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A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs

The programmability of RNA–RNA interactions through intermolecular base-pairing has been successfully exploited to design a variety of RNA devices that artificially regulate gene expression. An in silico design for interacting structured RNA sequences that satisfies multiple design criteria becomes...

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Detalles Bibliográficos
Autores principales: Taneda, Akito, Sato, Kengo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7962656/
https://www.ncbi.nlm.nih.gov/pubmed/33800268
http://dx.doi.org/10.3390/ijms22052720
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author Taneda, Akito
Sato, Kengo
author_facet Taneda, Akito
Sato, Kengo
author_sort Taneda, Akito
collection PubMed
description The programmability of RNA–RNA interactions through intermolecular base-pairing has been successfully exploited to design a variety of RNA devices that artificially regulate gene expression. An in silico design for interacting structured RNA sequences that satisfies multiple design criteria becomes a complex multi-objective problem. Although multi-objective optimization is a powerful technique that explores a vast solution space without empirical weights between design objectives, to date, no web service for multi-objective design of RNA switches that utilizes RNA–RNA interaction has been proposed. We developed a web server, which is based on a multi-objective design algorithm called MODENA, to design two interacting RNAs that form a complex in silico. By predicting the secondary structures with RactIP during the design process, we can design RNAs that form a joint secondary structure with an external pseudoknot. The energy barrier upon the complex formation is modeled by an interaction seed that is optimized in the design algorithm. We benchmarked the RNA switch design approaches (MODENA+RactIP and MODENA+RNAcofold) for the target structures based on natural RNA-RNA interactions. As a result, MODENA+RactIP showed high design performance for the benchmark datasets.
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spelling pubmed-79626562021-03-17 A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs Taneda, Akito Sato, Kengo Int J Mol Sci Article The programmability of RNA–RNA interactions through intermolecular base-pairing has been successfully exploited to design a variety of RNA devices that artificially regulate gene expression. An in silico design for interacting structured RNA sequences that satisfies multiple design criteria becomes a complex multi-objective problem. Although multi-objective optimization is a powerful technique that explores a vast solution space without empirical weights between design objectives, to date, no web service for multi-objective design of RNA switches that utilizes RNA–RNA interaction has been proposed. We developed a web server, which is based on a multi-objective design algorithm called MODENA, to design two interacting RNAs that form a complex in silico. By predicting the secondary structures with RactIP during the design process, we can design RNAs that form a joint secondary structure with an external pseudoknot. The energy barrier upon the complex formation is modeled by an interaction seed that is optimized in the design algorithm. We benchmarked the RNA switch design approaches (MODENA+RactIP and MODENA+RNAcofold) for the target structures based on natural RNA-RNA interactions. As a result, MODENA+RactIP showed high design performance for the benchmark datasets. MDPI 2021-03-08 /pmc/articles/PMC7962656/ /pubmed/33800268 http://dx.doi.org/10.3390/ijms22052720 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Taneda, Akito
Sato, Kengo
A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs
title A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs
title_full A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs
title_fullStr A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs
title_full_unstemmed A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs
title_short A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs
title_sort web server for designing molecular switches composed of two interacting rnas
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7962656/
https://www.ncbi.nlm.nih.gov/pubmed/33800268
http://dx.doi.org/10.3390/ijms22052720
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