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

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.

Structure of the 5′ untranslated region in SARS-CoV-2 genome and its specific recognition by innate immune systemviathe human oligoadenylate synthase 1

“…2 The characterization of the secondary structure of this RNA region indicates that it is organized in two distinct stem loops, of whom the first one (SL1) exhibits a remarkably high affinity for OAS1. 7,8 Furthermore, the SL1 structure has a crucial role in regulating the genome replication, and particularly the action of the RNA dependent RNA polymerase. 9,10 Models of the SL1 structure have been reported, based on secondary structure predictions, 11,12 and more recently on experimental data.…”

Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures

“…7). The assignments of SL1 and SL5a have been previously reported (35,36). Each of these 5′ domains contains bulges and/or other internal loops.…”

The 5′-terminal stem–loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH

“…Furthermore, the U13–A26 base pair adjacent to the internal loop was also shown to be labile, but significantly populated. Both U–A base pairs exhibited 2 h J NN couplings >4 Hz indicative for partial hydrogen bond formation ( 15 , 27 ).…”

“…NMR experiments for the assignment of the SL1 protons were carried out as previously described ( 27 ). For structure calculations, additional nuclear Overhauser enhancement and exchange spectroscopy (NOESY) spectra with homogeneous excitation profiles for nuclear Overhauser effect (NOE)-derived distance restraints were measured each for the exchangeable protons (in 5% D 2 O; pH 6.2, 283 K; 80 ms NOESY mixing time) and for non-exchangeable protons (in 99.95% D 2 O; pH 6.2, 298 K; 150, 200 and 300 ms NOESY mixing times), respectively.…”