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

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

doi:10.1007/s12104-021-10047-2

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

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

Authors

Christian Richter^#^{1

2}, Katharina F Hohmann^#^{1

2}, Sabrina Toews^{1

2}, Daniel Mathieu³, 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 Peter⁸, 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 Weigand⁸, Julia Wirmer-Bartoschek^{1

2}, Kerstin Witt^{1

2}, Jens Wöhnert^{2

5}, Harald Schwalbe^{11

12}, Anna Wacker^{13

14}

Affiliations

¹ Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany.
² Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany.
³ Bruker BioSpin, Silberstreifen 4, 76287, Rheinstetten, Germany.
⁴ BioNTech SE, An der Goldgrube 12, 55131, Mainz, Germany.
⁵ Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany.
⁶ Faculty of Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel.
⁷ Institute for Biophysical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany.
⁸ Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany.
⁹ EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany.
¹⁰ Deutero GmbH, Am Ring 29, 56288, Kastellaun, Germany.
¹¹ Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany. [email protected].
¹² Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany. [email protected].
¹³ Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany. [email protected].
¹⁴ Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany. [email protected].

^# Contributed equally.

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.

MeSH terms

5' Untranslated Regions*
Base Sequence
Carbon Isotopes
Nitrogen Isotopes*
Nuclear Magnetic Resonance, Biomolecular
Nucleic Acid Conformation
RNA, Viral* / chemistry
SARS-CoV-2*

Substances

5' Untranslated Regions
Nitrogen-15
Nitrogen Isotopes
RNA, Viral
Carbon-13
Carbon Isotopes

Abstract

MeSH terms

Substances

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