Opposite Effects of Potassium Ions on the Thermal Stability of i-Motif DNA in Different Buffer Systems.

i-motifs are noncanonical DNA structures formed the stack of intercalating hemi-protonated C: C base pairs in C-rich DNA strands and play essential roles in the regulation of gene expression. Here, we systematically investigated the impacts of K on i-motif DNA folding using different buffer systems. We found that i-motif structures display very different values at the same pH and ion strength in different buffer systems. More importantly, K disrupts the i-motif formed in the MES and Bis-Tris buffer; however, K stabilizes the i-motif in phosphate, citrate, and sodium cacodylate buffers. Next, we selected phosphate buffer and confirmed by single-molecule fluorescence resonance energy transfer that K indeed has the stabilizing effect on the folding of i-motif DNA from pH 5.8 to 8.0. Nonetheless, circular dichroism spectra further indicate that the structures formed by i-motif sequences at high K concentrations at neutral and alkaline pH are not i-motif but other types of higher-order structures and most likely C-hairpins. We finally proposed the mechanisms of how K plays the opposite roles in different buffer systems. The present study may provide new insights into our understanding of the formation and stability of i-motif DNA.