Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Sequence Dependence of Counterion Binding to DNA Oligomers Containing A-Tracts

The free solution mobility of a series of 26-bp DNA oligomers containing An- or AnTm-tracts has been measured by capillary electrophoresis in Tris-acetate and Tris-diethylmalonate buffers, to test the hypothesis that site-specific binding of monovalent counterions can occur in the narrow minor groove of A-tract-containing DNAs. Preferential counterion binding should be manifested as a decrease in mobility compared with that of an oligomer of same size containing a randomized sequence of the same composition. Since the expected mobility differences are very small, linearized pUC19 is used as a marker to correct for small day-to-day variations in the electroosmotic flow of the solvent. Many oligomers containing An-tracts migrate with approximately the same mobility as a randomized sequence of the same size, suggesting that preferential counterion binding to An-tract DNAs is not observed in Tris-acetate or Tris-diethylmalonate buffers. Oligomers containing the AnTm sequence motif migrate more slowly than An-tract-containing oligomers, suggesting that preferential counterion binding occurs for oligomers containing the ApT base-pair step.

The addition of K+ ions to Tris-acetate and Tris-diethylmalonate buffers leads to more complicated results. Oligomers containing A3-5-tracts migrate relatively more slowly in Tris-acetate buffers containing K+ ions than in the buffer alone, suggesting that K+ ions may bind to A-tract DNAs. In potassium diethylmalonate buffer (without Tris), several of the AnTm-tract oligomers migrate faster than expected, while an oligomer containing two phased A4-tracts migrates relatively slowly. By far slowest mobilities are observed for oligomers containing two phased A4T4-tracts or eight ApT base-pair steps, again suggesting that preferential counterion binding occurs more readily at the ApT base-pair step. The results also suggest that Tris and K+ ions may compete for binding to the An and AnTm sequence motifs.

Nancy C. Stellwagen*
Qian Dong

Department of Biochemistry
University of Iowa
Iowa City, IA 52242