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Vögele J, Duchardt-Ferner E, Bains JK, Knezic B, Wacker A, Sich C, Weigand J, Šponer J, Schwalbe H, Krepl M, Wöhnert J. Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV-2 genomic RNA. Nucleic Acids Res 2024; 52:6687-6706. [PMID: 38783391 PMCID: PMC11194097 DOI: 10.1093/nar/gkae349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 03/27/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
The single-stranded RNA genome of SARS-CoV-2 is highly structured. Numerous helical stem-loop structures interrupted by mismatch motifs are present in the functionally important 5'- and 3'-UTRs. These mismatches modulate local helical geometries and feature unusual arrays of hydrogen bonding donor and acceptor groups. However, their conformational and dynamical properties cannot be directly inferred from chemical probing and are difficult to predict theoretically. A mismatch motif (SL1-motif) consisting of three consecutive U•U base pairs is located in stem-loop 1 of the 3'-UTR. We combined NMR-spectroscopy and MD-simulations to investigate its structure and dynamics. All three U•U base pairs feature two direct hydrogen bonds and are as stable as Watson-Crick A:U base pairs. Plasmodium falciparum 25S rRNA contains a triple U•U mismatch motif (Pf-motif) differing from SL1-motif only with respect to the orientation of the two closing base pairs. Interestingly, while the geometry of the outer two U•U mismatches was identical in both motifs the preferred orientation of the central U•U mismatch was different. MD simulations and potassium ion titrations revealed that the potassium ion-binding mode to the major groove is connected to the different preferred geometries of the central base pair in the two motifs.
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Affiliation(s)
- Jennifer Vögele
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jasleen Kaur Bains
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
- Institute of Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Bozana Knezic
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
- Institute of Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Anna Wacker
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
- Institute of Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Christian Sich
- Volkswagen AG, Brieffach 1617/0, 38436 Wolfsburg, Germany
| | - Julia E Weigand
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
- Institute of Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Jens Wöhnert
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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2
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Mertinkus KR, Grün JT, Altincekic N, Bains JK, Ceylan B, Ferner JP, Frydman L, Fürtig B, Hengesbach M, Hohmann KF, Hymon D, Kim J, Knezic B, Novakovic M, Oxenfarth A, Peter SA, Qureshi NS, Richter C, Scherf T, Schlundt A, Schnieders R, Schwalbe H, Stirnal E, Sudakov A, Vögele J, Wacker A, Weigand JE, Wirmer-Bartoschek J, Martin MAW, Wöhnert J. 1H, 13C and 15N chemical shift assignment of the stem-loops 5b + c from the 5'-UTR of SARS-CoV-2. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:17-25. [PMID: 35178672 PMCID: PMC8853908 DOI: 10.1007/s12104-021-10053-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/16/2021] [Indexed: 06/14/2023]
Abstract
The ongoing pandemic of the respiratory disease COVID-19 is caused by the SARS-CoV-2 (SCoV2) virus. SCoV2 is a member of the Betacoronavirus genus. The 30 kb positive sense, single stranded RNA genome of SCoV2 features 5'- and 3'-genomic ends that are highly conserved among Betacoronaviruses. These genomic ends contain structured cis-acting RNA elements, which are involved in the regulation of viral replication and translation. Structural information about these potential antiviral drug targets supports the development of novel classes of therapeutics against COVID-19. The highly conserved branched stem-loop 5 (SL5) found within the 5'-untranslated region (5'-UTR) consists of a basal stem and three stem-loops, namely SL5a, SL5b and SL5c. Both, SL5a and SL5b feature a 5'-UUUCGU-3' hexaloop that is also found among Alphacoronaviruses. Here, we report the extensive 1H, 13C and 15N resonance assignment of the 37 nucleotides (nts) long sequence spanning SL5b and SL5c (SL5b + c), as basis for further in-depth structural studies by solution NMR spectroscopy.
