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Adeoye RI, Okaiyeto K, Igunnu A, Oguntibeju OO. Systematic mapping of DNAzymes research from 1995 to 2019. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:384-406. [PMID: 35343361 DOI: 10.1080/15257770.2022.2052318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
DNAzymes (catalytic DNA) have gained significant diagnostic and therapeutic applications with increasing research output over the years. Functional oligonucleotides are used as molecular recognition elements within biosensors for detection of analytes and viral infections such as SARS-CoV-2. DNAzymes are also applied for silencing and regulating cancer specific genes. However, there has not been any report on systematic analysis to track research status, reveal hotspots, and map knowledge in this field. Therefore, in the present study, research articles on DNAzymes from 1995 to 2019 were extracted from Web of Science (SCI-Expanded) after which, 1037 articles were imported into Rstudio (version 3.6.2) and analysed accordingly. The highest number of articles was published in 2019 (n = 138), while the least was in 1995 (n = 1). The articles were published across 216 journals by 2344 authors with 2337 multi-author and 7 single authors. The most prolific authors were Li Y (n = 47), Liu J (n = 46), Wang L (n = 33), Willner I (n = 33) and Zhang L (n = 33). The top three most productive countries were China (n = 2018), USA (n = 447) and Canada (n = 251). The most productive institutions were Hunan University, China (n = 141), University of Illinois, USA (n = 139) and Fuzhou University, China (n = 101). Despite the increasing interest in this field, international collaborations between institutions were very low which requires immediate attention to mitigate challenges such as limited funding, access to facilities, and existing knowledge gap.
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Affiliation(s)
- Raphael Idowu Adeoye
- Enzymology Unit, Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- Biochemistry Unit, Department of Chemistry and Biochemistry, College of Pure and Applied Sciences, Caleb University, Imota, Lagos, Nigeria
| | - Kunle Okaiyeto
- Phytomedicine and Phytochemistry Group, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
| | - Adedoyin Igunnu
- Enzymology Unit, Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Oluwafemi Omoniyi Oguntibeju
- Phytomedicine and Phytochemistry Group, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
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Araki H, Hagiwara S, Shinomiya R, Momotake A, Kotani H, Kojima T, Ochiai T, Shimada N, Maruyama A, Yamamoto Y. A cationic copolymer as a cocatalyst for a peroxidase-mimicking heme-DNAzyme. Biomater Sci 2021; 9:6142-6152. [PMID: 34346413 DOI: 10.1039/d1bm00949d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heme binds to a parallel-stranded G-quadruplex DNA to form a peroxidase-mimicking heme-DNAzyme. An interpolyelectrolyte complex between the heme-DNAzyme and a cationic copolymer possessing protonated amino groups was characterized and the peroxidase activity of the complex was evaluated to elucidate the effect of the polymer on the catalytic activity of the heme-DNAzyme. We found that the catalytic activity of the heme-DNAzyme is enhanced through the formation of the interpolyelectrolyte complex due to the general acid catalysis of protonated amino groups of the polymer, enhancing the formation of the iron(iv)oxo porphyrin π-cation radical intermediate known as Compound I. This finding indicates that the polymer with protonated amino groups can act as a cocatalyst for the heme-DNAzyme in the oxidation catalysis. We also found that the enhancement of the activity of the heme-DNAzyme by the polymer depends on the local heme environment such as the negative charge density in the proximity of the heme and substrate accessibility to the heme. These findings provide novel insights as to molecular design of the heme-DNAzyme for enhancing its catalytic activity.
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Affiliation(s)
- Haruka Araki
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Shota Hagiwara
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryosuke Shinomiya
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Hiroaki Kotani
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takahiko Kojima
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takuro Ochiai
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Naohiko Shimada
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Atsushi Maruyama
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan and Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8571, Japan
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Tsukakoshi K, Yamagishi Y, Kanazashi M, Nakama K, Oshikawa D, Savory N, Matsugami A, Hayashi F, Lee J, Saito T, Sode K, Khunathai K, Kuno H, Ikebukuro K. G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol. Nucleic Acids Res 2021; 49:6069-6081. [PMID: 34095949 PMCID: PMC8216272 DOI: 10.1093/nar/gkab388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 04/25/2021] [Accepted: 06/03/2021] [Indexed: 01/07/2023] Open
Abstract
Aptamers can control the biological functions of enzymes, thereby facilitating the development of novel biosensors. While aptamers that inhibit catalytic reactions of enzymes were found and used as signal transducers to sense target molecules in biosensors, no aptamers that amplify enzymatic activity have been identified. In this study, we report G-quadruplex (G4)-forming DNA aptamers that upregulate the peroxidase activity in myoglobin specifically for luminol. Using in vitro selection, one G4-forming aptamer that enhanced chemiluminescence from luminol by myoglobin's peroxidase activity was discovered. Through our strategy—in silico maturation, which is a genetic algorithm-aided sequence manipulation method, the enhancing activity of the aptamer was improved by introducing mutations to the aptamer sequences. The best aptamer conserved the parallel G4 property with over 300-times higher luminol chemiluminescence from peroxidase activity more than myoglobin alone at an optimal pH of 5.0. Furthermore, using hemin and hemin-binding aptamers, we demonstrated that the binding property of the G4 aptamers to heme in myoglobin might be necessary to exert the enhancing effect. Structure determination for one of the aptamers revealed a parallel-type G4 structure with propeller-like loops, which might be useful for a rational design of aptasensors utilizing the G4 aptamer-myoglobin pair.
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Affiliation(s)
- Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yasuko Yamagishi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Mana Kanazashi
- DENSO CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kenta Nakama
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daiki Oshikawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Akimasa Matsugami
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Fumiaki Hayashi
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Jinhee Lee
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | - Taiki Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | | | - Hitoshi Kuno
- DENSO CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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