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A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers
Loop–loop (also known as kissing) interactions between RNA hairpins are involved in several mechanisms in both prokaryotes and eukaryotes such as the regulation of the plasmid copy number or the dimerization of retroviral genomes. The stability of kissing complexes relies on loop parameters (base co...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872101/ https://www.ncbi.nlm.nih.gov/pubmed/27067541 http://dx.doi.org/10.1093/nar/gkw206 |
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author | Durand, Guillaume Dausse, Eric Goux, Emma Fiore, Emmanuelle Peyrin, Eric Ravelet, Corinne Toulmé, Jean-Jacques |
author_facet | Durand, Guillaume Dausse, Eric Goux, Emma Fiore, Emmanuelle Peyrin, Eric Ravelet, Corinne Toulmé, Jean-Jacques |
author_sort | Durand, Guillaume |
collection | PubMed |
description | Loop–loop (also known as kissing) interactions between RNA hairpins are involved in several mechanisms in both prokaryotes and eukaryotes such as the regulation of the plasmid copy number or the dimerization of retroviral genomes. The stability of kissing complexes relies on loop parameters (base composition, sequence and size) and base combination at the loop–loop helix - stem junctions. In order to identify kissing partners that could be used as regulatory elements or building blocks of RNA scaffolds, we analysed a pool of 5.2 × 10(6) RNA hairpins with randomized loops. We identified more than 50 pairs of kissing RNA hairpins. Two kissing motifs, 5′CCNY and 5′RYRY, generate highly stable complexes with K(D)s in the low nanomolar range. Such motifs were introduced in the apical loop of hairpin aptamers that switch between unfolded and folded state upon binding to their cognate target molecule, hence their name aptaswitch. The aptaswitch–ligand complex is specifically recognized by a second RNA hairpin named aptakiss through loop–loop interaction. Taking advantage of our kissing motif repertoire we engineered aptaswitch–aptakiss modules for purine derivatives, namely adenosine, GTP and theophylline and demonstrated that these molecules can be specifically and simultaneously detected by surface plasmon resonance or by fluorescence anisotropy. |
format | Online Article Text |
id | pubmed-4872101 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-48721012016-05-27 A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers Durand, Guillaume Dausse, Eric Goux, Emma Fiore, Emmanuelle Peyrin, Eric Ravelet, Corinne Toulmé, Jean-Jacques Nucleic Acids Res Synthetic Biology and Bioengineering Loop–loop (also known as kissing) interactions between RNA hairpins are involved in several mechanisms in both prokaryotes and eukaryotes such as the regulation of the plasmid copy number or the dimerization of retroviral genomes. The stability of kissing complexes relies on loop parameters (base composition, sequence and size) and base combination at the loop–loop helix - stem junctions. In order to identify kissing partners that could be used as regulatory elements or building blocks of RNA scaffolds, we analysed a pool of 5.2 × 10(6) RNA hairpins with randomized loops. We identified more than 50 pairs of kissing RNA hairpins. Two kissing motifs, 5′CCNY and 5′RYRY, generate highly stable complexes with K(D)s in the low nanomolar range. Such motifs were introduced in the apical loop of hairpin aptamers that switch between unfolded and folded state upon binding to their cognate target molecule, hence their name aptaswitch. The aptaswitch–ligand complex is specifically recognized by a second RNA hairpin named aptakiss through loop–loop interaction. Taking advantage of our kissing motif repertoire we engineered aptaswitch–aptakiss modules for purine derivatives, namely adenosine, GTP and theophylline and demonstrated that these molecules can be specifically and simultaneously detected by surface plasmon resonance or by fluorescence anisotropy. Oxford University Press 2016-05-19 2016-04-11 /pmc/articles/PMC4872101/ /pubmed/27067541 http://dx.doi.org/10.1093/nar/gkw206 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Synthetic Biology and Bioengineering Durand, Guillaume Dausse, Eric Goux, Emma Fiore, Emmanuelle Peyrin, Eric Ravelet, Corinne Toulmé, Jean-Jacques A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers |
title | A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers |
title_full | A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers |
title_fullStr | A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers |
title_full_unstemmed | A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers |
title_short | A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers |
title_sort | combinatorial approach to the repertoire of rna kissing motifs; towards multiplex detection by switching hairpin aptamers |
topic | Synthetic Biology and Bioengineering |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872101/ https://www.ncbi.nlm.nih.gov/pubmed/27067541 http://dx.doi.org/10.1093/nar/gkw206 |
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