Preferential counterion binding to A-tract DNA oligomers.
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.
Stellwagen
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Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA. nancy-stellwagen@uiowe.edu
Magnusdottir
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Gelfi
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Righetti
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D001483:Base Sequence; D019075:Electrophoresis, Capillary; D007477:Ions / Q000378:metabolism / Q000494:pharmacology; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D011061:Poly A / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D012965:Sodium Chloride / Q000378:metabolism* / Q000494:pharmacology; D012996:Solutions
D007477:Ions; D009838:Oligodeoxyribonucleotides; D012996:Solutions; D011061:Poly A; D012965:Sodium Chloride