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

被引:34
作者
Cepeda-Plaza, Marjorie [1 ]
McGhee, Claire E. [2 ]
Lu, Yi [2 ]
机构
[1] Univ Andres Bello, Sch Exact Sci, Dept Chem Sci, Republ 275, Santiago, Chile
[2] Univ Illinois, Dept Chem, 600 South Mathews Ave, Urbana, IL 61801 USA
基金
美国国家卫生研究院;
关键词
IN-VITRO SELECTION; RNA-CLEAVING DEOXYRIBOZYME; DELTA VIRUS RIBOZYME; ACTIVE-SITE GUANINE; METAL-IONS; HAIRPIN RIBOZYME; HAMMERHEAD RIBOZYME; CRYSTAL-STRUCTURE; TWISTER RIBOZYME; LIVING CELLS;
D O I
10.1021/acs.biochem.7b01096
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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; pK(a,N1) = 9.4) with analogues with a different pK(a) at the N-1 position, such as inosine (G14I; pK(a,N1)= 8.7), 2,6-diaminopurine (G14diAP; pK(a,N1) = 5.6), and 2-aminopurine (G14AP; pK(a,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.
引用
收藏
页码:1517 / 1522
页数:6
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