Binding of Nucleotides and Nucleosides to Per(6‐guanidino‐6‐deoxy)cyclodextrins in Solution

The binding of α‐, β‐, and γ‐per(6‐guanidino‐6‐deoxy)cyclodextrins (ag, bg, and gg, respectively) with nucleotides (5′‐dAMP, 5′‐AMP, and 5′‐dCMP) and nucleosides (2′‐dA and 2′‐dC) was studied with NMR spectroscopy in aqueous solution. Nucleotides formed strong complexes with bg and gg (not ag) through ditopic binding. Multiple Coulombic attractive forces between the guanidino groups and the single phosphate group of the nucleotides drove inclusion of the entire ribose ring into the cavity, in both deoxy‐ and ribonucleotides, whereas the base moiety was only partially included. In contrast, no interaction was observed between guanidino cyclodextrins and nucleosides. The prevailing stoichiometries in all nucleotide/bg and nucleotide/gg complexes were 1:2, except for 5′‐dAMP/bg where oligomeric aggregates formed. The anti orientation of the nucleotides was preserved upon inclusion. The populations of conformers due to ribose pucker, 2′‐ endo (S) and 3′‐ endo (N), were practically undisturbed by inclusion. Interestingly, in the nucleotide/bg complexes at 278 K two nucleotide conformers were observed with distinctly different signals in slow mutual exchange owing to cavity restriction and a slow ribose pucker rate, which resulted in the observation of 3′‐ endo (N) conformer separate from 2′‐ endo (S) conformer for the first time.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)