Folding of the thrombin aptamer into a G-quadruplex with Sr2+: Stability, heat, and hydration

It has been shown that the DNA aptamer d(G(2)T(2)G(2)TGTG(2)T(2)G(2)) adopt s an intraniolecular G-quadruplex structure in the presence of K+. Its affi nity for trombin has been associated with the inhibition of thrombin-cataly zed fibrin clot fort-nation. In this work, we used a combination of spectro scopy, calorimetry, density, and ultrasound techniques to determine the spe ctral characteristics, thermodynamics, and hydration effects for the format ion of G-quadruplexes with a variety of monovalent and divalent metal ions. The formation of cation-aptamer complexes is relatively fast and highly re producible. The comparison of their CD spectra and melting profiles as a fu nction of strand concentration shows that K+, Rb+, NH4+, Sr2+, and Ba2+-for m intramolecular cation-aptanter complexes with transition temperatures abo ve 25 degreesC. However, the cations Li+, Na+, Cs+, Mg2+, and Ca2+ form wea ker complexes at very low temperatures. This is consistent with the observa tion that metal ions with ionic radii in the range 1.3-1.5 Angstrom fit wel l within ' the two G-quartets of the complex, while the other cations canno t. The comparison of thermodynamic unfolding profiles of the Sr(2+)aptamer and K+-aptamer complexes shows that the Sr2+-aptamer complex is more stable , by similar to 18 degreesC, and unfolds with a lower endothermic heat of 8 .3 kcal/mol. This is in excellent agreement with the exothermic heats of -1 6.8 kcal/mol and -25.7 kcal/mol for the binding of Sr2+ and K+ to the aptam er, respectively. Furthermore, volume and compressibility parameters of cat ion binding show hydration effects resulting mainly from two contributions: the dehydration of both cation and guanine atomic groups and water uptake upon the folding of a single-strand into a G- quadruplex structure.