Preferential counterion binding to A-tract DNA oligomers.
Identifieur interne : 002401 ( PubMed/Checkpoint ); précédent : 002400; suivant : 002402Preferential counterion binding to A-tract DNA oligomers.
Auteurs : N C Stellwagen [États-Unis] ; S. Magnusdottir ; C. Gelfi ; P G RighettiSource :
- Journal of molecular biology [ 0022-2836 ] ; 2001.
Descripteurs français
- KwdFr :
- Chlorure de sodium (métabolisme), Chlorure de sodium (pharmacologie), Conformation d'acide nucléique (), Ions (métabolisme), Ions (pharmacologie), Oligodésoxyribonucléotides (), Oligodésoxyribonucléotides (génétique), Oligodésoxyribonucléotides (métabolisme), Poly A (), Poly A (génétique), Poly A (métabolisme), Solutions, Séquence nucléotidique, Électrophorèse capillaire.
- MESH :
- génétique : Oligodésoxyribonucléotides, Poly A.
- métabolisme : Chlorure de sodium, Ions, Oligodésoxyribonucléotides, Poly A.
- pharmacologie : Chlorure de sodium, Ions.
- Conformation d'acide nucléique, Oligodésoxyribonucléotides, Poly A, Solutions, Séquence nucléotidique, Électrophorèse capillaire.
English descriptors
- KwdEn :
- Base Sequence, Electrophoresis, Capillary, Ions (metabolism), Ions (pharmacology), Nucleic Acid Conformation (drug effects), Oligodeoxyribonucleotides (chemistry), Oligodeoxyribonucleotides (genetics), Oligodeoxyribonucleotides (metabolism), Poly A (chemistry), Poly A (genetics), Poly A (metabolism), Sodium Chloride (metabolism), Sodium Chloride (pharmacology), Solutions.
- MESH :
- chemical , chemistry : Oligodeoxyribonucleotides, Poly A.
- chemical , genetics : Oligodeoxyribonucleotides, Poly A.
- chemical , metabolism : Ions, Oligodeoxyribonucleotides, Poly A, Sodium Chloride.
- chemical , pharmacology : Ions, Sodium Chloride.
- drug effects : Nucleic Acid Conformation.
- Base Sequence, Electrophoresis, Capillary, Solutions.
Abstract
The free solution mobility of four 20 bp DNA oligomers, with and without A-tracts, has been measured by capillary electrophoresis in Tris-acetate buffer, to test the hypothesis that site-specific binding of monovalent counterions can occur in the narrow minor groove of A-tract DNAs. Preferential counterion binding has been proposed to cause A-tract bending because of asymmetric charge neutralization and collapse of the helix backbone toward the minor groove. Preferential counterion binding in A-tract DNAs should be manifested by a decrease in the electrophoretic mobility observed in free solution, compared to that of non-A-tract DNAs of the same size. Of the four sequences studied here, the slowest absolute mobility, indicative of the greatest counterion binding, was observed for a 20 bp oligomer containing two runs of A3T3 in phase with the helix repeat. A 20-mer containing phased CACA sequences migrated with the fastest mobility; 20-mers containing phased A5 tracts or phased runs of T3A3 migrated with intermediate mobilities. Very similar mobility differences were observed when 1-20 mM NaCl was added to the buffer. The results suggest that preferential counterion binding occurs in A-tract DNAs, especially those containing the AnTn sequence motif.
