Altering the orientation of a fused protein to the RNA-binding ribosomal protein L7Ae and its derivatives through circular permutation

Ohuchi, Shoji J.; Sagawa, Fumihiko; Sakamoto, Taiichi; Inoue, Tan

doi:10.1016/j.bbrc.2015.09.035

Cited by 3 publications

(3 citation statements)

References 13 publications

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“…The computer-generated model showed no structure deformation after functionalization (Figures S2), leading to the final design of equilateral triangle shaped nanoparticle (Figure B). Although similar nanoparticles have been reported, ,,,, none of them have been constructed based on the enzymatically processed motif. The designed triangular nanoparticle with the side length of approximately 20 nm holds a potential to be used in nanobiotechnology as a carrier of multiple functionalities or the platform for more complex, supramolecular constructs.…”

mentioning

confidence: 98%

“…RNA structural data can be found in various databases, − and such motifs are commonly used in RNA-tectonics approach . In fact, RNA alone and in complexes with other biomolecules was used to design and create various nanostructures. ,,,,− Few of such structures were shown to successfully deliver functional RNA fragments to the eukaryotic cells. ,,,− However, the RNA particles were used merely as structural scaffolds without biological function. In a majority of cases the regulatory fragments were activated via nucleolytic removal of the dsRNA from the scaffold ,,, or interaction with the cognate partner ,,− without indication that the motif itself had been processed.…”

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confidence: 99%

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Self-Assembling RNA Nanoparticle for Gene Expression Regulation in a Model System

Jedrzejczyk

Chworoś

2019

ACS Synth. Biol.

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In the search for enzymatically processed RNA fragments, we found the novel three-way junction motif. The structure prediction suggested the arrangement of helices at acute angle approx. 60°. This allows the design of a trimeric RNA nanoparticle that can be functionalized with multiple regulatory fragments. Such RNA nano-object of equilateral triangular shape was applied for gene expression regulation studies in two independent cellular systems. Biochemical and functional studies confirmed the predicted shape and structure of the nanoparticle. The regulatory siRNA fragments incorporated into the nanoparticle were effectively released and triggered gene silencing. The regulatory effect was prolonged when induced with structuralized RNA compared to unstructured siRNAs. In these studies, the enzymatic processing of the motif was utilized for function release from the nanoparticle, enabling simultaneous delivery of different regulatory functions. This methodology of sequence search, RNA structural prediction, and application for rational design opens a new way for creating enzymatically processed RNA nanoparticles.

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confidence: 98%

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confidence: 99%

Self-Assembling RNA Nanoparticle for Gene Expression Regulation in a Model System

Jedrzejczyk

Chworoś

2019

ACS Synth. Biol.

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“…This proved that the nanoparticles could serve as ON/OFF switches for cellular development. Orientation changes in the functional protein fused with L7Ae were shown in the eGFP modification [96]. The interaction of protein with the RNA part was improved by the circular permutation of the L7Ae native protein.…”

Section: Multifunctional Rna Nano-objectsmentioning

confidence: 99%

Designing synthetic RNA for delivery by nanoparticles

Jedrzejczyk

Gendaszewska‐Darmach

Pawłowska

et al. 2017

J. Phys.: Condens. Matter

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The rapid development of synthetic biology and nanobiotechnology has led to the construction of various synthetic RNA nanoparticles of different functionalities and potential applications. As they occur naturally, nucleic acids are an attractive construction material for biocompatible nanoscaffold and nanomachine design. In this review, we provide an overview of the types of RNA and nucleic acid's nanoparticle design, with the focus on relevant nanostructures utilized for gene-expression regulation in cellular models. Structural analysis and modeling is addressed along with the tools available for RNA structural prediction. The functionalization of RNA-based nanoparticles leading to prospective applications of such constructs in potential therapies is shown. The route from the nanoparticle design and modeling through synthesis and functionalization to cellular application is also described. For a better understanding of the fate of targeted RNA after delivery, an overview of RNA processing inside the cell is also provided.

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