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Affiliation(s)
- Klara R Mertinkus
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jan-Peter Ferner
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jihyun Kim
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Božana Knezic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
- Institute for Biochemistry, ETH Zürich, Hönggerbergring 64, 8093, Zürich, Switzerland
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | | | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Tali Scherf
- Department of Chemical Research Support, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Deutero GmbH, Am Ring 29, 56288, Kastellaun, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
| | - Elke Stirnal
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jennifer Vögele
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Maria A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
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LeBlanc RM, Kasprzak WK, Longhini AP, Olenginski LT, Abulwerdi F, Ginocchio S, Shields B, Nyman J, Svirydava M, Del Vecchio C, Ivanic J, Schneekloth JS, Shapiro BA, Dayie TK, Le Grice SFJ. Structural insights of the conserved "priming loop" of hepatitis B virus pre-genomic RNA. J Biomol Struct Dyn 2021; 40:9761-9773. [PMID: 34155954 PMCID: PMC10167916 DOI: 10.1080/07391102.2021.1934544] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/20/2021] [Indexed: 12/16/2022]
Abstract
Initiation of protein-primed (-) strand DNA synthesis in hepatitis B virus (HBV) requires interaction of the viral polymerase with a cis-acting regulatory signal, designated epsilon (ε), located at the 5'-end of its pre-genomic RNA (pgRNA). Binding of polymerase to ε is also necessary for pgRNA encapsidation. While the mechanistic basis of this interaction remains elusive, mutagenesis studies suggest its internal 6-nt "priming loop" provides an important structural contribution. ε might therefore be considered a promising target for small molecule interventions to complement current nucleoside-analog based anti-HBV therapies. An ideal prerequisite to any RNA-directed small molecule strategy would be a detailed structural description of this important element. Herein, we present a solution NMR structure for HBV ε which, in combination with molecular dynamics and docking simulations, reports on a flexible ligand "pocket", reminiscent of those observed in proteins. We also demonstrate the binding of the selective estrogen receptor modulators (SERMs) Raloxifene, Bazedoxifene, and a de novo derivative to the priming loop.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Regan M. LeBlanc
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Wojciech K. Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Andrew P. Longhini
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Lukasz T. Olenginski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Fardokht Abulwerdi
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Stefano Ginocchio
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Brigit Shields
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Julie Nyman
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Maryia Svirydava
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | | | - Joseph Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Bruce A. Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Theodore Kwaku Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
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Brillet K, Martinez-Zapien D, Bec G, Ennifar E, Dock-Bregeon AC, Lebars I. Different views of the dynamic landscape covered by the 5'-hairpin of the 7SK small nuclear RNA. RNA (NEW YORK, N.Y.) 2020; 26:1184-1197. [PMID: 32430362 PMCID: PMC7430674 DOI: 10.1261/rna.074955.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
The 7SK small nuclear RNA (7SKsnRNA) plays a key role in the regulation of RNA polymerase II by sequestrating and inhibiting the positive transcription elongation factor b (P-TEFb) in the 7SK ribonucleoprotein complex (7SKsnRNP), a process mediated by interaction with the protein HEXIM. P-TEFb is also an essential cellular factor recruited by the viral protein Tat to ensure the replication of the viral RNA in the infection cycle of the human immunodeficiency virus (HIV-1). Tat promotes the release of P-TEFb from the 7SKsnRNP and subsequent activation of transcription, by displacing HEXIM from the 5'-hairpin of the 7SKsnRNA. This hairpin (HP1), comprising the signature sequence of the 7SKsnRNA, has been the subject of three independent structural studies aimed at identifying the structural features that could drive the recognition by the two proteins, both depending on arginine-rich motifs (ARM). Interestingly, four distinct structures were determined. In an attempt to provide a comprehensive view of the structure-function relationship of this versatile RNA, we present here a structural analysis of the models, highlighting how HP1 is able to adopt distinct conformations with significant impact on the compactness of the molecule. Since these models are solved under different conditions by nuclear magnetic resonance (NMR) and crystallography, the impact of the buffer composition on the conformational variation was investigated by complementary biophysical approaches. Finally, using isothermal titration calorimetry, we determined the thermodynamic signatures of the Tat-ARM and HEXIM-ARM peptide interactions with the RNA, showing that they are associated with distinct binding mechanisms.
