Optimizing the kinetics and thermodynamics of DNA i-motif folding

Under slightly acidic conditions, single cytidine-rich DNA strands can form four-stranded structures called i-motifs. The stability of the i-motif structure is based on the intercalation of hemiprotonated C-C(+) base pairs. In addition, the stability of these structures is influenced by pH, temperature, salt concentration, number of cytidines per C-rich stretch, and length of sequence; it also depends on the nucleotides in the connecting loop regions. Here, we investigated the influence of the loop nucleotides on i-motif stability, structure, and kinetics of folding, in five structures with the same loop-size but different adenosine and thymidine residues within the loop. The stabilities of the i-motif structures were determined by CD melting, and structure and kinetics of folding were studied by static and time-resolved NMR experiments.