Crystal structures and identification of novel Cd(2+)-specific DNA aptamer

Cadmium (Cd) is one of the most toxic heavy metals. Exposure to Cd can impair the functions of the kidney, respiratory system, reproductive system and skeletal system. Cd(2+)-binding aptamers have been extensively utilized in the development of Cd(2+)-detecting devices; however, the underlying mechanisms remain elusive. This study reports four Cd(2+)-bound DNA aptamer structures, representing the only Cd(2+)-specific aptamer structures available to date. In all the structures, the Cd(2+)-binding loop (CBL-loop) adopts a compact, double-twisted conformation and the Cd(2+) ion is mainly coordinated with the G9, C12 and G16 nucleotides. Moreover, T11 and A15 within the CBL-loop form one regular Watson–Crick pair and stabilize the conformation of G9. The conformation of G16 is stabilized by the G8–C18 pair of the stem. By folding and/or stabilizing the CBL-loop, the other four nucleotides of the CBL-loop also play important roles in Cd(2+) binding. Similarly to the native sequence, crystal structures, circular dichroism spectrum and isothermal titration calorimetry analysis confirm that several variants of the aptamer can recognize Cd(2+). This study not only reveals the underlying basis for the binding of Cd(2+) ions with the aptamer, but also extends the sequence for the construction of novel metal–DNA complex.