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Affiliation(s)
- Karl Brillet
- Université de Strasbourg, Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, F-67084 Strasbourg, France
| | - Denise Martinez-Zapien
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Guillaume Bec
- Université de Strasbourg, Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, F-67084 Strasbourg, France
| | - Eric Ennifar
- Université de Strasbourg, Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, F-67084 Strasbourg, France
| | - Anne-Catherine Dock-Bregeon
- Laboratory of Integrative Biology of Marine Models (LBI2M), Sorbonne University-CNRS UMR 8227, Station Biologique de Roscoff, 29680 Roscoff Cedex, France
| | - Isabelle Lebars
- Université de Strasbourg, Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, F-67084 Strasbourg, France
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5
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Schnieders R, Keyhani S, Schwalbe H, Fürtig B. More than Proton Detection-New Avenues for NMR Spectroscopy of RNA. Chemistry 2020; 26:102-113. [PMID: 31454110 PMCID: PMC6973061 DOI: 10.1002/chem.201903355] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleic acid oligonucleotides (RNAs) play pivotal roles in cellular function (riboswitches), chemical biology applications (SELEX-derived aptamers), cell biology and biomedical applications (transcriptomics). Furthermore, a growing number of RNA forms (long non-coding RNAs, circular RNAs) but also RNA modifications are identified, showing the ever increasing functional diversity of RNAs. To describe and understand this functional diversity, structural studies of RNA are increasingly important. However, they are often more challenging than protein structural studies as RNAs are substantially more dynamic and their function is often linked to their structural transitions between alternative conformations. NMR is a prime technique to characterize these structural dynamics with atomic resolution. To extend the NMR size limitation and to characterize large RNAs and their complexes above 200 nucleotides, new NMR techniques have been developed. This Minireview reports on the development of NMR methods that utilize detection on low-γ nuclei (heteronuclei like 13 C or 15 N with lower gyromagnetic ratio than 1 H) to obtain unique structural and dynamic information for large RNA molecules in solution. Experiments involve through-bond correlations of nucleobases and the phosphodiester backbone of RNA for chemical shift assignment and make information on hydrogen bonding uniquely accessible. Previously unobservable NMR resonances of amino groups in RNA nucleobases are now detected in experiments involving conformational exchange-resistant double-quantum 1 H coherences, detected by 13 C NMR spectroscopy. Furthermore, 13 C and 15 N chemical shifts provide valuable information on conformations. All the covered aspects point to the advantages of low-γ nuclei detection experiments in RNA.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Sara Keyhani
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
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The yeast C/D box snoRNA U14 adopts a "weak" K-turn like conformation recognized by the Snu13 core protein in solution. Biochimie 2019; 164:70-82. [PMID: 30914254 DOI: 10.1016/j.biochi.2019.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/20/2019] [Indexed: 01/09/2023]
Abstract
Non-coding RNAs associate with proteins to form ribonucleoproteins (RNPs), such as ribosome, box C/D snoRNPs, H/ACA snoRNPs, ribonuclease P, telomerase and spliceosome to ensure cell viability. The assembly of these RNA-protein complexes relies on the ability of the RNA to adopt the correct bound conformation. K-turn motifs represent ubiquitous binding platform for proteins found in several cellular environment. This structural motif has an internal three-nucleotide bulge flanked on its 3' side by a G•A/A•G tandem pairs followed by one or two non-Watson-Crick pairs, and on its 5' side by a classical RNA helix. This peculiar arrangement induces a strong curvature of the phosphodiester backbone, which makes it conducive to multiple tertiary interactions. SNU13/Snu13p (Human/Yeast) binds specifically the U14 C/D box snoRNA K-turn sequence motif. This event is the prerequisite to promote the assembly of the RNP, which contains NOP58/Nop58 and NOP56/Nop56 core proteins and the 2'-O-methyl-transferase, Fibrillarin/Nop1p. The U14 small nucleolar RNA is a conserved non-coding RNA found in yeast and vertebrates required for the pre-rRNA maturation and ribose methylation. Here, we report the solution structure of the free U14 snoRNA K-turn motif (kt-U14) as determined by Nuclear Magnetic Resonance. We demonstrate that a major fraction of free kt-U14 adopts a pre-folded conformation similar to protein bound K-turn, even in the absence of divalent ions. In contrast to the kt-U4 or tyrS RNA, kt-U14 displays a sharp bent in the phosphodiester backbone. The U•U and G•A tandem base pairs are formed through weak hydrogen bonds. Finally, we show that the structure of kt-U14 is stabilized upon Snu13p binding. The structure of the free U14 RNA is the first reference example for the canonical motifs of the C/D box snoRNA family.
