ArticleNucleic acids research2026
A potential RNA-RNA distal interaction competing with a functional pseudoknot in the 3'-untranslated region of SARS-like coronaviruses.
Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
In the 3' untranslated region of betacoronaviruses, a pseudoknot involving stem-loop 3SL2 has been proposed to form a binding site for the viral RNA polymerase enabling the initiation of negative-sense RNA synthesis during the processes of virus replication and discontinuous transcription. Based on bioinformatic analyses and a mutagenesis strategy monitored with electrophoretic experiments and viral replication assays, we report that, in addition to the local pseudoknot in the 3'UTR, 3SL2 can establish a distal tertiary contact with an exposed sequence in the ORF7b gene located 1847 nucleotides upstream in the SARS-CoV-2 genome. The bases involved in this contact are highly conserved in all SARS-like coronaviruses and sequencing data indicate that this motif may form an alternative polymerase binding site enabling the synthesis of non-canonical subgenomic RNA. These findings provide a foundation for investigating the molecular mechanisms governing the processes of replication, discontinuous transcription, and recombination in these viruses.
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