Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Preferential Counterion Binding to A-tract DNAs

The preferential binding of monovalent counterions to A-tract-containing DNAs has been investigated by capillary electrophoresis, comparing the mobility of a random-sequence 26-bp oligomer with the mobilities observed for 26-bp oligomers containing various types of A-tracts. All solutions contained 200 mM diethylmalonate as the buffering anion plus various concentrations of NH4+, Li+, Na+, K+, or Tris+ as the test counterion. The solutions also contained appropriate concentrations of the ?non-binding? tetrapropyl (TPA+) or tetrabutyl (TBA+) ammonium ions, to keep the total ionic strength constant. In general, A-tract-containing DNA oligomers have different free solution mobilities than a random oligomer of the same size. The mobility of an A-tract-containing oligomer (but not the random oligomer) decreases with increasing concentrations of NH4+, Li+, Na+, K+, or Tris+ ions, eventually reaching a plateau mobility at high concentrations of the test ion. Hence, A-tract DNAs bind more monovalent cations than oligomers of the same size without A-tracts. Surprisingly, the A-tract-containing oligomers have two different cation binding sites, termed the high affinity and low affinity sites. TBA+ ions are too large to bind to either site. TPA+ ions bind strongly to the high affinity site but not to the low affinity site. For the high affinity site, in solutions without TPA+, Li+ = Tris+ = NH4+ > Na+ = K+. For the low affinity site, Li+ = Tris+ ≥ NH4+ > Na+ > K+, with the exact order of cation binding depending somewhat on A-tract sequence. No preferential counterion binding is observed in the low affinity site if the oligomers are first equilibrated with netropsin, which binds in the minor grooves of A-tract DNAs. Hence, the low affinity site is located in the A-tract minor groove. Cation binding affinity increases with A-tract length and is not affected by the phasing of the A-tracts, suggesting that preferential counterion binding reflects DNA sequence, rather than bending.

Nancy C. Stellwagen*
Qian Dong
Earle Stellwagen

Department of Biochemistry
University of Iowa
Iowa City, IA 52242

*Fax: 319-335-9570
Email: nancy-stellwagen@uiowa.edu