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7
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Applications of NMR to structure determination of RNAs large and small. Arch Biochem Biophys 2017; 628:42-56. [PMID: 28600200 DOI: 10.1016/j.abb.2017.06.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 05/31/2017] [Accepted: 06/04/2017] [Indexed: 02/07/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to investigate the structure and dynamics of RNA, because many biologically important RNAs have conformationally flexible structures, which makes them difficult to crystallize. Functional, independently folded RNA domains, range in size between simple stem-loops of as few as 10-20 nucleotides, to 50-70 nucleotides, the size of tRNA and many small ribozymes, to a few hundred nucleotides, the size of more complex RNA enzymes and of the functional domains of non-coding transcripts. In this review, we discuss new methods for sample preparation, assignment strategies and structure determination for independently folded RNA domains of up to 100 kDa in molecular weight.
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Bourbigot S, Dock-Bregeon AC, Eberling P, Coutant J, Kieffer B, Lebars I. Solution structure of the 5'-terminal hairpin of the 7SK small nuclear RNA. RNA (NEW YORK, N.Y.) 2016; 22:1844-1858. [PMID: 27852926 PMCID: PMC5113205 DOI: 10.1261/rna.056523.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/10/2016] [Indexed: 05/10/2023]
Abstract
The small nuclear 7SK RNA regulates RNA polymerase II (RNA Pol II) transcription, by sequestering and inhibiting the positive transcription elongation factor b (P-TEFb). P-TEFb is stored in the 7SK ribonucleoprotein (RNP) that contains the three nuclear proteins Hexim1, LaRP7, and MePCE. P-TEFb interacts with the protein Hexim1 and the 7SK RNA. Once P-TEFb is released from the 7SK RNP, it activates transcription by phosphorylating the C-terminal domain of RNA Pol II. P-TEFb also plays a crucial role in the replication of the human immunodeficiency virus HIV-1, through its recruitment by the viral transactivator Tat. Previous work demonstrated that the protein Tat promotes the release of P-TEFb from the 7SK RNP through direct binding to the 7SK RNA. Hexim1 and Tat proteins both comprise conserved and similar arginine-rich motifs that were identified to bind the 7SK RNA at a repeated GAUC site located at the top of the 5'-terminal hairpin (HPI). Here, we report the solution structure of this region as determined by nuclear magnetic resonance, to identify HPI structural features recognized by Hexim1 and Tat. The HPI solution structure displays an elongated shape featuring four helical segments interrupted by one internal loop and three bulges with distinct folds. In particular, the repeated GAUC motif adopts a pre-organized geometry. Our results suggest that the binding of Hexim1 and Tat to the 7SK RNA could originate from a conformational selection of this motif, highlighting how RNA local structure could lead to an adaptive recognition of their partners.
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Affiliation(s)
- Sarah Bourbigot
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Anne-Catherine Dock-Bregeon
- Department of Functional Genomics, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 75005 Paris, France
| | - Pascal Eberling
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Jérôme Coutant
- Bruker BioSpin SAS, BP 10002, 67166 Wissembourg Cedex, France
| | - Bruno Kieffer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Isabelle Lebars
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
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9
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Chemo-enzymatic labeling for rapid assignment of RNA molecules. Methods 2016; 103:11-7. [PMID: 27090003 DOI: 10.1016/j.ymeth.2016.03.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 03/17/2016] [Accepted: 03/22/2016] [Indexed: 11/22/2022] Open
Abstract
Even though Nuclear Magnetic Resonance (NMR) spectroscopy is one of the few techniques capable of determining atomic resolution structures of RNA, it is constrained by two major problems of chemical shift overlap of resonances and rapid signal loss due to line broadening. Emerging tools to tackle these problems include synthesis of atom specifically labeled or chemically modified nucleotides. Herein we review the synthesis of these nucleotides, the design and production of appropriate RNA samples, and the application and analysis of the NMR experiments that take advantage of these labels.
