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Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy.
Wacker, Anna; Weigand, Julia E; Akabayov, Sabine R; Altincekic, Nadide; Bains, Jasleen Kaur; Banijamali, Elnaz; Binas, Oliver; Castillo-Martinez, Jesus; Cetiner, Erhan; Ceylan, Betül; Chiu, Liang-Yuan; Davila-Calderon, Jesse; Dhamotharan, Karthikeyan; Duchardt-Ferner, Elke; Ferner, Jan; Frydman, Lucio; Fürtig, Boris; Gallego, José; Grün, J Tassilo; Hacker, Carolin; Haddad, Christina; Hähnke, Martin; Hengesbach, Martin; Hiller, Fabian; Hohmann, Katharina F; Hymon, Daniel; de Jesus, Vanessa; Jonker, Henry; Keller, Heiko; Knezic, Bozana; Landgraf, Tom; Löhr, Frank; Luo, Le; Mertinkus, Klara R; Muhs, Christina; Novakovic, Mihajlo; Oxenfarth, Andreas; Palomino-Schätzlein, Martina; Petzold, Katja; Peter, Stephen A; Pyper, Dennis J; Qureshi, Nusrat S; Riad, Magdalena; Richter, Christian; Saxena, Krishna; Schamber, Tatjana; Scherf, Tali; Schlagnitweit, Judith; Schlundt, Andreas; Schnieders, Robbin.
  • Wacker A; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Weigand JE; Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
  • Akabayov SR; Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel.
  • Altincekic N; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Bains JK; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Banijamali E; Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden.
  • Binas O; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Castillo-Martinez J; School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain.
  • Cetiner E; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Ceylan B; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Chiu LY; Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
  • Davila-Calderon J; Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
  • Dhamotharan K; Institute for Molecular Biosciences.
  • Duchardt-Ferner E; Institute for Molecular Biosciences.
  • Ferner J; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Frydman L; Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel.
  • Fürtig B; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Gallego J; School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain.
  • Grün JT; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Hacker C; Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany.
  • Haddad C; Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
  • Hähnke M; Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany.
  • Hengesbach M; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Hiller F; Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany.
  • Hohmann KF; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Hymon D; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • de Jesus V; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Jonker H; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Keller H; Institute for Molecular Biosciences.
  • Knezic B; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Landgraf T; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Löhr F; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Luo L; Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden.
  • Mertinkus KR; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Muhs C; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Novakovic M; Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel.
  • Oxenfarth A; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Palomino-Schätzlein M; School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain.
  • Petzold K; Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden.
  • Peter SA; Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
  • Pyper DJ; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Qureshi NS; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Riad M; Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden.
  • Richter C; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Saxena K; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Schamber T; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
  • Scherf T; Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel.
  • Schlagnitweit J; Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden.
  • Schlundt A; Institute for Molecular Biosciences.
  • Schnieders R; Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.
Nucleic Acids Res ; 48(22): 12415-12435, 2020 12 16.
Article in English | MEDLINE | ID: covidwho-917705
Semantic information from SemMedBD (by NLM)
1. Pharmaceutical Preparations INTERACTS_WITH RNA
Subject
Pharmaceutical Preparations
Predicate
INTERACTS_WITH
Object
RNA
2. Pharmaceutical Preparations TREATS 2019 novel coronavirus
Subject
Pharmaceutical Preparations
Predicate
TREATS
Object
2019 novel coronavirus
3. Interventional procedure USES Binde
Subject
Interventional procedure
Predicate
USES
Object
Binde
4. Basis INTERACTS_WITH RNA
Subject
Basis
Predicate
INTERACTS_WITH
Object
RNA
5. Magnetic Resonance Imaging USES Basis
Subject
Magnetic Resonance Imaging
Predicate
USES
Object
Basis
6. Pharmaceutical Preparations INTERACTS_WITH RNA
Subject
Pharmaceutical Preparations
Predicate
INTERACTS_WITH
Object
RNA
7. Pharmaceutical Preparations TREATS 2019 novel coronavirus
Subject
Pharmaceutical Preparations
Predicate
TREATS
Object
2019 novel coronavirus
8. Interventional procedure USES Binder, device
Subject
Interventional procedure
Predicate
USES
Object
Binder, device
9. Basis INTERACTS_WITH RNA
Subject
Basis
Predicate
INTERACTS_WITH
Object
RNA
10. Magnetic Resonance Imaging USES Basis
Subject
Magnetic Resonance Imaging
Predicate
USES
Object
Basis
ABSTRACT
The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5' end, the ribosomal frameshift segment and the 3'-untranslated region (3'-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: RNA, Viral / Magnetic Resonance Spectroscopy / SARS-CoV-2 / COVID-19 / Nucleic Acid Conformation Limits: Humans Language: English Journal: Nucleic Acids Res Year: 2020 Document Type: Article Affiliation country: Nar

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Full text: Available Collection: International databases Database: MEDLINE Main subject: RNA, Viral / Magnetic Resonance Spectroscopy / SARS-CoV-2 / COVID-19 / Nucleic Acid Conformation Limits: Humans Language: English Journal: Nucleic Acids Res Year: 2020 Document Type: Article Affiliation country: Nar