i-Motif-forming sequences are present in or near the regulatory regions of >40% of all genes, including known oncogenes. We report here the results of a biophysical characterization and computational study of an ensemble of Intramolecular i-motifs that model the polypyrimidine sequence in the human c-MYC P1 promoter. Circular dichroism results demonstrate that the mutant sequence (5'-CTT TCC TAC CCTCCC TAC CCT AA-3′) can adopt multiple "i-motif-like," classical i-motif, and single-stranded structures as a function of pH. The classical i-motif structures are predominant in the pH range 4.2-5.2. The "i-motif-like" and single-stranded structures are the most significant species in solution at pH higher and lower, respectively, than that range. Differential scanning calorimetry results demonstrate an equilibrium mixture of at least three i-motif folded conformations with T m values of 38.1, 46.6, and 49.5°C at pH 5.0. The proposed ensemble of three folded conformations includes the three lowest-energy conformations obtained by computational modeling and two folded conformers that were proposed in a previous NMR study. The NMR study did not report the most stable conformer found in this study. © 2010 by the Biophysical Society.
Dettler, J. M., Buscaglia, R., Cui, J. J., Cashman, D., Blynn, M., & Lewis, E. A. (2010). Biophysical characterization of an ensemble of intramolecular i-Motifs formed by the human c-MYC NHE III1 P1 promoter mutant sequence. Biophysical Journal, 99(2), 561–567. https://doi.org/10.1016/j.bpj.2010.04.042