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

Authors
  • Cepeda-Plaza, Marjorie1
  • McGhee, Claire E2
  • Lu, Yi2
  • 1 Department of Chemical Sciences, School of Exact Sciences , Universidad Andres Bello , República 275 , Santiago , Chile. , (Chile)
  • 2 Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States. , (United States)
Type
Published Article
Journal
Biochemistry
Publisher
American Chemical Society
Publication Date
Mar 06, 2018
Volume
57
Issue
9
Pages
1517–1522
Identifiers
DOI: 10.1021/acs.biochem.7b01096
PMID: 29389111
Source
Medline
License
Unknown

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; p Ka,N1 = 9.4) with analogues with a different p Ka at the N1 position, such as inosine (G14I; p Ka,N1 = 8.7), 2,6-diaminopurine (G14diAP; p Ka,N1 = 5.6), and 2-aminopurine (G14AP; p Ka,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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