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Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation

The three-dimensional (3D) structures of many biomacromolecules have been solved to reveal the functions of these molecules. However, these 3D structures have rarely been applied to constructing efficient molecular devices that function in living cells. Here, we demonstrate a 3D structure-based mole...

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Detalles Bibliográficos
Autores principales: Kashida, Shunnichi, Inoue, Tan, Saito, Hirohide
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467064/
https://www.ncbi.nlm.nih.gov/pubmed/22810207
http://dx.doi.org/10.1093/nar/gks668
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author Kashida, Shunnichi
Inoue, Tan
Saito, Hirohide
author_facet Kashida, Shunnichi
Inoue, Tan
Saito, Hirohide
author_sort Kashida, Shunnichi
collection PubMed
description The three-dimensional (3D) structures of many biomacromolecules have been solved to reveal the functions of these molecules. However, these 3D structures have rarely been applied to constructing efficient molecular devices that function in living cells. Here, we demonstrate a 3D structure-based molecular design principle for constructing short hairpin RNA (shRNA)-mediated genetic information converters; these converters respond to specific proteins and trigger the desired gene expression by modulating the function of the RNA-processing enzyme Dicer. The inhibitory effect on Dicer cleavage against the shRNA designed to specifically bind to U1A spliceosomal protein was correlated with the degree of steric hindrance between Dicer and the shRNA-protein complex in vitro: The level of the hindrance was predicted based on the models. Moreover, the regulation of gene expression was achieved by using the shRNA converters designed to bind to the target U1A or nuclear factor-κB (NF-κB) p50 proteins expressed in human cells. The 3D molecular design approach is widely applicable for developing new devices in synthetic biology.
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spelling pubmed-34670642012-10-10 Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation Kashida, Shunnichi Inoue, Tan Saito, Hirohide Nucleic Acids Res Synthetic Biology and Chemistry The three-dimensional (3D) structures of many biomacromolecules have been solved to reveal the functions of these molecules. However, these 3D structures have rarely been applied to constructing efficient molecular devices that function in living cells. Here, we demonstrate a 3D structure-based molecular design principle for constructing short hairpin RNA (shRNA)-mediated genetic information converters; these converters respond to specific proteins and trigger the desired gene expression by modulating the function of the RNA-processing enzyme Dicer. The inhibitory effect on Dicer cleavage against the shRNA designed to specifically bind to U1A spliceosomal protein was correlated with the degree of steric hindrance between Dicer and the shRNA-protein complex in vitro: The level of the hindrance was predicted based on the models. Moreover, the regulation of gene expression was achieved by using the shRNA converters designed to bind to the target U1A or nuclear factor-κB (NF-κB) p50 proteins expressed in human cells. The 3D molecular design approach is widely applicable for developing new devices in synthetic biology. Oxford University Press 2012-10 2012-07-18 /pmc/articles/PMC3467064/ /pubmed/22810207 http://dx.doi.org/10.1093/nar/gks668 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Synthetic Biology and Chemistry
Kashida, Shunnichi
Inoue, Tan
Saito, Hirohide
Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation
title Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation
title_full Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation
title_fullStr Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation
title_full_unstemmed Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation
title_short Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation
title_sort three-dimensionally designed protein-responsive rna devices for cell signaling regulation
topic Synthetic Biology and Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467064/
https://www.ncbi.nlm.nih.gov/pubmed/22810207
http://dx.doi.org/10.1093/nar/gks668
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