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Dagenais P, Legault P. In Vitro Selection of Varkud Satellite Ribozyme Variants that Cleave a Modified Stem-Loop Substrate. Methods Mol Biol 2021; 2167:61-77. [PMID: 32712915 DOI: 10.1007/978-1-0716-0716-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In vitro selection is an established approach to create artificial ribozymes with defined activities or to modify the properties of naturally occurring ribozymes. For the Varkud satellite ribozyme of Neurospora, an in vitro selection protocol based on its phosphodiester bond cleavage activity has not been previously reported. Here, we describe a simple protocol for cleavage-based in vitro selection that we recently used to identify variants of the Varkud satellite ribozyme able to target and cleave a non-natural stem-loop substrate derived from the HIV-1 TAR RNA. It allows quick selection of active ribozyme variants from the transcription reaction based on the size of the self-cleavage product without the need for RNA labeling. This results in a streamlined procedure that is easily adaptable to engineer ribozymes with new activities.
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Affiliation(s)
- Pierre Dagenais
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada.
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Nomura Y, Yamazaki K, Amano R, Takada K, Nagata T, Kobayashi N, Tanaka Y, Fukunaga J, Katahira M, Kozu T, Nakamura Y, Haishima Y, Torigoe H, Sakamoto T. Conjugation of two RNA aptamers improves binding affinity to AML1 Runt domain. J Biochem 2017; 162:431-436. [PMID: 28992043 DOI: 10.1093/jb/mvx049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/19/2017] [Indexed: 12/22/2022] Open
Abstract
To develop a high-affinity aptamer against AML1 Runt domain, two aptamers were conjugated based on their structural information. The newly designed aptamer Apt14 was generated by the conjugation of two RNA aptamers (Apt1 and Apt4) obtained by SELEX against AML1 Runt domain, resulting in improvement in its binding performance. The residues of AML1 Runt domain in contact with Apt14 were predicted in silico and confirmed by mutation and NMR analyses. It was suggested that the conjugated internal loop renders additional contacts and is responsible for the enhancement in the binding affinity. Conjugation of two aptamers that bind to different sites of the target protein is a facile and robust strategy to develop an aptamer with higher performance.
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Affiliation(s)
- Yusuke Nomura
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku 162-8601, Tokyo, Japan.,Division of Medical Devices, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Kaori Yamazaki
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku 162-8601, Tokyo, Japan
| | - Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Kenta Takada
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Naohiro Kobayashi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoichiro Tanaka
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806, Japan
| | - Junichi Fukunaga
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806, Japan
| | - Yoshikazu Nakamura
- RIBOMIC Inc, 3-16-13 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan.,Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yuji Haishima
- Division of Medical Devices, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku 162-8601, Tokyo, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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Rudchenko MN, Zamyatnin AA. Prospects for using self-assembled nucleic acid structures. BIOCHEMISTRY (MOSCOW) 2016; 80:391-9. [PMID: 25869355 DOI: 10.1134/s000629791504001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
According to the central dogma in molecular biology, nucleic acids are assigned with key functions on storing and executing genetic information in any living cell. However, features of nucleic acids are not limited only with properties providing template-dependent biosynthetic processes. Studies of DNA and RNA unveiled unique features of these polymers able to make various self-assembled three-dimensional structures that, among other things, use the complementarity principle. Here, we review various self-assembled nucleic acid structures as well as application of DNA and RNA to develop nanomaterials, molecular automata, and nanodevices. It can be expected that in the near future results of these developments will allow designing novel next-generation diagnostic systems and medicinal drugs.
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Affiliation(s)
- M N Rudchenko
- Research Division, Hospital for Special Surgery, New York, NY 10021, USA.
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Fujita Y, Tanaka T, Furuta H, Ikawa Y. Functional roles of a tetraloop/receptor interacting module in a cyclic di-GMP riboswitch. J Biosci Bioeng 2011; 113:141-5. [PMID: 22074990 DOI: 10.1016/j.jbiosc.2011.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 09/26/2011] [Accepted: 10/07/2011] [Indexed: 12/27/2022]
Abstract
Riboswitches are a class of structural RNAs that regulate transcription and translation through specific recognition of small molecules. Riboswitches are attractive not only as drug targets for novel antibiotics but also as modular tools for controlling gene expression. Sequence comparison of a class of riboswitches that sense cyclic di-GMP (type-I c-di-GMP riboswitches) revealed that this type of riboswitch frequently shows a GAAA loop/receptor interaction between P1 and P3 elements. In the crystal structures of a type-I c-di-GMP riboswitch from Vibrio cholerae (the Vc2 riboswitch), the GNRA loop/receptor interaction assembled P2 and P3 stems to organize a ligand-binding pocket. In this study, the functional importance of the GAAA loop-receptor interaction in the Vc2 riboswitch was examined. A series of variant Vc2 riboswitches with mutations in the GAAA loop/receptor interaction were assayed for their switching abilities. In mutants with mutations in the P2 GAAA loop, expression of the reporter gene was reduced to approximately 40% - 60% of that in the wild-type. However, mutants in which the P3 receptor motif was substituted with base pairs were as active as the wild-type. These results suggested that the GAAA loop/receptor interaction does not simply establish the RNA 3D structure but docking of P2 GAAA loop reduces the flexibility of the GAAA receptor motif in the P3 element. This mechanism was supported by a variant riboswitch bearing a theophylline aptamer module in P3 the structural rigidity of which could be modulated by the small molecule theophylline.
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Affiliation(s)
- Yuki Fujita
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan
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Maeda Y, Furuta H, Ikawa Y. Trans-acting RNAs as molecular probes for monitoring time-dependent structural change of an RNA complex adapting two structures. J Biosci Bioeng 2010; 111:370-6. [PMID: 21163698 DOI: 10.1016/j.jbiosc.2010.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 11/02/2010] [Accepted: 11/15/2010] [Indexed: 01/04/2023]
Abstract
As dynamic structural changes are pivotal for the functions of some classes of RNA molecule, it is important to develop methods to monitor structural changes in RNA in a time-dependent manner without chemical modification. Based on previous reports that trans-acting RNAs can be used as probes for analysis and control of 3D structures of target RNAs, we applied this method to monitor time-dependent structural changes in RNA. We designed and performed a proof-of-principle study using a simple model RNA complex that adopts two different structures as a target. The time-dependent structural changes in the target RNA were successfully monitored using two trans-acting RNAs, which stably form a ternary complex with the bimolecular target RNA and act as a catalyst to join two RNA fragments of the target complex, respectively.
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Affiliation(s)
- Yuri Maeda
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
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