TY - JOUR
T1 - Evidence of a General Acid-Base Catalysis Mechanism in the 8-17 DNAzyme
AU - Cepeda-Plaza, Marjorie
AU - McGhee, Claire E.
AU - Lu, Yi
N1 - Publisher Copyright:
© 2018 American Chemical Society.
PY - 2018/3/6
Y1 - 2018/3/6
N2 - 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 next to the cleavage site, is involved in proton transfer at the catalytic site. In contrast, we did not find any evidence of G1.1 being involved in acid-base catalysis. These results support general acid-base catalysis as a feasible strategy used in DNA catalysis, as in RNA and protein enzymes.
AB - 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 next to the cleavage site, is involved in proton transfer at the catalytic site. In contrast, we did not find any evidence of G1.1 being involved in acid-base catalysis. These results support general acid-base catalysis as a feasible strategy used in DNA catalysis, as in RNA and protein enzymes.
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U2 - 10.1021/acs.biochem.7b01096
DO - 10.1021/acs.biochem.7b01096
M3 - Article
C2 - 29389111
AN - SCOPUS:85043318639
SN - 0006-2960
VL - 57
SP - 1517
EP - 1522
JO - Biochemistry
JF - Biochemistry
IS - 9
ER -