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Kensinger, Adam H. ; Makowski, Joseph A. ; Pellegrene, Kendy A. ; Imperatore, Joshua A. ; Cunningham, Caylee L. ; Frye, Caleb J. ; Lackey, Patrick E. ; Mihailescu, Mihaela Rita ; Evanseck, Jeffrey D. ( , ACS Physical Chemistry Au)
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Imperatore, Joshua A. ; Cunningham, Caylee L. ; Pellegrene, Kendy A. ; Brinson, Robert G. ; Marino, John P. ; Evanseck, Jeffrey D. ; Mihailescu, Mihaela Rita ( , Nucleic Acids Research)
Abstract The ongoing COVID-19 pandemic highlights the necessity for a more fundamental understanding of the coronavirus life cycle. The causative agent of the disease, SARS-CoV-2, is being studied extensively from a structural standpoint in order to gain insight into key molecular mechanisms required for its survival. Contained within the untranslated regions of the SARS-CoV-2 genome are various conserved stem-loop elements that are believed to function in RNA replication, viral protein translation, and discontinuous transcription. While the majority of these regions are variable in sequence, a 41-nucleotide s2m element within the genome 3′ untranslated region is highly conserved among coronaviruses and three other viral families. In this study, we demonstrate that the SARS-CoV-2 s2m element dimerizes by forming an intermediate homodimeric kissing complex structure that is subsequently converted to a thermodynamically stable duplex conformation. This process is aided by the viral nucleocapsid protein, potentially indicating a role in mediating genome dimerization. Furthermore, we demonstrate that the s2m element interacts with multiple copies of host cellular microRNA (miRNA) 1307-3p. Taken together, our results highlight the potential significance of the dimer structures formed by the s2m element in key biological processes and implicate the motif as a possible therapeutic drug target for COVID-19 and other coronavirus-related diseases.