Installation of orthogonality to the interface that assembles two modular domains in the Tetrahymena group I ribozyme

Tanaka, Takahiro; Furuta, Hiroyuki; Ikawa, Yoshiya

doi:10.1016/j.jbiosc.2013.10.008

Cited by 12 publications

(21 citation statements)

References 41 publications

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“…When the concentrations were reduced, the amount of product from P5abc/DP5 decreased more rapidly than for 3a+ 4c:o nly 18 % for P5abc/DP5 but 60 %f or 3a+ 4c,w ith 62.5 nm ribozyme and activator.T his is consistentw ith the stability of bimolecular complexesa sd etermined by an electrophoretic mobility shift (EMS) assay,i nw hich P5abc/DP5 with the orKL/orLRi nterface did not form stably in the presence of 5 mm Mg 2 + . [24] In contrast, 3a+ 4a formed ac omplex in the presence of 5mm Mg 2 + ( Figure 2C). Thus, in the tecto-GIRz system,a ssembly of aP 5abc/DP5 complex on one side is strongly assisted by a P5abc/DP5 complexo nthe opposite side.…”

Section: P1 Duplex In One Ribozyme Enhances the Activity Of The Complmentioning

confidence: 94%

“…Large structures of such modular ribozymes can be used as RNA units for large nanostructures. Their assembly is supported by multiple RNA–RNA interactions; their assembly is often rationally controllable because of the structural modularity . For example, RNaseP can be divided into two large domains: the catalytic domain (C‐domain) and the specificity domain (S‐domain).…”

Section: Introductionmentioning

confidence: 99%

“…An LR interaction (P5b–P6) and a KM interaction (P5c–P2) have been shown to support interdomain association between P5abc and ΔP5 . Previously, we replaced LR and KM with artificial variant motifs (the GGAA loop‐R(1) motif LR pair generated through in vitro evolution, and M3 KM interaction designed rationally) . This indicated that the large structural domains of the Tetrahymena ribozyme can be manipulated as if they were expanded versions of small RNA motifs; these were used as modular tools for the bottom‐up construction of RNA nanostructures and their assembly.…”

Section: Introductionmentioning

confidence: 99%

“…Their assembly is supported by multiple RNA-RNA interactions; their assembly is often rationally controllable because of the structuralm odularity. [24] For example, RNaseP can be divided into two large domains:t he catalytic domain (C-domain) and the specificity domain (S-domain). Separately prepared C-and S-domain RNAs can assemble noncovalently to reconstitute the RNaseP ribozymes.…”

Section: Introductionmentioning

confidence: 99%

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Tecto‐GIRz: Engineered Group I Ribozyme the Catalytic Ability of Which Can Be Controlled by Self‐Dimerization

et al. 2016

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RNA is a promising biomaterial for self-assembly of nano-sized structures with a wide range of applications in nanotechnology and synthetic biology. Several RNA-based nanostructures have been reported, but most are unrelated to intracellular RNA, which possesses modular structures that are sufficiently large and complex to serve as catalysts to promote sophisticated chemical reactions. In this study, we designed dimeric RNA structures based on the Tetrahymena group I ribozyme. The resulting dimeric RNAs (tecto group I ribozyme; tecto-GIRz) exhibit catalytic ability that depended on controlled dimerization, by which a pair of ribozymes can be activated to perform cleavage and splicing reactions of two distinct substrates. Modular redesign of complex RNA structures affords large ribozymes for use as modules in RNA nanotechnology and RNA synthetic biology.

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Section: P1 Duplex In One Ribozyme Enhances the Activity Of The Complmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Tecto‐GIRz: Engineered Group I Ribozyme the Catalytic Ability of Which Can Be Controlled by Self‐Dimerization

et al. 2016

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“…Self-oligomerization of the unit RNA yielded a mixture of assembled structures containing both triangular trimers and square tetramers. The selective formation of the desired structure was achieved by designing orthogonal interfaces between P5abc and ΔP5 modules [ 17 , 20 ]. In the orthogonal interfaces, we employed a non-natural RNA–RNA interacting motif, i.e., GGAA/R(GGAA), which belongs to the same RNA motif family (GNRA/receptor motif family) as the natural counterpart GAAA/R(GAAA) [ 21 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

Artificial RNA Motifs Expand the Programmable Assembly between RNA Modules of a Bimolecular Ribozyme Leading to Application to RNA Nanostructure Design

Rahman

Matsumura

Ikawa

2017

Biology

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A bimolecular ribozyme consisting of a core ribozyme (ΔP5 RNA) and an activator module (P5abc RNA) has been used as a platform to design assembled RNA nanostructures. The tight and specific assembly between the P5abc and ΔP5 modules depends on two sets of intermodule interactions. The interface between P5abc and ΔP5 must be controlled when designing RNA nanostructures. To expand the repertoire of molecular recognition in the P5abc/ΔP5 interface, we modified the interface by replacing the parent tertiary interactions in the interface with artificial interactions. The engineered P5abc/ΔP5 interfaces were characterized biochemically to identify those suitable for nanostructure design. The new interfaces were used to construct 2D-square and 1D-array RNA nanostructures.

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Flexible Assembly of Engineered Tetrahymena Ribozymes Forming Polygonal RNA Nanostructures with Catalytic Ability

Mori

Suzuki

et al. 2021

ChemBioChem

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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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Installation of orthogonality to the interface that assembles two modular domains in the Tetrahymena group I ribozyme

Cited by 12 publications

References 41 publications

Tecto‐GIRz: Engineered Group I Ribozyme the Catalytic Ability of Which Can Be Controlled by Self‐Dimerization

Tecto‐GIRz: Engineered Group I Ribozyme the Catalytic Ability of Which Can Be Controlled by Self‐Dimerization

Artificial RNA Motifs Expand the Programmable Assembly between RNA Modules of a Bimolecular Ribozyme Leading to Application to RNA Nanostructure Design

Flexible Assembly of Engineered Tetrahymena Ribozymes Forming Polygonal RNA Nanostructures with Catalytic Ability

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