PT  - JOURNAL ARTICLE
AU  - Caylee L. Cunningham
AU  - Caleb J. Frye
AU  - Joseph A. Makowski
AU  - Adam H. Kensinger
AU  - Morgan Shine
AU  - Ella J. Milback
AU  - Patrick E. Lackey
AU  - Jeffrey D. Evanseck
AU  - Mihaela-Rita Mihailescu
TI  - Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p
AID  - 10.1101/2023.02.10.528014
DP  - 2023 Jan 01
TA  - bioRxiv
PG  - 2023.02.10.528014
4099  - http://biorxiv.org/content/early/2023/02/10/2023.02.10.528014.short
4100  - http://biorxiv.org/content/early/2023/02/10/2023.02.10.528014.full
AB  - The stem loop 2 motif (s2m), a highly conserved 41-nucleotide hairpin structure in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome, serves as an attractive therapeutic target that may have important roles in the virus life cycle or interactions with the host. However, the conserved s2m in Delta SARS-CoV-2, a previously dominant variant characterized by high infectivity and disease severity, has received relatively less attention than that of the original SARS-CoV-2 virus. The focus of this work is to identify and define the s2m changes between Delta and SARS-CoV-2 and subsequent impact of those changes upon the s2m dimerization and interactions with the host microRNA miR-1307-3p. Bioinformatics analysis of the GISAID database targeting the s2m element reveals a greater than 99% correlation of a single nucleotide mutation at the 15th position (G15U) in Delta SARS-CoV-2. Based on 1H NMR assignments comparing the imino proton resonance region of s2m and the G15U at 19°C, we find that the U15-A29 base pair closes resulting in a stabilization of the upper stem without overall secondary structure deviation. Increased stability of the upper stem did not affect the chaperone activity of the viral N protein, as it was still able to convert the kissing dimers formed by s2m G15U into a stable duplex conformation, consistent with the s2m reference. However, we find that the s2m G15U mutation drastically reduces the binding affinity of the host miR-1307-3p. These findings demonstrate that the observed G15U mutation alters the secondary structure of s2m with subsequent impact on viral binding of host miR-1307-3p, with potential consequences on the immune response.Competing Interest StatementThe authors have declared no competing interest.