Efficient Guest Inclusion by β-Cyclodextrin Attached to the Ends of DNA Oligomers upon Hybridization to Various DNA Conjugates

Two types of 5′-β-CyD-DNA conjugates were synthesized using two different strategies and were hybridized with cDNA conjugates bearing various possible guest compounds at the 3′ ends. One of the β-CyD conjugates was synthesized on the basis of solid-phase postmodification of DNA with a monoamino-β-CyD derivative on a synthesis column for automated DNA synthesis. The other β-CyD conjugate was synthesized by the solution-phase coupling of DNA with a monomercapto-β-CyD derivative using a heterobifunctional cross-coupling reagent. When these 5′-β-CyD-DNA conjugates were hybridized with cDNA conjugates bearing 1-adamantaneacetic acid at the 3′ ends, significant stabilization of the duplexes was observed as compared with the control duplex without β-CyD. Duplexes of 5′-β-CyD-DNA conjugates and complementary 3′-dansyl-glycine-DNA conjugates were also moderately stabilized. Thermodynamic measurements revealed that the host−guest inclusion interactions between β-CyD and 1-adamantaneacetic acid or dansyl-glycine are roughly as strong as those found in bulk solution even if they are tethered to the ends of the DNA.