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. 2021 Oct;15(2):467-474.
doi: 10.1007/s12104-021-10047-2. Epub 2021 Aug 28.

1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2

Christian Richter #  1   2 , Katharina F Hohmann #  1   2 , Sabrina Toews  1   2 , Daniel Mathieu  3 , Nadide Altincekic  1   2 , Jasleen Kaur Bains  1   2 , Oliver Binas  1   2   4 , Betül Ceylan  1   2 , Elke Duchardt-Ferner  2   5 , Jan Ferner  1   2 , Boris Fürtig  1   2 , J Tassilo Grün  1   2   6 , Martin Hengesbach  1   2 , Daniel Hymon  1   2 , Hendrik R A Jonker  1   2 , Bozana Knezic  1   2 , Sophie M Korn  2   5 , Tom Landgraf  1   2 , Frank Löhr  2   7 , Stephen A Peter  8 , Dennis J Pyper  1   2 , Nusrat S Qureshi  1   2   9 , Andreas Schlundt  2   5 , Robbin Schnieders  1   2   10 , Elke Stirnal  1   2 , Alexey Sudakov  1   2 , Jennifer Vögele  2   5 , Julia E Weigand  8 , Julia Wirmer-Bartoschek  1   2 , Kerstin Witt  1   2 , Jens Wöhnert  2   5 , Harald Schwalbe  11   12 , Anna Wacker  13   14
Affiliations

1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2

Christian Richter et al. Biomol NMR Assign. 2021 Oct.

Abstract

The stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7-33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses. SL1 is present in genomic SARS-CoV-2 RNA as well as in all subgenomic mRNA species produced by the virus during replication, thus representing a ubiquitous cis-regulatory RNA with potential functions at all stages of the viral life cycle. We present here the 1H, 13C and 15N chemical shift assignment of the 29 nucleotides-RNA construct 5_SL1, which denotes the native 27mer SL1 stabilized by an additional terminal G-C base-pair.

Keywords: 5'-UTR; COVID19-NMR; SARS-CoV-2; SL1; Solution NMR spectroscopy.

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Conflict of interest statement

The authors declare the following competing financial interest(s): Daniel Mathieu is an employee of Bruker BioSpin.

Figures

Fig. 1
Fig. 1
a Secondary structure of 5_SL1 and its genomic position within the 5'-UTR of the SARS-CoV-2 genome. b Detection of the W–C base-pairs U13-A26 and U17-A22 in the lrHNN-COSY experiment (Table 1, XIII.). Adenosine C2H2 resonances (lower spectrum, 1H,13C-HSQC) were used to assign the 2J-N1H2 diagonal peaks and the corresponding uridine N3 cross peaks. Note that the A12 N1H2 resonance is broadened beyond detection. The U13-A22 and U17-A22 correlations are shown in black, the other base-pairs in grey in panel a
Fig. 2
Fig. 2
Plot of γFIT against PFIT as calculated from ribose 13C chemical shifts according to (Cherepanov et al. 2010). Residues from the apical loop are marked in red, bulge residues in black. C34 is omitted due to its low-field C2′ chemical shift typical for the 3'-terminal nucleotide, resulting in exceptionally high values of the canonical coordinates
Fig. 3
Fig. 3
Expanded region of the 2D 1H,1H TOCSY experiment (Table 1, XIV.) correlating pyrimidine H5–H6 proton chemical shifts via their 3J coupling. Linewidths are approximately inversely proportional to the base order parameter, resulting in sharp signals for flexible residues that exhibit a lower than the global τc. 1D traces for selected residues are shown in the 2D. The flexible loop residues U18, C19, and C20 and the non-native 3'-terminal c34 are highlighted in red; helical residues U9 and U11 are shown in black
See this image and copyright information in PMC

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