I-motif structures formed in the human c-MYC promoter are highly dynamic-insights into sequence redundancy and I-motif stability

The GC-rich nuclease hypersensitivity element III₁ (NHE III₁) of the c-MYC promoter largely controls the transcriptional activity of the c-MYC oncogene. The C-rich strand in this region can form I-motif DNA secondary structures. We determined the folding pattern of the major I-motif formed in the NHE III₁, which can be formed at near-neutral pH. While we find that the I-motif formed in the four 3′ consecutive runs of cytosines appears to be the most favored, our results demonstrate that the C-rich strand of the c-MYC NHE III₁ exhibits a high degree of dynamic equilibration. Using a trisubstituted oligomer of this region, we determined the formation of two equilibrating loop isomers, one of which contains a flipped-out cytosine. Our results indicate that the intercalative cytosine⁺-cytosine base pairs are not always necessary for an intramolecular Imotif. The dynamic character of the c-MYC I-motif is intrinsic to the NHE III¹ sequence and appears to provide stability to the c-MYC I-motif.