A box-in-box supramolecular assembly for the highly selective recognition of natural, epigenetically and chemically modified cytosines in water

A novel tetracationic macrocycle (1) was synthesized as a size-complementary cation for recognizing sulfonatocalix[4]arene (SC4H) anions. Complexation between 1 and SC4H resulted in the pH-responsive formation of a novel box-in-box supramolecular assembly (14+·SC44−), in which the lower rim of SC4H fits snugly into 1. Comprehensive characterization using NMR spectroscopy, isothermal titration calorimetry, and fluorescence spectroscopy revealed the high-affinity binding of 1 with SC4H in solution, which was consistent with the solid-state supramolecular structure determined by single-crystal X-ray diffraction analysis and TEM observations. Notably, the supramolecular assembly exhibited selectivity towards natural, chemically and epigenetically modified cytosines in water. In particular, it showed distinct affinities and binding modes towards cytosine (CTS, electron-rich) and 5-fluorocytosine (5F-CTS, electron-deficient), giving rise to ternary assemblies (14+·SC44−@CTS and 14+·SC44−@5F-CTS) through rare collaborative encapsulation. These three-component assemblies were characterized in the solid state through SC-XRD and in solution through NMR and ITC analyses (enthalpy-driven for CTS and entropy-driven for 5F-CTS), along with theoretical calculations. Considering their different binding affinities (ca. 103), the supramolecular assembly was utilized for the selective separation of CTS and 5F-CTS, which was found to preferentially encapsulate the natural CTS in a competitive mixture (1 : 1), leaving the unnatural 5F-CTS (antifungal agent) with a purity significantly higher than that obtained by the previously reported procedure. In addition, the supramolecular assembly was found to bind the epigenetically and chemically modified cytosines (5-methylcytosine and 5-hydroxymethylcytosine; gemcitabine and cytarabine). The method developed here provided a powerful tool for the efficient recognition of natural, epigenetically and chemically modified cytosines and the separation of the antifungal drug.