Conformational preferences of DNA from the promoter regions of the c-MYC, VEGF, and Bcl-2 oncogenes

We characterized the conformational preferences of DNA in an equimolar mixture of complementary G-rich and C-rich strands from the promoter regions of the c-MYC, VEGF, and Bcl-2 oncogenes. Our CD-based approach presupposes that the CD spectrum of such a mixture is the spectral sum of the constituent duplex, G-quadruplex, i-motif, and coiled conformations. Spectra were acquired over a range of temperatures at different pH and concentrations of KCl. Each spectrum was unmixed in terms of the predetermined spectra of the constituent conformational states to obtain the corresponding weighting factors for their fractional contributions to the total population of DNA. The temperature-dependences of those contributions then were analyzed in concert according to a model based on a thermodynamic representation of the underlying equilibria. Comparison of the conformational data on the c-MYC, VEGF, and Bcl-2 DNA reveals that the distribution of conformational states depends on the specific DNA sequence and is modulated by environmental factors. Under the physiological conditions of room temperature, neutral pH, and elevated concentrations of potassium ions, the duplex conformation coexists with the G-quadruplex conformation in proportions that depend on the sequence. This observed conformational diversity has biological implications suggesting a novel, thermodynamically controlled mechanism for the regulation of gene expression. In that hypothesis, a specific distribution of duplex and tetraplex conformations in a promoter region is fine-tuned to maintain the healthy level of gene expression. Any deviation from a healthy distribution of conformational states may result in pathology stemming from up- or downregulation of the gene.