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Box-shaped ribozyme octamer formed by face-to-face dimerization of a pair of square-shaped ribozyme tetramers. J Biosci Bioeng 2022; 134:195-202. [PMID: 35810135 DOI: 10.1016/j.jbiosc.2022.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/21/2022]
Abstract
Naturally occurring ribozymes with defined three-dimensional (3D) structures serve as promising platforms for the design and construction of artificial RNA nanostructures. We constructed a hexameric ribozyme nanostructure by face-to-face dimerization of a pair of triangular ribozyme trimers, unit RNAs of which were derived from the Tetrahymena group I ribozyme. In this study, we have expanded the dimerization strategy to a square-shaped ribozyme tetramer by introducing four pillar units. The resulting box-shaped nanostructures, which contained eight ribozyme units, can be assembled from either four or two components of their unit RNAs.
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Yu K, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. A hexameric ribozyme nanostructure formed by double-decker assembly of a pair of triangular ribozyme trimers. Chembiochem 2022; 23:e202100573. [PMID: 35088928 DOI: 10.1002/cbic.202100573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/29/2021] [Indexed: 11/12/2022]
Abstract
The modular architecture of naturally occurring ribozymes makes them a promising class of structural platforms to design and assemble three-dimensional (3D) RNA nanostructures, into which the catalytic ability of the platform ribozyme can be installed. We have constructed and analyzed RNA nanostructures with polygonal-shaped (closed) ribozyme oligomers by assembling unit RNAs derived from the Tetrahymena group I intron with a typical modular architecture. In this study, we dimerized ribozyme trimers with a triangular shape by introducing three pillar units. The resulting double-decker nanostructures containing six ribozyme units were characterized biochemically and their structures were observed by atomic force microscopy. The double-decker hexamers exhibited higher catalytic activity than the parent ribozyme trimers.
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Affiliation(s)
- Kai Yu
- University of Toyama: Toyama Daigaku, Department of Chemistry, JAPAN
| | - Kumi Hidaka
- Kyoto University: Kyoto Daigaku, Department of Chemistry, JAPAN
| | | | | | | | - Yoshiya Ikawa
- University of Toyama, Chemistry, Gofuku 3190, 930-8555, Toyama, JAPAN
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Dobirul Islam M, Motiar Rahman M, Matsumura S, Ikawa Y. Effects of chain length of polyethylene glycol molecular crowders on a mutant Tetrahymena group I ribozyme lacking large peripheral module. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:867-883. [PMID: 34402751 DOI: 10.1080/15257770.2021.1956531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
While current group I ribozymes use several distinct strategies to function under conditions of low Mg2+ concentration (≤ 3 mM), a deletion mutant of the Tetrahymena ribozyme (ΔP5 ribozyme) is virtually inactive with 3 mM Mg2+ due to removal of the large peripheral module, P5abc, supporting the active conformation of the core module. We investigated the molecular crowding effects of synthetic polyethylene glycols (PEGs) on the activity of the ΔP5 ribozyme. Among PEG molecules with different chain lengths, PEG600 improved the activity of the ΔP5 ribozyme most effectively in the presence of 3 mM Mg2+.
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Affiliation(s)
- Md Dobirul Islam
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
| | - Md Motiar Rahman
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
| | - Shigeyoshi Matsumura
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan.,Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Yoshiya Ikawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan.,Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
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Tsuruga R, Uehara N, Suzuki Y, Furuta H, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Oligomerization of a modular ribozyme assembly of which is controlled by a programmable RNA–RNA interface between two structural modules. J Biosci Bioeng 2019; 128:410-415. [DOI: 10.1016/j.jbiosc.2019.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/14/2022]
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Rahman MM, Matsumura S, Ikawa Y. Effects of molecular crowding on a bimolecular group I ribozyme and its derivative that self-assembles to form ribozyme oligomers. Biochem Biophys Res Commun 2018; 507:136-141. [DOI: 10.1016/j.bbrc.2018.10.188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 10/29/2018] [Indexed: 01/04/2023]
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Gulshan MA, Tsuji K, Matsumura S, Higuchi T, Umezawa N, Ikawa Y. Distinct modulation of group I ribozyme activity among stereoisomers of a synthetic pentamine with structural constraints. Biochem Biophys Res Commun 2018; 504:698-703. [PMID: 30213632 DOI: 10.1016/j.bbrc.2018.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 09/03/2018] [Indexed: 11/25/2022]
Abstract
Among cationic molecules that can modulate ribozyme activities, polyamines act as both activator and inhibitor of ribozyme reactions partly due to their structural flexibility. Restriction of structural flexibility of polyamines may allow them to emphasize particular modulation effects. We examined eight stereoisomers of a synthetic pentamine bearing three cyclopentane rings. In the reaction of a structurally unstable group I ribozyme, three stereoisomers exhibited distinct effects as inhibitor, an additive with a neutral effect, and also as an activator.
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Affiliation(s)
- Mst Ara Gulshan
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan; Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan
| | - Kasumi Tsuji
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan; Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan; Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan.
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Gulshan MA, Matsumura S, Higuchi T, Umezawa N, Ikawa Y. Comparative study of polyethylene polyamines as activator molecules for a structurally unstable group I ribozyme. Biosci Biotechnol Biochem 2018; 82:1404-1407. [PMID: 29699448 DOI: 10.1080/09168451.2018.1465811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Polyamines are a promising class of molecules that can modulate RNA enzyme activities. To analyze the effects of the number of amine moieties systematically, we employed four polyamines sharing dimethylene units to connect amine moieties. As a model RNA enzyme, we used a structurally unstable group I ribozyme, which was activated most and least efficiently by tetraethylenepentamine and diethylenetriamine respectively.
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Affiliation(s)
- Mst Ara Gulshan
- a Department of Chemistry, Graduate School of Science and Engineering , University of Toyama , Toyama , Japan.,b Graduate School of Innovative Life Science , University of Toyama , Toyama , Japan
| | - Shigeyoshi Matsumura
- a Department of Chemistry, Graduate School of Science and Engineering , University of Toyama , Toyama , Japan
| | - Tsunehiko Higuchi
- c Graduate School of Pharmaceutical Sciences , Nagoya City University , Nagoya , Japan
| | - Naoki Umezawa
- c Graduate School of Pharmaceutical Sciences , Nagoya City University , Nagoya , Japan
| | - Yoshiya Ikawa
- a Department of Chemistry, Graduate School of Science and Engineering , University of Toyama , Toyama , Japan
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