Characterization and comparison of synthetic immobile and mobile Holliday junctions.
Identifieur interne : 002A24 ( Ncbi/Merge ); précédent : 002A23; suivant : 002A25Characterization and comparison of synthetic immobile and mobile Holliday junctions.
Auteurs : T. Shida ; H. Iwasaki ; H. Shinagawa ; Y. KyogokuSource :
- Journal of biochemistry [ 0021-924X ] ; 1996.
Descripteurs français
- KwdFr :
- ADN (), ADN (métabolisme), ADN (synthèse chimique), Dichroïsme circulaire, Données de séquences moléculaires, Dénaturation d'acide nucléique, Endodeoxyribonucleases (métabolisme), Liaison aux protéines, Oligodésoxyribonucléotides (), Oligodésoxyribonucléotides (métabolisme), Oligodésoxyribonucléotides (synthèse chimique), Protéines Escherichia coli, Protéines bactériennes (métabolisme), Recombinaison génétique, Spectrophotométrie UV, Séquence nucléotidique, Électrophorèse sur gel de polyacrylamide.
- MESH :
- métabolisme : ADN, Endodeoxyribonucleases, Oligodésoxyribonucléotides, Protéines bactériennes.
- synthèse chimique : ADN, Oligodésoxyribonucléotides.
- ADN, Dichroïsme circulaire, Données de séquences moléculaires, Dénaturation d'acide nucléique, Liaison aux protéines, Oligodésoxyribonucléotides, Protéines Escherichia coli, Recombinaison génétique, Spectrophotométrie UV, Séquence nucléotidique, Électrophorèse sur gel de polyacrylamide.
English descriptors
- KwdEn :
- Bacterial Proteins (metabolism), Base Sequence, Circular Dichroism, DNA (chemical synthesis), DNA (chemistry), DNA (metabolism), Electrophoresis, Polyacrylamide Gel, Endodeoxyribonucleases (metabolism), Escherichia coli Proteins, Molecular Sequence Data, Nucleic Acid Denaturation, Oligodeoxyribonucleotides (chemical synthesis), Oligodeoxyribonucleotides (chemistry), Oligodeoxyribonucleotides (metabolism), Protein Binding, Recombination, Genetic, Spectrophotometry, Ultraviolet.
- MESH :
- chemical , chemical synthesis : DNA, Oligodeoxyribonucleotides.
- chemical , chemistry : DNA, Oligodeoxyribonucleotides.
- chemical , metabolism : Bacterial Proteins, DNA, Endodeoxyribonucleases, Oligodeoxyribonucleotides.
- Base Sequence, Circular Dichroism, Electrophoresis, Polyacrylamide Gel, Escherichia coli Proteins, Molecular Sequence Data, Nucleic Acid Denaturation, Protein Binding, Recombination, Genetic, Spectrophotometry, Ultraviolet.
Abstract
Eight synthetic Holliday junction (HJ) oligonucleotides containing an immobile or a mobile junction were characterized by gel electrophoresis, ultraviolet absorption and circular dichroism (CD) spectroscopy. Four 24-mer deoxyribonucleotides formed stable immobile and mobile HJs in 0.1 M NaCl at 5 muM strand concentration at room temperature. However, the immobile HJ constructed from four 18-mers was less stable, and four 12-mers did not form the HJ structure under the conditions used. A comparison of the melting profiles of the HJs with those of the duplexes corresponding to the arms of four-way junctions indicated that the thermal stability of the HJ was similar to that of the individual arm and the cooperativity of the melting behavior of the HJ was relatively higher than that of the individual arm duplex. The Tms of the mobile HJs containing 4, 6, 8, and 10 base-pair homologous cores at junctions were essentially identical with that of the immobile HJ of the same size. There is a tendency that the HJ containing a larger homologous core region becomes more resistant to thermal denaturation. The addition of divalent metal cations, Mg2+ and Ca2+, to the solutions of the HJs raised their melting temperatures. The difference found for the CD spectra of the HJs which differ only in the arrangement of the HJ depended primarily upon the DNA sequence flanking the junction. The RuvC protein binds to the immobile and mobile HJs, regardless of the presence and the size of the homologous core at the junction.
