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Mori Y, Oi H, Suzuki Y, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Flexible Assembly of Engineered Tetrahymena Ribozymes Forming Polygonal RNA Nanostructures with Catalytic Ability. Chembiochem 2021; 22:2168-2176. [PMID: 33876531 DOI: 10.1002/cbic.202100109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/11/2021] [Indexed: 11/11/2022]
Abstract
Ribozymes with modular architecture constitute an attractive class of structural platforms for design and construction of nucleic acid nanostructures with biological functions. Through modular engineering of the Tetrahymena ribozyme, we have designed unit RNAs (L-RNAs), assembly of which formed ribozyme-based closed trimers and closed tetramers. Their catalytic activity was dependent on oligomer formation. In this study, the structural variety of L-RNA oligomers was extended by tuning their structural elements, yielding closed pentamers and closed hexamers. Their assembly properties were analyzed by electrophoretic mobility shift assay (EMSA) and atomic force microscopy (AFM).
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Affiliation(s)
- Yuki Mori
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, 930-8555, Toyama, Japan
| | - Hiroki Oi
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, 930-8555, Toyama, Japan
| | - Yuki Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, 606-8502, Kyoto, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, 930-8555, Toyama, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, 930-8555, Toyama, Japan
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An RNA Triangle with Six Ribozyme Units Can Promote a Trans-Splicing Reaction through Trimerization of Unit Ribozyme Dimers. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11062583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Ribozymes are catalytic RNAs that are attractive platforms for the construction of nanoscale objects with biological functions. We designed a dimeric form of the Tetrahymena group I ribozyme as a unit structure in which two ribozymes were connected in a tail-to-tail manner with a linker element. We introduced a kink-turn motif as a bent linker element of the ribozyme dimer to design a closed trimer with a triangular shape. The oligomeric states of the resulting ribozyme dimers (kUrds) were analyzed biochemically and observed directly by atomic force microscopy (AFM). Formation of kUrd oligomers also triggered trans-splicing reactions, which could be monitored with a reporter system to yield a fluorescent RNA aptamer as the trans-splicing product.
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Mitchell C, Polanco JA, DeWald L, Kress D, Jaeger L, Grabow WW. Responsive self-assembly of tectoRNAs with loop-receptor interactions from the tetrahydrofolate (THF) riboswitch. Nucleic Acids Res 2020; 47:6439-6451. [PMID: 31045210 PMCID: PMC6614920 DOI: 10.1093/nar/gkz304] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 03/22/2019] [Accepted: 04/16/2019] [Indexed: 12/17/2022] Open
Abstract
Naturally occurring RNAs are known to exhibit a high degree of modularity, whereby specific structural modules (or motifs) can be mixed and matched to create new molecular architectures. The modular nature of RNA also affords researchers the ability to characterize individual structural elements in controlled synthetic contexts in order to gain new and critical insights into their particular structural features and overall performance. Here, we characterized the binding affinity of a unique loop–receptor interaction found in the tetrahydrofolate (THF) riboswitch using rationally designed self-assembling tectoRNAs. Our work suggests that the THF loop–receptor interaction has been fine-tuned for its particular role as a riboswitch component. We also demonstrate that the thermodynamic stability of this interaction can be modulated by the presence of folinic acid, which induces a local structural change at the level of the loop–receptor. This corroborates the existence of a THF binding site within this tertiary module and paves the way for its potential use as a THF responsive module for RNA nanotechnology and synthetic biology.
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Affiliation(s)
- Charles Mitchell
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA
| | - Julio A Polanco
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Laura DeWald
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA
| | - Dustin Kress
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Wade W Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA
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Catalytic RNA, ribozyme, and its applications in synthetic biology. Biotechnol Adv 2019; 37:107452. [DOI: 10.1016/j.biotechadv.2019.107452] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/21/2022]
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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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Rahman MM, Matsumura S, Ikawa Y. Oligomerization of a Bimolecular Ribozyme Modestly Rescues its Structural Defects that Disturb Interdomain Assembly to Form the Catalytic Site. J Mol Evol 2018; 86:431-442. [DOI: 10.1007/s00239-018-9862-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/07/2018] [Indexed: 12/31/2022]
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Mineral Surface-Templated Self-Assembling Systems: Case Studies from Nanoscience and Surface Science towards Origins of Life Research. Life (Basel) 2018; 8:life8020010. [PMID: 29738443 PMCID: PMC6027067 DOI: 10.3390/life8020010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/26/2018] [Accepted: 05/03/2018] [Indexed: 01/20/2023] Open
Abstract
An increasing body of evidence relates the wide range of benefits mineral surfaces offer for the development of early living systems, including adsorption of small molecules from the aqueous phase, formation of monomeric subunits and their subsequent polymerization, and supramolecular assembly of biopolymers and other biomolecules. Each of these processes was likely a necessary stage in the emergence of life on Earth. Here, we compile evidence that templating and enhancement of prebiotically-relevant self-assembling systems by mineral surfaces offers a route to increased structural, functional, and/or chemical complexity. This increase in complexity could have been achieved by early living systems before the advent of evolvable systems and would not have required the generally energetically unfavorable formation of covalent bonds such as phosphodiester or peptide bonds. In this review we will focus on various case studies of prebiotically-relevant mineral-templated self-assembling systems, including supramolecular assemblies of peptides and nucleic acids, from nanoscience and surface science. These fields contain valuable information that is not yet fully being utilized by the origins of life and astrobiology research communities. Some of the self-assemblies that we present can promote the formation of new mineral surfaces, similar to biomineralization, which can then catalyze more essential prebiotic reactions; this could have resulted in a symbiotic feedback loop by which geology and primitive pre-living systems were closely linked to one another even before life’s origin. We hope that the ideas presented herein will seed some interesting discussions and new collaborations between nanoscience/surface science researchers and origins of life/astrobiology researchers.
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Gulshan MA, Rahman MM, Matsumura S, Higuchi T, Umezawa N, Ikawa Y. Biogenic triamine and tetraamine activate core catalytic ability of Tetrahymena group I ribozyme in the absence of its large activator module. Biochem Biophys Res Commun 2018; 496:594-600. [DOI: 10.1016/j.bbrc.2018.01.085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 01/11/2018] [Indexed: 10/18/2022]
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