Interaction of DNA A-Tract Oligomers with Monovalent Cations

Abstract

We have characterized a series of 26 bp oligonucleotides containing either one or two A-tracts of variable length, sequence and phasing using capillary electrophoresis. The cation concentration was varied at constant ionic strength by gradually replacing tetrabutylammonium cations in the background electrolyte with the monovalent cation of interest. Three distinct A-tract conformations were detected as the monovalent cation concentration was increased, termed fast, normal and slow because of their electrophoretic mobilities relative to that of a random oligomer containing the same number of base pairs. None of the conformational changes are associated with A-tract bending since they are independent of phasing. Cooperative transitions between the different conformations are produced by the preferential complexation of monovalent cations in the millimolar concentration range. The complexation of Li+, NH4+ and Tris+ is similar and ubiquitous while the complexation of Na+ and K+ is weaker and dependent on A-tract sequence. The stability of the fast and slow conformations as well as their interactions with monovalent cations is markedly diminished by increasing the AT content of the sequences flanking the A-tracts.