DOI: 10.1093/oxfordjournals.jbchem.a021292
PubMed: 8743565
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pubmed:8743565Le document en format XML
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Shida</name><affiliation><nlm:affiliation>Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Nagano.</nlm:affiliation><wicri:noCountry code="subField">Nagano</wicri:noCountry></affiliation></author><author><name sortKey="Iwasaki, H" sort="Iwasaki, H" uniqKey="Iwasaki H" first="H" last="Iwasaki">H. Iwasaki</name></author><author><name sortKey="Shinagawa, H" sort="Shinagawa, H" uniqKey="Shinagawa H" first="H" last="Shinagawa">H. Shinagawa</name></author><author><name sortKey="Kyogoku, Y" sort="Kyogoku, Y" uniqKey="Kyogoku Y" first="Y" last="Kyogoku">Y. Kyogoku</name></author></analytic><series><title level="j">Journal of biochemistry</title><idno type="ISSN">0021-924X</idno><imprint><date when="1996" type="published">1996</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacterial Proteins (metabolism)</term><term>Base Sequence</term><term>Circular Dichroism</term><term>DNA (chemical synthesis)</term><term>DNA (chemistry)</term><term>DNA (metabolism)</term><term>Electrophoresis, Polyacrylamide Gel</term><term>Endodeoxyribonucleases (metabolism)</term><term>Escherichia coli Proteins</term><term>Molecular Sequence Data</term><term>Nucleic Acid Denaturation</term><term>Oligodeoxyribonucleotides (chemical synthesis)</term><term>Oligodeoxyribonucleotides (chemistry)</term><term>Oligodeoxyribonucleotides (metabolism)</term><term>Protein Binding</term><term>Recombination, Genetic</term><term>Spectrophotometry, Ultraviolet</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>ADN (métabolisme)</term><term>ADN (synthèse chimique)</term><term>Dichroïsme circulaire</term><term>Données de séquences moléculaires</term><term>Dénaturation d'acide nucléique</term><term>Endodeoxyribonucleases (métabolisme)</term><term>Liaison aux protéines</term><term>Oligodésoxyribonucléotides ()</term><term>Oligodésoxyribonucléotides (métabolisme)</term><term>Oligodésoxyribonucléotides (synthèse chimique)</term><term>Protéines Escherichia coli</term><term>Protéines bactériennes (métabolisme)</term><term>Recombinaison génétique</term><term>Spectrophotométrie UV</term><term>Séquence nucléotidique</term><term>Électrophorèse sur gel de polyacrylamide</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemical synthesis" xml:lang="en"><term>DNA</term><term>Oligodeoxyribonucleotides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>Oligodeoxyribonucleotides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Bacterial Proteins</term><term>DNA</term><term>Endodeoxyribonucleases</term><term>Oligodeoxyribonucleotides</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term><term>Endodeoxyribonucleases</term><term>Oligodésoxyribonucléotides</term><term>Protéines bactériennes</term></keywords><keywords scheme="MESH" qualifier="synthèse chimique" xml:lang="fr"><term>ADN</term><term>Oligodésoxyribonucléotides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Circular Dichroism</term><term>Electrophoresis, Polyacrylamide Gel</term><term>Escherichia coli Proteins</term><term>Molecular Sequence Data</term><term>Nucleic Acid Denaturation</term><term>Protein Binding</term><term>Recombination, Genetic</term><term>Spectrophotometry, Ultraviolet</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Dichroïsme circulaire</term><term>Données de séquences moléculaires</term><term>Dénaturation d'acide nucléique</term><term>Liaison aux protéines</term><term>Oligodésoxyribonucléotides</term><term>Protéines Escherichia coli</term><term>Recombinaison génétique</term><term>Spectrophotométrie UV</term><term>Séquence nucléotidique</term><term>Électrophorèse sur gel de polyacrylamide</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Eight synthetic Holliday junction (HJ) oligonucleotides containing an immobile or a mobile junction were characterized by gel electrophoresis, ultraviolet absorption and circular dichroism (CD) spectroscopy. Four 24-mer deoxyribonucleotides formed stable immobile and mobile HJs in 0.1 M NaCl at 5 muM strand concentration at room temperature. However, the immobile HJ constructed from four 18-mers was less stable, and four 12-mers did not form the HJ structure under the conditions used. A comparison of the melting profiles of the HJs with those of the duplexes corresponding to the arms of four-way junctions indicated that the thermal stability of the HJ was similar to that of the individual arm and the cooperativity of the melting behavior of the HJ was relatively higher than that of the individual arm duplex. The Tms of the mobile HJs containing 4, 6, 8, and 10 base-pair homologous cores at junctions were essentially identical with that of the immobile HJ of the same size. There is a tendency that the HJ containing a larger homologous core region becomes more resistant to thermal denaturation. The addition of divalent metal cations, Mg2+ and Ca2+, to the solutions of the HJs raised their melting temperatures. The difference found for the CD spectra of the HJs which differ only in the arrangement of the HJ depended primarily upon the DNA sequence flanking the junction. The RuvC protein binds to the immobile and mobile HJs, regardless of the presence and the size of the homologous core at the junction.