><term>ss</term><term>single strand(ed)</term></item><item><term>SSC</term><term>0.15 M NaCl/0.015 M Na3 · citrate pH 7.6</term></item><item><term>Taq polymerase</term><term>DNA polymerase isolated from Thermus aquaticus YT1</term></item><item><term>TBE</term><term>tick-borne encephalitis</term></item><item><term>WN</term><term>West Nile virus</term></item><item><term>YF</term><term>yellow fever virus</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="1991-08-10">Modified</change><change when="1991">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-ZV12H3NM-L/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Elsevier, elements deleted: tail"><istex:xmlDeclaration>version="1.0" encoding="utf-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//ES//DTD journal article DTD version 4.5.2//EN//XML" URI="art452.dtd" name="istex:docType"></istex:docType><istex:document><converted-article version="4.5.2" docsubtype="fla"><item-info><jid>GENE</jid><aid>9190433C</aid><ce:pii>0378-1119(91)90433-C</ce:pii><ce:doi>10.1016/0378-1119(91)90433-C</ce:doi><ce:copyright type="unknown" year="1991"></ce:copyright></item-info><head><ce:title>Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA</ce:title><ce:author-group><ce:author><ce:given-name>P.Maruthi</ce:given-name><ce:surname>Mohan</ce:surname><ce:cross-ref refid="FN1"><ce:sup>∗</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>R.</ce:given-name><ce:surname>Padmanabhan</ce:surname><ce:cross-ref refid="COR1"><ce:sup>∗</ce:sup></ce:cross-ref></ce:author><ce:affiliation><ce:textfn>Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103 U.S.A.</ce:textfn></ce:affiliation><ce:correspondence id="COR1"><ce:label>∗</ce:label><ce:text>Correspondence to: Dr. R. Padmanabhan, Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 39th and Rainbow Blvd., Kansas City, KS 66103 U.S.A. Tel. (913)588-7018; Fax (913)588-4903.</ce:text></ce:correspondence><ce:footnote id="FN1"><ce:label>∗</ce:label><ce:note-para>Present address: Department of Biochemistry, Osmania University, Hyderabad-500007 (A.P.) (India) Tel. (091) 842-868951 (Ext. 245); Fax (91) 842-869020.</ce:note-para></ce:footnote></ce:author-group><ce:date-received day="6" month="11" year="1989"></ce:date-received><ce:date-revised day="10" month="8" year="1991"></ce:date-revised><ce:date-accepted day="14" month="8" year="1991"></ce:date-accepted><ce:miscellaneous>Received by J.R. Putnak</ce:miscellaneous><ce:abstract><ce:section-title>Abstract</ce:section-title><ce:abstract-sec><ce:simple-para>The 3'-terminal sequences of flavivirus genomes within approx. 100 nucleotides (nt) have been suggested to have a highly conserved secondary structure, as based on the known nt sequence data and free-energy calculations using computer programs. To test the existence of a secondary structure in solution, we devised a strategy to generate truncated RNA molecules from about 0.3–1.4 kb in length, having the same polarity and nt sequence as dengue virus type 2 (DEN-2) RNA (New Guinea-C strain). When these labeled RNA molecules were digested by RNase A, and analyzed by denaturing polyacrylamide-gel electrophoresis, three resistant fragments of 16, 20 and 23 nt in length were reproducibly obtained. To examine whether these RNase A-resistant (RNase<ce:sup>R</ce:sup>) fragments emerged from a stable secondary structure formed in solution consisting of 3'-terminal sequences, hybridization of the RNase<ce:sup>R</ce:sup> fragments to four chemically synthesized oligodeoxyribonucleotides (oligos), complementary to nt 1–24, 25–48, 49–72, and 73–96 from the 3' terminus of DEN-2 RNA, followed by RNase H digestion were carried out. Oligos complementary to nt 25–48 and 49–72 from the 3' end of DEN-2 RNA were sufficient to render all three RNase<ce:sup>R</ce:sup> fragments susceptible to RNase H digestion. These data indicate that a stable secondary structure is formed in solution involving nt 18–67 from the 3' terminus. The potential use of these unique transcripts to identify the viral and/or host proteins which might interact at the 3' terminus of DEN-2 RNA during initiation of replication is discussed.