Conformer Analysis of a Biological G-Quadruplex Element in the Human c-MYC Promoter by Native Polyacrylamide Gel Electrophoresis

The G-quadruplexes undergo complex folding and conformation exchanges. G-quadruplex stability is substantially influenced by sequence, buffer and temperature. Mutational analysis together with nuclear magnetic resonance spectroscopy (NMR), X-ray crystallography and circular dichroism spectroscopy has been proved to be a powerful approach for G-quadruplex structural analysis. Herein, we used DNA sequence mutation and native polyacrylamide gel electrophoresis to investigate the topology and conformations of a G-quadruplex model molecule Pu18 found in the human c-MYC promoter. The guanines (G6, G9 or G18) which were not contributable to G-tetrad formation in c-MYC Pu18 sequence were mutated to thymine or adenine. We screened the buffer and temperature of gel electrophoresis for Pu18. Gel electrophoresis showed that two of the four conformers of c-MYC Pu18 in 100 mM K+ buffer were resolved, which was in accordance with the conformations as determined by the 1H NMR spectra in previous studies. This technique is expected as a general methodology for its easy operation and low cost to facilitate uncovering more yet unidentified G-quadruplex folds and functions, with the assistance of other analytical methods like NMR, X-ray crystallography and circular dichroism spectroscopy.