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">8743565</PMID><DateCompleted><Year>1996</Year><Month>10</Month><Day>24</Day></DateCompleted><DateRevised><Year>2019</Year><Month>05</Month><Day>12</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0021-924X</ISSN><JournalIssue CitedMedium="Print"><Volume>119</Volume><Issue>4</Issue><PubDate><Year>1996</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Journal of biochemistry</Title><ISOAbbreviation>J. Biochem.</ISOAbbreviation></Journal><ArticleTitle>Characterization and comparison of synthetic immobile and mobile Holliday junctions.</ArticleTitle><Pagination><MedlinePgn>653-8</MedlinePgn></Pagination><Abstract><AbstractText>Eight synthetic Holliday junction (HJ) oligonucleotides containing an immobile or a mobile junction were characterized by gel electrophoresis, ultraviolet absorption and circular dichroism (CD) spectroscopy. Four 24-mer deoxyribonucleotides formed stable immobile and mobile HJs in 0.1 M NaCl at 5 muM strand concentration at room temperature. However, the immobile HJ constructed from four 18-mers was less stable, and four 12-mers did not form the HJ structure under the conditions used. A comparison of the melting profiles of the HJs with those of the duplexes corresponding to the arms of four-way junctions indicated that the thermal stability of the HJ was similar to that of the individual arm and the cooperativity of the melting behavior of the HJ was relatively higher than that of the individual arm duplex. The Tms of the mobile HJs containing 4, 6, 8, and 10 base-pair homologous cores at junctions were essentially identical with that of the immobile HJ of the same size. There is a tendency that the HJ containing a larger homologous core region becomes more resistant to thermal denaturation. The addition of divalent metal cations, Mg2+ and Ca2+, to the solutions of the HJs raised their melting temperatures. The difference found for the CD spectra of the HJs which differ only in the arrangement of the HJ depended primarily upon the DNA sequence flanking the junction. The RuvC protein binds to the immobile and mobile HJs, regardless of the presence and the size of the homologous core at the junction.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Shida</LastName><ForeName>T</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Nagano.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Iwasaki</LastName><ForeName>H</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Shinagawa</LastName><ForeName>H</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Kyogoku</LastName><ForeName>Y</ForeName><Initials>Y</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Biochem</MedlineTA><NlmUniqueID>0376600</NlmUniqueID><ISSNLinking>0021-924X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D001426">Bacterial Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D029968">Escherichia coli Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009838">Oligodeoxyribonucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C069806">ruvC protein, E coli</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.-</RegistryNumber><NameOfSubstance UI="D004706">Endodeoxyribonucleases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001426" MajorTopicYN="N">Bacterial Proteins</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002942" MajorTopicYN="N">Circular Dichroism</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000138" MajorTopicYN="N">chemical synthesis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004591" MajorTopicYN="N">Electrophoresis, Polyacrylamide Gel</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004706" MajorTopicYN="N">Endodeoxyribonucleases</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D029968" MajorTopicYN="Y">Escherichia coli Proteins</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009691" MajorTopicYN="N">Nucleic Acid Denaturation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009838" MajorTopicYN="N">Oligodeoxyribonucleotides</DescriptorName><QualifierName UI="Q000138" MajorTopicYN="N">chemical synthesis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011485" MajorTopicYN="N">Protein Binding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011995" MajorTopicYN="Y">Recombination, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013056" MajorTopicYN="N">Spectrophotometry, Ultraviolet</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>1996</Year><Month>4</Month><Day>1</Day></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>1996</Year><Month>4</Month><Day>1</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>1996</Year><Month>4</Month><Day>1</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">8743565</ArticleId><ArticleId IdType="doi">10.1093/oxfordjournals.jbchem.a021292</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list></list><tree><noCountry><name sortKey="Iwasaki, H" sort="Iwasaki, H" uniqKey="Iwasaki H" first="H" last="Iwasaki">H. Iwasaki</name><name sortKey="Kyogoku, Y" sort="Kyogoku, Y" uniqKey="Kyogoku Y" first="Y" last="Kyogoku">Y. Kyogoku</name><name sortKey="Shida, T" sort="Shida, T" uniqKey="Shida T" first="T" last="Shida">T. Shida</name><name sortKey="Shinagawa, H" sort="Shinagawa, H" uniqKey="Shinagawa H" first="H" last="Shinagawa">H. Shinagawa</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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