Preferential counterion binding to A-tract DNA oligomers

Nancy C. Stellwagen, Soffia Magnusdottir, Cecilia Gelfi, Pier Giorgio Righetti

Research output: Contribution to journalArticlepeer-review


The free solution mobility of four 20 bp Dna oligomers, with and without A-tracts, has been measured by capillary electrophoresis in Trisacetate 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.

Original languageEnglish
Pages (from-to)1025-1033
Number of pages9
JournalJournal of Molecular Biology
Issue number5
Publication statusPublished - Feb 2 2001


  • Capillary electrophoresis
  • Counterion binding
  • DNA bending
  • Dna oligonucleotide
  • Free solution mobility

ASJC Scopus subject areas

  • Virology


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