DNA and RNA guanine-rich oligonucleotides can form non-canonical structures called G-quadruplexes or "G4" that are based on the stacking of G-quartets. The role of DNA and RNA G4 is documented in eukaryotic cells and in pathogens such as viruses. Yet, G4 have been identified only in a few RNA viruses, including the Flaviviridae family. In this study, we analysed the last 157 nucleotides at the 3'end of the HCV (-) strand. This sequence is known to be the minimal sequence required for an efficient RNA replication. Using bioinformatics and biophysics, we identified a highly conserved G4-prone sequence located in the stem-loop IIy' of the negative strand. We also showed that the formation of this G-quadruplex inhibits the in vitro RNA synthesis by the RdRp. Furthermore, Phen-DC3, a specific G-quadruplex binder, is able to inhibit HCV viral replication in cells in conditions where no cytotoxicity was measured. Considering that this domain of the negative RNA strand is well conserved among HCV genotypes, G4 ligands could be of interest for new antiviral therapies.

Institute of Biophysics Academy of Sciences of the Czech Republic 612 65 Brno Czech Republic

Univ Bordeaux ARNA laboratory INSERM U1212 CNRS UMR 5320 IECB F 33600 Pessac France

Univ Bordeaux CNRS UMR5234 MFP laboratory F 33000 Bordeaux France

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Sci Rep. 2019 May 23;9(1):7954. doi: 10.1038/s41598-019-43445-7. PubMed

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