</ce:simple-para></ce:abstract-sec></ce:abstract><ce:keywords><ce:section-title>Keywords</ce:section-title><ce:keyword><ce:text>Recombinant DNA</ce:text></ce:keyword><ce:keyword><ce:text>flavivirus</ce:text></ce:keyword><ce:keyword><ce:text>in vitro transcription</ce:text></ce:keyword><ce:keyword><ce:text>polymerase chain reaction</ce:text></ce:keyword><ce:keyword><ce:text>RNase A cleavage sites</ce:text></ce:keyword><ce:keyword><ce:text>RNase H mapping</ce:text></ce:keyword></ce:keywords><ce:keywords class="abr"><ce:section-title>Abbreviations</ce:section-title><ce:keyword><ce:text>bp</ce:text><ce:keyword><ce:text>base pair(s)</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>cDNA</ce:text><ce:keyword><ce:text>DNA complementary to viral RNA</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>DEN-2</ce:text><ce:keyword><ce:text>dengue virus type 2</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>dNTP</ce:text><ce:keyword><ce:text>deoxynucleoside triphosphates</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>ds</ce:text><ce:keyword><ce:text>double strand(ed)</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>DTT</ce:text><ce:keyword><ce:text>dithiothreitol</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>JE</ce:text><ce:keyword><ce:text>Japanese encephalitis virus</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>kb</ce:text><ce:keyword><ce:text>kilobase(s) or 1000 bp</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>MVE</ce:text><ce:keyword><ce:text>Murray valley encephalitis virus</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>NGS-C</ce:text><ce:keyword><ce:text>New Guinea strain C</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>nt</ce:text><ce:keyword><ce:text>nucleotide(s)</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>oligo</ce:text><ce:keyword><ce:text>oligodeoxyribonucleotide</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>ORF</ce:text><ce:keyword><ce:text>open reading frame</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>PCR</ce:text><ce:keyword><ce:text>polymerase chain reaction</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>PolIk</ce:text><ce:keyword><ce:text>Klenow (large) fragment of <ce:italic>E. coli</ce:italic> DNA polymerase I</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text><ce:small-caps>r</ce:small-caps></ce:text><ce:keyword><ce:text>resistance/resistant</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>RNase<ce:sup>R</ce:sup></ce:text><ce:keyword><ce:text>resistant to RNase A digestion</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>ss</ce:text><ce:keyword><ce:text>single strand(ed)</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>SSC</ce:text><ce:keyword><ce:text>0.15 M NaCl/0.015 M Na<ce:inf>3</ce:inf> · citrate pH 7.6</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text><ce:italic>Taq</ce:italic> polymerase</ce:text><ce:keyword><ce:text>DNA polymerase isolated from <ce:italic>Thermus aquaticus</ce:italic> YT1</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>TBE</ce:text><ce:keyword><ce:text>tick-borne encephalitis</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>WN</ce:text><ce:keyword><ce:text>West Nile virus</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>YF</ce:text><ce:keyword><ce:text>yellow fever virus</ce:text></ce:keyword></ce:keyword></ce:keywords></head></converted-article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo><title>Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA</title></titleInfo><name type="personal"><namePart type="given">P.Maruthi</namePart><namePart type="family">Mohan</namePart><affiliation>Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103 U.S.A.</affiliation><description>Present address: Department of Biochemistry, Osmania University, Hyderabad-500007 (A.P.) (India) Tel. (091) 842-868951 (Ext. 245); Fax (91) 842-869020.</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">R.</namePart><namePart type="family">Padmanabhan</namePart><affiliation>Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103 U.S.A.</affiliation><description>Correspondence to: Dr. R. Padmanabhan, Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 39th and Rainbow Blvd., Kansas City, KS 66103 U.S.A. Tel. (913)588-7018; Fax (913)588-4903.</description><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="Full-length article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">1991</dateIssued><dateModified encoding="w3cdtf">1991-08-10</dateModified><copyrightDate encoding="w3cdtf">1991</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><abstract lang="en">Abstract: The 3'-terminal sequences of flavivirus genomes within approx. 