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10
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Nowakowski M, Saxena S, Stanek J, Żerko S, Koźmiński W. Applications of high dimensionality experiments to biomolecular NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 90-91:49-73. [PMID: 26592945 DOI: 10.1016/j.pnmrs.2015.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 07/03/2015] [Accepted: 07/03/2015] [Indexed: 05/23/2023]
Abstract
High dimensionality NMR experiments facilitate resonance assignment and precise determination of spectral parameters such as coupling constants. Sparse non-uniform sampling enables acquisition of experiments of high dimensionality with high resolution in acceptable time. In this review we present and compare some significant applications of NMR experiments of dimensionality higher than three in the field of biomolecular studies in solution.
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Affiliation(s)
- Michał Nowakowski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Saurabh Saxena
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Jan Stanek
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Szymon Żerko
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland.
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11
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Saxena S, Stanek J, Cevec M, Plavec J, Koźmiński W. C4'/H4' selective, non-uniformly sampled 4D HC(P)CH experiment for sequential assignments of (13)C-labeled RNAs. JOURNAL OF BIOMOLECULAR NMR 2014; 60:91-98. [PMID: 25205465 PMCID: PMC4207962 DOI: 10.1007/s10858-014-9861-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/01/2014] [Indexed: 05/30/2023]
Abstract
A through bond, C4'/H4' selective, "out and stay" type 4D HC(P)CH experiment is introduced which provides sequential connectivity via H4'(i)-C4'(i)-C4'(i-1)-H4'(i-1) correlations. The (31)P dimension (used in the conventional 3D HCP experiment) is replaced with evolution of better dispersed C4' dimension. The experiment fully utilizes (13)C-labeling of RNA by inclusion of two C4' evolution periods. An additional evolution of H4' is included to further enhance peak resolution. Band selective (13)C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the of C4'-C3' and C4'-C5' homonuclear couplings. For reasonable resolution, non-uniform sampling is employed in all indirect dimensions. To reduce sensitivity losses, multiple quantum coherences are preserved during shared-time evolution and coherence transfer delays. In the experiment the intra-nucleotide peaks are suppressed whereas inter-nucleotide peaks are enhanced to reduce the ambiguities. The performance of the experiment is verified on a fully (13)C, (15)N-labeled 34-nt hairpin RNA comprising typical structure elements.
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Affiliation(s)
- Saurabh Saxena
- Biological and Chemical Research Centre (CENT III), Faculty of Chemistry, University of Warsaw, Pasteura1, 02093 Warsaw, Poland
| | - Jan Stanek
- Biological and Chemical Research Centre (CENT III), Faculty of Chemistry, University of Warsaw, Pasteura1, 02093 Warsaw, Poland
| | - Mirko Cevec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova ulica 19, 1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova ulica 19, 1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Dunajska cesta 156, 1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva cesta 5, 1000 Ljubljana, Slovenia
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre (CENT III), Faculty of Chemistry, University of Warsaw, Pasteura1, 02093 Warsaw, Poland
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12
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Krähenbühl B, El Bakkali I, Schmidt E, Güntert P, Wider G. Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments. JOURNAL OF BIOMOLECULAR NMR 2014; 59:87-93. [PMID: 24771326 DOI: 10.1007/s10858-014-9829-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 04/16/2014] [Indexed: 06/03/2023]
Abstract
A fast, robust and reliable strategy for automated sequential resonance assignment for uniformly [(13)C, (15)N]-labeled RNA via its phosphodiester backbone is presented. It is based on a series of high-dimensional through-bond APSY experiments: a 5D HCP-CCH COSY, a 4D H1'C1'CH TOCSY for ribose resonances, a 5D HCNCH for ribose-to-base connection, a 4D H6C6C5H5 TOCSY for pyrimidine resonances, and a 4D H8C8(C)C2H2 TOCSY for adenine resonances. The utilized pulse sequences are partially novel, and optimized to enable long evolution times in all dimensions. The highly precise APSY peak lists derived with these experiments could be used directly for reliable automated resonance assignment with the FLYA algorithm. This approach resulted in 98 % assignment completeness for all (13)C-(1)H, (15)N1/9 and (31)P resonances of a stem-loop with 14 nucleotides.
