Evidence of a General Acid-Base Catalysis Mechanism in the 8-17 DNAzyme
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Date
2018-03
Profesor/a GuÃa
Facultad/escuela
Idioma
en
Journal Title
Journal ISSN
Volume Title
Publisher
American Chemical Society
Nombre de Curso
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CC BY-NC-ND 4.0
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Abstract
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. © 2018 American Chemical Society.
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Indexación Scopus
Keywords
Catalytic DNA, RNA-cleaving DNA 10-23, Metal Ion
Citation
Biochemistry Volume 57, Issue 9, Pages 1517 - 15226 March 2018
DOI
10.1021/acs.biochem.7b01096