Preferential counterion binding to A-tract DNA oligomers.
Identifieur interne : 003429 ( Main/Exploration ); précédent : 003428; suivant : 003430Preferential 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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Le document en format XML
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Magnusdottir</name></author><author><name sortKey="Gelfi, C" sort="Gelfi, C" uniqKey="Gelfi C" first="C" last="Gelfi">C. Gelfi</name></author><author><name sortKey="Righetti, P G" sort="Righetti, P G" uniqKey="Righetti P" first="P G" last="Righetti">P G Righetti</name></author></analytic><series><title level="j">Journal of molecular biology</title><idno type="ISSN">0022-2836</idno><imprint><date when="2001" type="published">2001</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Electrophoresis, Capillary</term><term>Ions (metabolism)</term><term>Ions (pharmacology)</term><term>Nucleic Acid Conformation (drug effects)</term><term>Oligodeoxyribonucleotides (chemistry)</term><term>Oligodeoxyribonucleotides (genetics)</term><term>Oligodeoxyribonucleotides (metabolism)</term><term>Poly A (chemistry)</term><term>Poly A (genetics)</term><term>Poly A (metabolism)</term><term>Sodium Chloride (metabolism)</term><term>Sodium Chloride (pharmacology)</term><term>Solutions</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Chlorure de sodium (métabolisme)</term><term>Chlorure de sodium (pharmacologie)</term><term>Conformation d'acide nucléique ()</term><term>Ions (métabolisme)</term><term>Ions (pharmacologie)</term><term>Oligodésoxyribonucléotides ()</term><term>Oligodésoxyribonucléotides (génétique)</term><term>Oligodésoxyribonucléotides (métabolisme)</term><term>Poly A ()</term><term>Poly A (génétique)</term><term>Poly A (métabolisme)</term><term>Solutions</term><term>Séquence nucléotidique</term><term>Électrophorèse capillaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Oligodeoxyribonucleotides</term><term>Poly A</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Oligodeoxyribonucleotides</term><term>Poly A</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Ions</term><term>Oligodeoxyribonucleotides</term><term>Poly A</term><term>Sodium Chloride</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Ions</term><term>Sodium Chloride</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Nucleic Acid Conformation</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Oligodésoxyribonucléotides</term><term>Poly A</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Chlorure de sodium</term><term>Ions</term><term>Oligodésoxyribonucléotides</term><term>Poly A</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Chlorure de sodium</term><term>Ions</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Electrophoresis, Capillary</term><term>Solutions</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Conformation d'acide nucléique</term><term>Oligodésoxyribonucléotides</term><term>Poly A</term><term>Solutions</term><term>Séquence nucléotidique</term><term>Électrophorèse capillaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><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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