Monovalent cation localization in DNA A‐tracts with different sequences

Abstract

AbstractThe free solution mobilities of 26‐base pair (bp) DNA oligomers containing A‐tracts with and without internal ApT steps have been measured by capillary electrophoresis, using the mobility of a 26‐bp random‐sequence oligomer as a reference. The background electrolytes (BGEs) contained mixtures of Li+ and tetrapropylammonium (TPA+) ions, keeping the total cation concentration constant at 0.3 M. The mobility ratios equaled 1.00 in 0.3 M TPA+, indicating that the A‐tract and reference oligomers had the same B‐form conformation in this BGE. With increasing [Li+], the mobility ratio decreased as Li+ ions became localized in the A‐tract minor groove, suggesting that the A‐tract was now in the B* conformation. If the A‐tract contained an internal ApT step and the oligomer contained less than ∼50% A + T, the mobility ratio reached a reduced plateau value that remained constant as the [Li+] increased to 0.3 M. However, for A‐tracts without an internal ApT step and for A‐tracts embedded in oligomers containing more than 50% A + T, the mobility ratios increased again at high [Li+], eventually reaching a plateau value of 1.00. Hence, DNA A‐tracts in solution appear to exist as mixtures of the B and B* conformations, with the fractional concentration of each conformer depending on the [Li+], the A‐tract sequence, and the total A + T content of the oligomer.