100 nucleotides (nt) have been suggested to have a highly conserved secondary structure, as based on the known nt sequence data and free-energy calculations using computer programs. To test the existence of a secondary structure in solution, we devised a strategy to generate truncated RNA molecules from about 0.3–1.4 kb in length, having the same polarity and nt sequence as dengue virus type 2 (DEN-2) RNA (New Guinea-C strain). When these labeled RNA molecules were digested by RNase A, and analyzed by denaturing polyacrylamide-gel electrophoresis, three resistant fragments of 16, 20 and 23 nt in length were reproducibly obtained. To examine whether these RNase A-resistant (RNaseR) fragments emerged from a stable secondary structure formed in solution consisting of 3'-terminal sequences, hybridization of the RNaseR fragments to four chemically synthesized oligodeoxyribonucleotides (oligos), complementary to nt 1–24, 25–48, 49–72, and 73–96 from the 3' terminus of DEN-2 RNA, followed by RNase H digestion were carried out. Oligos complementary to nt 25–48 and 49–72 from the 3' end of DEN-2 RNA were sufficient to render all three RNaseR fragments susceptible to RNase H digestion. These data indicate that a stable secondary structure is formed in solution involving nt 18–67 from the 3' terminus. The potential use of these unique transcripts to identify the viral and/or host proteins which might interact at the 3' terminus of DEN-2 RNA during initiation of replication is discussed.</abstract><note>Received by J.R. Putnak</note><subject><genre>Keywords</genre><topic>Recombinant DNA</topic><topic>flavivirus</topic><topic>in vitro transcription</topic><topic>polymerase chain reaction</topic><topic>RNase A cleavage sites</topic><topic>RNase H mapping</topic></subject><subject><genre>Abbreviations</genre><topic>bp : base pair(s)</topic><topic>cDNA : DNA complementary to viral RNA</topic><topic>DEN-2 : dengue virus type 2</topic><topic>dNTP : deoxynucleoside triphosphates</topic><topic>ds : double strand(ed)</topic><topic>DTT : dithiothreitol</topic><topic>JE : Japanese encephalitis virus</topic><topic>kb : kilobase(s) or 1000 bp</topic><topic>MVE : Murray valley encephalitis virus</topic><topic>NGS-C : New Guinea strain C</topic><topic>nt : nucleotide(s)</topic><topic>oligo : oligodeoxyribonucleotide</topic><topic>ORF : open reading frame</topic><topic>PCR : polymerase chain reaction</topic><topic>PolIk : Klenow (large) fragment of E. coli DNA polymerase I</topic><topic>r : resistance/resistant</topic><topic>RNaseR : resistant to RNase A digestion</topic><topic>ss : single strand(ed)</topic><topic>SSC : 0.15 M NaCl/0.015 M Na3 · citrate pH 7.6</topic><topic>Taq polymerase : DNA polymerase isolated from Thermus aquaticus YT1</topic><topic>TBE : tick-borne encephalitis</topic><topic>WN : West Nile virus</topic><topic>YF : yellow fever virus</topic></subject><relatedItem type="host"><titleInfo><title>Gene</title></titleInfo><titleInfo type="abbreviated"><title>GENE</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">1991</dateIssued></originInfo><identifier type="ISSN">0378-1119</identifier><identifier type="PII">S0378-1119(00)X0425-8</identifier><part><date>1991</date><detail type="volume"><number>108</number><caption>vol.</caption></detail><detail type="issue"><number>2</number><caption>no.</caption></detail><extent unit="issue-pages"><start>167</start><end>321</end></extent><extent unit="pages"><start>185</start><end>191</end></extent></part></relatedItem><identifier type="istex">1B390769465343ADD7601B585787C5C63C5896C9</identifier><identifier type="ark">ark:/67375/6H6-ZV12H3NM-L</identifier><identifier type="DOI">10.1016/0378-1119(91)90433-C</identifier><identifier type="PII">0378-1119(91)90433-C</identifier><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M">elsevier</recordContentSource></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-ZV12H3NM-L/record.json</uri></json:item></metadata></istex></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Istex/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001575 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Istex/Corpus/biblio.hfd -nk 001575 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Istex
|étape= Corpus
|type= RBID
|clé= ISTEX:1B390769465343ADD7601B585787C5C63C5896C9
|texte= Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA
}}
| This area was generated with Dilib version V0.6.33. |  |