Book of Abstracts: Albany 2007
June 19-23 2007
Unfolding Thermodynamics of G-quadruplexes
We use a combination of spectroscopic (UV and circular dichroism) and calorimetric (differential scanning and pressure perturbation) techniques to determine complete thermodynamic profiles for the unfolding of the following fundamental G-quadruplexes: d(GGT2GGTGTGGT2GG) (G2) and d(GGGT2GGGTGTGGGT2GGG) (G3), where the bases in italics correspond to loops; and other sequences containing base substitutions in the loops.
The unfolding thermodynamic profiles and Hess cycles for pairs of molecules were used to resolve the following energetic contributions: (a) stacking of two G-quartets, which is then applied to determine the loop and single strand contributions of other biologically relevant G-quadruplexes; (b) removal of methyl groups from the loops, by substituting all T?s for U?s in G2 and G3; (c) base substitutions of guanine in the TGT loop of G2, and for the inclusion of additional thymines in the T2 loops of this quadruplex; and (d) the unfolding volumes of G2.
The results are summarized as follows: (a) the favorable formation of a G-quartet stack is accompanied by an enthalpy-entropy compensation, uptake of ions and release of water molecules. After subtracting the contribution of the G-quartet stack(s) from the thermodynamic folding profiles of each quadruplex; the presence of loops and/or single strands stabilizes G-quadruplexes. (b) The removal of six methyl groups from the loops of G2 and G3, yielded more stable G-quadruplexes, due to a slightly higher release of structural water, and a similar thermodynamic profile for the formation of a G-quartet stack. (c) The base substitutions of guanine in the TGT loop and the inclusion of T4 loops yielded more stable G-quadruplexes, due to increased base-base stacking contributions within the loops. (d) The resulting unfolding volumes are consistent with the net uptake of water molecules.
Department of Pharmaceutical Sciences