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Affiliation(s)
- Barbara Krähenbühl
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
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13
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Richter T, Berger S. A NMR method to determine the anomeric specificity of glucose phosphorylation. Bioorg Med Chem 2013; 21:2710-4. [DOI: 10.1016/j.bmc.2013.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 03/08/2013] [Accepted: 03/12/2013] [Indexed: 11/17/2022]
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14
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Richter C, Kovacs H, Buck J, Wacker A, Fürtig B, Bermel W, Schwalbe H. 13C-direct detected NMR experiments for the sequential J-based resonance assignment of RNA oligonucleotides. JOURNAL OF BIOMOLECULAR NMR 2010; 47:259-69. [PMID: 20544375 PMCID: PMC2900595 DOI: 10.1007/s10858-010-9429-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Accepted: 05/24/2010] [Indexed: 05/08/2023]
Abstract
We present here a set of (13)C-direct detected NMR experiments to facilitate the resonance assignment of RNA oligonucleotides. Three experiments have been developed: (1) the (H)CC-TOCSY-experiment utilizing a virtual decoupling scheme to assign the intraresidual ribose (13)C-spins, (2) the (H)CPC-experiment that correlates each phosphorus with the C4' nuclei of adjacent nucleotides via J(C,P) couplings and (3) the (H)CPC-CCH-TOCSY-experiment that correlates the phosphorus nuclei with the respective C1',H1' ribose signals. The experiments were applied to two RNA hairpin structures. The current set of (13)C-direct detected experiments allows direct and unambiguous assignment of the majority of the hetero nuclei and the identification of the individual ribose moieties following their sequential assignment. Thus, (13)C-direct detected NMR methods constitute useful complements to the conventional (1)H-detected approach for the resonance assignment of oligonucleotides that is often hindered by the limited chemical shift dispersion. The developed methods can also be applied to large deuterated RNAs.
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Affiliation(s)
- Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/M, Germany
| | - Helena Kovacs
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Janina Buck
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/M, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/M, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/M, Germany
- Present Address: Max F. Perutz Laboratories, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen, 76287 Rheinstetten, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/M, Germany
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15
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Schmidtke SR, Duchardt-Ferner E, Weigand JE, Suess B, Wöhnert J. NMR resonance assignments of an engineered neomycin-sensing riboswitch RNA bound to ribostamycin and tobramycin. BIOMOLECULAR NMR ASSIGNMENTS 2010; 4:115-118. [PMID: 20306311 DOI: 10.1007/s12104-010-9223-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 01/25/2010] [Indexed: 05/29/2023]
Abstract
The neomycin-sensing riboswitch is an engineered riboswitch developed to regulate gene expression in vivo in the lower eukaryote Saccharomyces cerevisiae upon binding to neomycin B. With a size of only 27nt it is the smallest functional riboswitch element identified so far. It binds not only neomycin B but also related aminoglycosides of the 2'-deoxystreptamine class with high affinity. The regulatory activity, however, strongly depends on the identity of the aminoglycoside. As a prerequisite for the structure determination of riboswitch-ligand complexes we report here the (1)H, (15)N, (13)C and partial (31)P chemical shift assignments for the minimal functional 27nt neomycin sensing riboswitch RNA in complex with the 4,5-linked neomycin analog ribostamycin and the 4,6-linked aminoglycoside tobramycin.
