About: Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2

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About: Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2 Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2
Creator	Gallo, Juan Bañobre-López, Manuel Belmonte-Reche, Efres Gonzalez, Carlos Serrano-Chacón, Israel
source	BioRxiv
abstract	In this paper we report the analysis of the 2019-nCoV genome and related viruses using an upgraded version of the open-source algorithm G4-iM Grinder. This version improves the functionality of the software, including an easy way to determine the potential biological features affected by the candidates found. The quadruplex definitions of the algorithm were optimized for 2019-nCoV. Using a lax quadruplex definition ruleset, which accepts amongst other parameters two residue G- and C-tracks, hundreds of potential quadruplex candidates were discovered. These sequences were evaluated by their in vitro formation probability, their position in the viral RNA, their uniqueness and their conservation rates (calculated in over three thousand different COVID-19 clinical cases and sequenced at different times and locations during the ongoing pandemic). These results were compared sequentially to other Coronaviridae members, other Group IV (+)ssRNA viruses and the entire realm. Sequences found in common with other species were further analyzed and characterized. Sequences with high scores unique to the 2019-nCoV were studied to investigate the variations amongst similar species. Quadruplex formation of the best candidates was then confirmed experimentally. Using NMR and CD spectroscopy, we found several highly stable RNA quadruplexes that may be suitable theranostic targets against the 2019-nCoV. GRAPHICAL ABSTRACT
has issue date	2020-08-20(xsd:dateTime)
bibo:doi	10.1101/2020.08.19.257493
has license	biorxiv
sha1sum (hex)	9e5bf34d9f119e78bd3e388b990cc8d2593d17d4
schema:url	https://doi.org/10.1101/2020.08.19.257493
resource representing a document's title	Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2
schema:publication	bioRxiv
resource representing a document's body	covid:9e5bf34d9f119e78bd3e388b990cc8d2593d17d4#body_text
is schema:about of	named entity 'algorithm' named entity 'sequenced' named entity 'easy' named entity 'cases' named entity 'formation' »more»

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