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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...

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Autores principales: Durand, Guillaume, Dausse, Eric, Goux, Emma, Fiore, Emmanuelle, Peyrin, Eric, Ravelet, Corinne, Toulmé, Jean-Jacques
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
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.
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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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