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Affiliation(s)
- Sina R Schmidtke
- Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität Frankfurt/M, Max-von-Laue-Str 9, 60438 Frankfurt, Germany
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16
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Rinnenthal J, Richter C, Nozinovic S, Fürtig B, Lopez JJ, Glaubitz C, Schwalbe H. RNA phosphodiester backbone dynamics of a perdeuterated cUUCGg tetraloop RNA from phosphorus-31 NMR relaxation analysis. JOURNAL OF BIOMOLECULAR NMR 2009; 45:143-55. [PMID: 19636800 DOI: 10.1007/s10858-009-9343-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 06/19/2009] [Indexed: 05/13/2023]
Abstract
We have analyzed the relaxation properties of all (31)P nuclei in an RNA cUUCGg tetraloop model hairpin at proton magnetic field strengths of 300, 600 and 900 MHz in solution. Significant H, P dipolar contributions to R (1) and R (2) relaxation are observed in a protonated RNA sample at 600 MHz. These contributions can be suppressed using a perdeuterated RNA sample. In order to interpret the (31)P relaxation data (R (1), R (2)), we measured the (31)P chemical shift anisotropy (CSA) by solid-state NMR spectroscopy under various salt and hydration conditions. A value of 178.5 ppm for the (31)P CSA in the static state (S (2) = 1) could be determined. In order to obtain information about fast time scale dynamics we performed a modelfree analysis on the basis of our relaxation data. The results show that subnanosecond dynamics detected around the phosphodiester backbone are more pronounced than the dynamics detected for the ribofuranosyl and nucleobase moieties of the individual nucleotides (Duchardt and Schwalbe, J Biomol NMR 32:295-308, 2005; Ferner et al., Nucleic Acids Res 36:1928-1940, 2008). Furthermore, the dynamics of the individual phosphate groups seem to be correlated to the 5' neighbouring nucleobases.
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Affiliation(s)
- Jörg Rinnenthal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, Frankfurt/Main, Germany
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17
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Watrin M, Dausse E, Lebars I, Rayner B, Bugaut A, Toulmé JJ. Aptamers targeting RNA molecules. Methods Mol Biol 2009; 535:79-105. [PMID: 19377979 DOI: 10.1007/978-1-59745-557-2_6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Oligonucleotides complementary to RNA sequences interact poorly with folded target regions. In vitro selection of oligonucleotides carried out against RNA structures have led to aptamers that frequently differ from antisense sequences, but rather take advantage of non-double-stranded peculiarities of the target. Studies along this line provide information about tertiary RNA architectures as well as their interaction with ligand of interest. We describe here a genomic SELEX approach and its application to the recognition of stem-loop structures prone to the formation of kissing complexes. We also provide technical details for running a procedure termed 2D-SELEX that takes advantage of both in vitro selection and dynamic combinatorial chemistry. This allows selecting aptamer derivatives containing modified nucleotides that cannot be incorporated by polymerases. Last we present in vitro transcription conditions under which large amounts of RNA, suitable for NMR structural studies, can be obtained. These different aspects of the SELEX technology have been applied to the trans-activating responsive element of the human immunodeficiency virus type 1, which is crucial for the transcription of the retroviral genome.
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Affiliation(s)
- Marguerite Watrin
- Institut Européen de Chimie et Biologie, Pessac, France, Université Victor Segalen, Bordeaux, France
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18
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Hennig M, Williamson JR, Brodsky AS, Battiste JL. Recent advances in RNA structure determination by NMR. ACTA ACUST UNITED AC 2008; Chapter 7:Unit 7.7. [PMID: 18428875 DOI: 10.1002/0471142700.nc0707s02] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Despite recent advances in the solution of NMR structures of RNA and RNA-ligand complexes, the rate limiting step remains the gathering of a large number of NOE and torsion restraints. Additional sources of information for structure determination of larger RNA molecules have recently become available, and it is possible to supplement NOE and J-coupling data with the measurement of dipolar couplings and cross-correlated relaxation rates in high-resolution NMR spectroscopy.
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Affiliation(s)
- M Hennig
- The Scripps Research Institute, La Jolla, California, USA
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19
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Abstract
This chapter reviews the methodologies for RNA structure determination by liquid-state nuclear magnetic resonance (NMR). The routine production of milligram quantities of isotopically labeled RNA remains critical to the success of NMR-based structure studies. The standard method for the preparation of isotopically labeled RNA for structural studies in solution is in vitro transcription from DNA oligonucleotide templates using T7 RNA polymerase and unlabeled or isotopically labeled nucleotide triphosphates (NTPs). The purification of the desired RNA can be performed by either denaturing polyacrylamide gel electrophoresis (PAGE) or anion-exchange chromatography. Our basic strategy for studying RNA in solution by NMR is outlined. The topics covered include RNA resonance assignment, restraint collection, and the structure calculation process. Selected examples of NMR spectra are given for a correctly folded 30 nucleotide-containing RNA.
