Backbone equilibrium in mismatched DNA influenced by solution conditions.

The impact of solution conditions on the 31P isotropic chemical shifts of DNA phosphates and therefore the sequence-dependent backbone conformational equilibrium has not been well-documented. There are no previous studies of DNA backbone equilibrium in the presence of crowding agents, nor any on mismatched DNA. A systematic study of several experimental conditions (Na+ concentration, K+ concentration, Mg2+ concentration, pH, the presence of PEG molecular crowders) was performed and the effect quantified in mismatched DNA compared to a canonical control sequence. Na+ concentration, pH and crowding agents have only a minimal effect on the backbone equilibrium (<5 % perturbation on backbone populations). But in the mismatched DNA, both K+ and Mg2+ shift the backbone equilibrium on both DNA strands but most significantly perturb the phosphates in proximity to the mismatch. This indicates a possible role of counterions in mismatch recognition or nucleotide flipping, and suggests knowledge of solutions conditions continue to be relevant for conformational processes.