Energetic and Hydration Contributions of the Removal of Methyl Groups From Thymine to Form Uracil in G-Quadruplexes

A combination of spectroscopic and calorimetric techniques is used to investigate the unfolding of two G-quadruplexes: d(G2U2G2UGUG2U2G2), G2-U, and d(G2T2G2TGTG2T2G2), G2. The comparisons of their thermodynamic data allow us to elucidate the role of methylation on the energetic and hydration properties accompanying their stable formation. The favorable formation of each G-quadruplex results from the characteristic enthalpy−entropy compensation, uptake of ions, and release of water molecules. The loops of G2-U and G2 contribute favorably to their formation, and the absence of methyl groups stabilizes the G-quadruplex. The unfolding of G2-U produces a larger ΔV, indicating a difference in the hydration states of the two oligonucleotides, while the opposite signs between ΔΔG° with the ΔΔV suggest that the differential hydration reflects structural, or hydrophobic, water is involved in the unfolding of G-quadruplexes.