Interaction of minor groove ligands with G-quadruplexes: Thermodynamic contributions of the number of quartets, T–U substitutions, and conformation

In the presence of specific metal ions, DNA oligonucleotides containing guanine repeat sequences can adopt G-quadruplex structures. In this work, we used a combination of spectroscopic and calorimetric techniques to investigate the conformation and unfolding thermodynamics of the K+-form of five G-quadruplexes with sequences: d(G2T2G2TGTG2T2G2), G2, d(G3T2G3TGTG3T2G3), G3, their analogs where T is replaced with U, G2-U and G3-U, and r(G2U2G2UGUG2U2G2), rG2. These G-quadruplexes show CD spectra characteristic of the “chair” conformation (G2 and G2-U), or “basket” conformation (rG2); or a mixture of these two conformers (G3 and G3-U). Thermodynamic profiles show that the favorable folding of each G-quadruplex results from the typical compensation of a favorable enthalpy and unfavorable entropy contributions. G-quadruplex stability increase in the following order (in ΔG°20): rG2 (−1.3 kcal/mol) < G2 < G2-U

► Quadruplex conformation: “chair” (G2 & G2-U), “basket” (rG2); and both (G3 & G3-U).
► DSC profiles showed the following order of stability: rG2 < G2 < G2-U < G3-U < G3.
► Netropsin and distamycin yielded exothermic binding enthalpies of ∼−10.8 kcal/mol.
► Isotherms yielded affinities of ∼8 × 104 and 1:1 stoichiometries.
► Thermodynamic binding profiles suggest binding to the terminal G-quartets and loops.