ArticlePloS one2021
Potential G-quadruplexes and i-Motifs in the SARS-CoV-2.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 61 citations in OpenAlex.
- Recent advances in functional studies of coronavirus NSP13 helicase and challenges in inhibitor development.Virulence · 2026Review
- An ATP-Driven N Protein-DDX21 Molecular Switch Dynamically Controls SARS-CoV-2 RNA G-Quadruplex Heterogeneity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- How loop lengths shape topological preferences of two-tetrad G-quadruplexes.Nucleic acids research · 2026Article
- In Search of the Most Significant Potential G-Quadruplexes in SARS-CoV-2 RNA: Genomic Analysis.Viruses · 2026Article
- Paradoxical G-quadruplex distribution in coronavirus genomes reveals functional constraints and antiviral therapeutic opportunities.Virus research · 2026Article
- Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5' UTR of the viral genome.Microbiology spectrum · 2025Article
- From RNA sequence to its three-dimensional structure: geometrical structure, stability and dynamics of selected fragments of SARS-CoV-2 RNA.NAR genomics and bioinformatics · 2024Article
- Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA.Genome research · 2024Article
- Stabilization of G-Quadruplex Structures of the SARS-CoV-2 Genome by TMPyP4, BRACO19, and PhenDC3.International journal of molecular sciences · 2024Article
- On Water Arrangements in Right- and Left-Handed DNA Structures.Molecules (Basel, Switzerland) · 2024Review
- TMPRSS2 isoform 1 downregulation by G-quadruplex stabilization induces SARS-CoV-2 replication arrest.BMC biology · 2024Article
- G-Quadruplexes in the Viral Genome: Unlocking Targets for Therapeutic Interventions and Antiviral Strategies.Viruses · 2023Review
- Stabilization of the Quadruplex-Forming G-Rich Sequences in the Rhinovirus Genome Inhibits Uncoating-Role of NaViruses · 2023Article
- Article
- Unlocking G-Quadruplexes as Targets and Tools against COVID-19.Chinese journal of chemistry · 2022Article
- Recent advances in applying G-quadruplex for SARS-CoV-2 targeting and diagnosis: A review.International journal of biological macromolecules · 2022Review
- Binding Properties of RNA Quadruplex of SARS-CoV-2 to Berberine Compared to Telomeric DNA Quadruplex.International journal of molecular sciences · 2022Article
- G-Quadruplex DNA as a Target in Pathogenic Bacteria: Efficacy of an Extended Naphthalene Diimide Ligand and Its Mode of Action.Journal of medicinal chemistry · 2022Article
- Major Achievements in the Design of Quadruplex-Interactive Small Molecules.Pharmaceuticals (Basel, Switzerland) · 2022Review
- Modulation of the Conformational Space of SARS-CoV-2 RNA Quadruplex RG-1 by Cellular Components and the Amyloidogenic Peptides α-Synuclein and hIAPP.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Quadruplex structures have been identified in a plethora of organisms where they play important functions in the regulation of molecular processes, and hence have been proposed as therapeutic targets for many diseases. In this paper we report the extensive bioinformatic analysis of the SARS-CoV-2 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 SARS-CoV-2. Using a lax quadruplex definition ruleset, which accepts amongst other parameters two residue G- and C-tracks, 512 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 seventeen thousand different COVID-19 clinical cases and sequenced at different times and locations during the ongoing pandemic). These results were then compared subsequently to other Coronaviridae members, other Group IV (+)ssRNA viruses and the entire viral realm. Sequences found in common with other viral species were further analyzed and characterized. Sequences with high scores unique to the SARS-CoV-2 were studied to investigate the variations amongst similar species. Quadruplex formation of the best candidates were then confirmed experimentally. Using NMR and CD spectroscopy, we found several highly stable RNA quadruplexes that may be suitable therapeutic targets for the SARS-CoV-2.
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