Flanking AT base pairs affect the localization of monovalent cations in DNA A‐tracts

Abstract

Capillary electrophoresis has been used to measure the free solution mobilities of a series of 26‐base pair (bp) DNA oligomers containing two phased A4T1in‐tracts embedded in flanking sequences containing 0 to 11 additional AT bps. A random‐sequence 26‐bp oligomer with 12 isolated AT bps was used as the reference. Mobility ratios (A‐tract/reference) were measured in background electrolytes (BGEs) containing mixtures of small monovalent cations and tetrabutylammonium (TBA⁺) or tetrapropylammonium (TPA⁺) ions. The mobility ratios observed in 0.3 M TBA⁺ were >1.00, suggesting that the TBA⁺ ions had formed electrostatic contact pairs with the AT bp in the reference and in the A‐tract flanking sequences, decreasing the mobilities of both oligomers. The TBA–AT pairing interactions could be eliminated by increasing the concentration of small monovalent cations in the BGE. In 0.3 M TPA⁺, electrostatic contact pairs were formed with the AT bps in the flanking sequences and in the A‐tracts. Interestingly, the shapes of the mobility ratio profiles observed for the A4T1in‐tract oligomers depended on the total number of A + T residues in the oligomer.