Thermodynamic Effect of Complementary Hydrogen Bond Base Pairing on Aromatic Stacking Interaction in the Guanine-X-Trp Complex (X=Adenine, Guanine, Cytosine, Thymin.

Abstract

Four kinds of X-Trp (X=adenine, guanine, cytosine, thymine) were synthesized as model compounds to investigate the effect of complementary hydrogen bond base pairing on the stacking interaction of Trp with nucleic acid base. Association constants (Ka) of these compounds with two guanine derivatives (9-ethylguanine and 9-ethyl-7-methylguanine) were determined by Eadie-Hofstee plots of 1H-NMR titration experiments, and the thermodynamic parameters (ΔH, ΔS and ΔG) for the respective complexes were obtained by van't Hoff analyses based on the temperature dependence of the Ka values. The complexes were characterized by enthalpy/entropy compensations, where the interaction of cytosine-Trp with guanine derivatives was largely enthalpy-driven, accompanied by a small entropy component, whereas those of remaining complexes were all associated with a large increase in entropy, accompanied by a small positive enthalpy component. The present insight on the binding of X-Trp with a guanine base provides a thermodynamic basis for the importance of cooperative hydrogen bond pairing and aromatic stacking interactions in the specific recognition of a nucleic acid base pair by protein.