DOI: 10.1006/jmbi.2000.4362
PubMed: 11162111
Affiliations:
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Preferential counterion binding has been proposed to cause A-tract bending because of asymmetric charge neutralization and collapse of the helix backbone toward the minor groove. Preferential counterion binding in A-tract DNAs should be manifested by a decrease in the electrophoretic mobility observed in free solution, compared to that of non-A-tract DNAs of the same size. Of the four sequences studied here, the slowest absolute mobility, indicative of the greatest counterion binding, was observed for a 20 bp oligomer containing two runs of A3T3 in phase with the helix repeat. A 20-mer containing phased CACA sequences migrated with the fastest mobility; 20-mers containing phased A5 tracts or phased runs of T3A3 migrated with intermediate mobilities. Very similar mobility differences were observed when 1-20 mM NaCl was added to the buffer. The results suggest that preferential counterion binding occurs in A-tract DNAs, especially those containing the AnTn sequence motif.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">11162111</PMID><DateCompleted><Year>2001</Year><Month>03</Month><Day>15</Day></DateCompleted><DateRevised><Year>2017</Year><Month>09</Month><Day>22</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0022-2836</ISSN><JournalIssue CitedMedium="Print"><Volume>305</Volume><Issue>5</Issue><PubDate><Year>2001</Year><Month>Feb</Month><Day>02</Day></PubDate></JournalIssue><Title>Journal of molecular biology</Title><ISOAbbreviation>J. Mol. Biol.</ISOAbbreviation></Journal><ArticleTitle>Preferential counterion binding to A-tract DNA oligomers.</ArticleTitle><Pagination><MedlinePgn>1025-33</MedlinePgn></Pagination><Abstract><AbstractText>The free solution mobility of four 20 bp DNA oligomers, with and without A-tracts, has been measured by capillary electrophoresis in Tris-acetate buffer, to test the hypothesis that site-specific binding of monovalent counterions can occur in the narrow minor groove of A-tract DNAs. Preferential counterion binding has been proposed to cause A-tract bending because of asymmetric charge neutralization and collapse of the helix backbone toward the minor groove. Preferential counterion binding in A-tract DNAs should be manifested by a decrease in the electrophoretic mobility observed in free solution, compared to that of non-A-tract DNAs of the same size. Of the four sequences studied here, the slowest absolute mobility, indicative of the greatest counterion binding, was observed for a 20 bp oligomer containing two runs of A3T3 in phase with the helix repeat. A 20-mer containing phased CACA sequences migrated with the fastest mobility; 20-mers containing phased A5 tracts or phased runs of T3A3 migrated with intermediate mobilities. Very similar mobility differences were observed when 1-20 mM NaCl was added to the buffer. The results suggest that preferential counterion binding occurs in A-tract DNAs, especially those containing the AnTn sequence motif.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Stellwagen</LastName><ForeName>N C</ForeName><Initials>NC</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA. nancy-stellwagen@uiowe.edu</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Magnusdottir</LastName><ForeName>S</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Gelfi</LastName><ForeName>C</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Righetti</LastName><ForeName>P G</ForeName><Initials>PG</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>E.0893</GrantID><Agency>Telethon</Agency><Country>Italy</Country></Grant><Grant><GrantID>GM29690</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Mol Biol</MedlineTA><NlmUniqueID>2985088R</NlmUniqueID><ISSNLinking>0022-2836</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D007477">Ions</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009838">Oligodeoxyribonucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012996">Solutions</NameOfSubstance></Chemical><Chemical><RegistryNumber>24937-83-5</RegistryNumber><NameOfSubstance UI="D011061">Poly A</NameOfSubstance></Chemical><Chemical><RegistryNumber>451W47IQ8X</RegistryNumber><NameOfSubstance UI="D012965">Sodium Chloride</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019075" MajorTopicYN="N">Electrophoresis, Capillary</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007477" MajorTopicYN="N">Ions</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName><QualifierName UI="Q000494" MajorTopicYN="N">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009838" MajorTopicYN="N">Oligodeoxyribonucleotides</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011061" MajorTopicYN="N">Poly A</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012965" MajorTopicYN="N">Sodium Chloride</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName><QualifierName UI="Q000494" MajorTopicYN="N">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012996" MajorTopicYN="N">Solutions</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2001</Year><Month>2</Month><Day>13</Day><Hour>11</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2001</Year><Month>3</Month><Day>17</Day><Hour>10</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2001</Year><Month>2</Month><Day>13</Day><Hour>11</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">11162111</ArticleId><ArticleId IdType="doi">10.1006/jmbi.2000.4362</ArticleId><ArticleId IdType="pii">S0022-2836(00)94362-6</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Iowa</li></region><settlement><li>Iowa City</li></settlement><orgName><li>Université de l'Iowa</li></orgName></list><tree><noCountry><name sortKey="Gelfi, C" sort="Gelfi, C" uniqKey="Gelfi C" first="C" last="Gelfi">C. Gelfi</name><name sortKey="Magnusdottir, S" sort="Magnusdottir, S" uniqKey="Magnusdottir S" first="S" last="Magnusdottir">S. Magnusdottir</name><name sortKey="Righetti, P G" sort="Righetti, P G" uniqKey="Righetti P" first="P G" last="Righetti">P G Righetti</name></noCountry><country name="États-Unis"><region name="Iowa"><name sortKey="Stellwagen, N C" sort="Stellwagen, N C" uniqKey="Stellwagen N" first="N C" last="Stellwagen">N C Stellwagen</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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