Evidence of a General Acid/Base Catalysis Mechanism in the 8-17 DNAzyme

DNAzymes are catalytic DNA molecules that can perform a variety of reactions. Although advances have been made in obtaining DNAzymes via in vitro selection and many of them have been developed into sensors and imaging agents for metal ions, bacteria, and other molecules, the structural features responsible for these enzymatic reactions are still not well understood. Previous studies of the 8–17 DNAzyme have suggested conserved guanines close to the phosphodiester transfer site may play a role in the catalytic reaction. To identify the specific guanine and functional group of the guanine responsible for the reaction, we herein report the effects of replacing G1.1 and G14 (G; pKa,N1 = 9.4) with analogues with a different pKa at the N1 position, such as inosine (G14I; pKa,N1 = 8.7), 2,6-diaminopurine (G14diAP; pKa,N1 = 5.6), and 2-aminopurine (G14AP; pKa,N1 = 3.8) on pH-dependent reaction rates. A comparison of the pH dependence of the reaction rates of these DNAzymes demonstrated that G14 in the bulge loop ...