Thermodynamics of i-tetraplex formation in the nuclease hypersensitive element of human c-myc promoter

Abstract

More than 85% of c-myc transcription is controlled by the nuclease hypersensitive element III₁ upstream of the P1 promoter of this oncogene. The purine-rich sequence in the anti-sense strand forms a G-quadruplex, which has been recently implicated in colorectal cancer, and is proposed as a silencer element [Proc. Natl. Acad. Sci. USA 101 (2004) 6140]. This prompted us to characterize the thermodynamics and proton/counterion effect of the complementary pyrimidine-rich sequence, which forms a C-tetraplex. We report the thermodynamic parameters for folding of the pyrimidine-rich DNA fragment from this region into a C-tetraplex. At 20°C, we observed a ΔG of −10.36 ± 0.13 kcal mol⁻¹ with favorable enthalpy (ΔH = −75.99±0.99 kcal mol⁻¹) and unfavorable entropy (TΔS = −65.63±0.88 kcal mol⁻¹) at pH 5.3 in 20 mM NaCl for tetraplex folding. Similar characteristic stabilizing enthalpy and destabilizing entropy were observed at other pH and ionic strengths. Folding was induced by uptake of about two to three protons per mole of tetraplex while a marginal (0.5–1 mol/mol) counterion uptake was observed. In the context of current understanding of c-myc transcription we envisage a role of the i-motif in remodeling the G-quadruplex silencer.