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Catalysts 2017, 7(12), 355; doi:10.3390/catal7120355

Catalytic Activities of Ribozymes and DNAzymes in Water and Mixed Aqueous Media

1
Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
2
Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
*
Author to whom correspondence should be addressed.
Received: 1 November 2017 / Revised: 13 November 2017 / Accepted: 20 November 2017 / Published: 23 November 2017
(This article belongs to the Special Issue Homogeneous Catalysis and Mechanisms in Water and Biphasic Media)
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Abstract

Catalytic nucleic acids are regarded as potential therapeutic agents and biosensors. The catalytic activities of nucleic acid enzymes are usually investigated in dilute aqueous solutions, although the physical properties of the reaction environment inside living cells and that in the area proximal to the surface of biosensors in which they operate are quite different from those of pure water. The effect of the molecular environment is also an important focus of research aimed at improving and expanding nucleic acid function by addition of organic solvents to aqueous solutions. In this study, the catalytic activities of RNA and DNA enzymes (hammerhead ribozyme, 17E DNAzyme, R3C ribozyme, and 9DB1 DNAzyme) were investigated using 21 different mixed aqueous solutions comprising organic compounds. Kinetic measurements indicated that these enzymes can display enhanced catalytic activity in mixed solutions with respect to the solution containing no organic additives. Correlation analyses revealed that the turnover rate of the reaction catalyzed by hammerhead ribozyme increased in a medium with a lower dielectric constant than water, and the turnover rate of the reaction catalyzed by 17E DNAzyme increased in conditions that increased the strength of DNA interactions. On the other hand, R3C ribozyme and 9DB1 DNAzyme displayed no significant turnover activity, but their single-turnover rates increased in many mixed solutions. Our data provide insight into the activity of catalytic nucleic acids under various conditions that are applicable to the medical and technology fields, such as in living cells and in biosensors. View Full-Text
Keywords: ribozyme; DNAzyme; rate constant; melting temperature; molecular crowding; polyethylene glycol ribozyme; DNAzyme; rate constant; melting temperature; molecular crowding; polyethylene glycol
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Nakano, S.-I.; Horita, M.; Kobayashi, M.; Sugimoto, N. Catalytic Activities of Ribozymes and DNAzymes in Water and Mixed Aqueous Media. Catalysts 2017, 7, 355.

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