Dissecting the Conformational\nHeterogeneity of Stem-Loop\nSubstructures of the Fifth Element in the 5′-Untranslated Region\nof SARS-CoV‑2

Throughout the family of coronaviruses, structured RNA\nelements\nwithin the 5′ region of the genome are highly conserved. The\nfifth stem-loop element from SARS-CoV-2 (5_SL5) represents an example\nof an RNA structural element, repeatedly occurring in coronaviruses.\nIt contains a conserved, repetitive fold within its substructures\nSL5a and SL5b. We herein report the detailed characterization of the\nstructure and dynamics of elements SL5a and SL5b that are located\nimmediately upstream of the SARS-CoV-2 ORF1a/b start codon. Exploiting\nthe unique ability of solution NMR methods, we show that the structures\nof both apical loops are modulated by structural differences in the\nremote parts located in their stem regions. We further integrated\nour high-resolution models of SL5a/b into the context of full-length\n5_SL5 structures by combining different structural biology methods.\nFinally, we evaluated the impact of the two most common VoC mutations\nwithin 5_SL5 with respect to individual base-pair stability.