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20
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Fürtig B, Wenter P, Reymond L, Richter C, Pitsch S, Schwalbe H. Conformational Dynamics of Bistable RNAs Studied by Time-Resolved NMR Spectroscopy. J Am Chem Soc 2007; 129:16222-9. [DOI: 10.1021/ja076739r] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Boris Fürtig
- Contribution from the Johann Wolfgang Goethe University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max von Laue-Str. 7, 60438 Frankfurt, Germany, and École Polytechnique Fédérale de Lausanne Laboratory of Nucleic Acid Chemistry, EPFL-BCH 1015 Lausanne, Switzerland
| | - Philipp Wenter
- Contribution from the Johann Wolfgang Goethe University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max von Laue-Str. 7, 60438 Frankfurt, Germany, and École Polytechnique Fédérale de Lausanne Laboratory of Nucleic Acid Chemistry, EPFL-BCH 1015 Lausanne, Switzerland
| | - Luc Reymond
- Contribution from the Johann Wolfgang Goethe University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max von Laue-Str. 7, 60438 Frankfurt, Germany, and École Polytechnique Fédérale de Lausanne Laboratory of Nucleic Acid Chemistry, EPFL-BCH 1015 Lausanne, Switzerland
| | - Christian Richter
- Contribution from the Johann Wolfgang Goethe University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max von Laue-Str. 7, 60438 Frankfurt, Germany, and École Polytechnique Fédérale de Lausanne Laboratory of Nucleic Acid Chemistry, EPFL-BCH 1015 Lausanne, Switzerland
| | - Stefan Pitsch
- Contribution from the Johann Wolfgang Goethe University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max von Laue-Str. 7, 60438 Frankfurt, Germany, and École Polytechnique Fédérale de Lausanne Laboratory of Nucleic Acid Chemistry, EPFL-BCH 1015 Lausanne, Switzerland
| | - Harald Schwalbe
- Contribution from the Johann Wolfgang Goethe University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max von Laue-Str. 7, 60438 Frankfurt, Germany, and École Polytechnique Fédérale de Lausanne Laboratory of Nucleic Acid Chemistry, EPFL-BCH 1015 Lausanne, Switzerland
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21
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Gaudin C, Ghazal G, Yoshizawa S, Elela SA, Fourmy D. Structure of an AAGU tetraloop and its contribution to substrate selection by yeast RNase III. J Mol Biol 2006; 363:322-31. [PMID: 16979185 DOI: 10.1016/j.jmb.2006.08.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 08/04/2006] [Accepted: 08/07/2006] [Indexed: 10/24/2022]
Abstract
RNase III enzymes are a highly conserved family of proteins that specifically cleave double-stranded RNA (dsRNA). These proteins are involved in a variety of cellular functions, including the processing of many non-coding RNAs, mRNA decay, and RNA interference. In yeast Rnt1p, a dsRNA-binding domain (dsRBD) recognizes its substrate by interacting with stems capped with conserved AGNN tetraloops. The enzyme uses the tetraloop to cut 14nt to 16nt away into the stem in a ruler-like mechanism. The solution structure of Rnt1p dsRBD complexed to one of its small nucleolar (sno) RNA substrate revealed non-sequence-specific contacts with the sugar-phosphate backbone in the minor groove of the AGNN fold and the two non-conserved tetraloop nucleotides. Recently, a new form of Rnt1p substrates lacking the conserved AGNN sequence but instead harboring an AAGU tetraloop was found at the 5' end of snoRNA 48 precursor. Here, we report the solution structure of this hairpin capped with an AAGU tetraloop. Some of the stacking interactions and the position of the turn in the sugar-phosphate backbone are similar to the one observed in the AGNN loop structure; however, the AAGU sequence adopts a different conformation. The most striking difference was found at the 3' end of the loop where Rnt1p interacts with AGNN substrates. The last nucleotide is extruded from the AAGU tetraloop structure in contrast to the compact AGNN fold. The AAGU hairpin structure suggests that Rnt1p recognizes substrates with different tetraloop structures, indicating that the structural repertoire specifically recognized by Rnt1p is larger than previously anticipated.
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Affiliation(s)
- Cyril Gaudin
- Laboratoire de RMN, ICSN-CNRS 1 ave de la terrasse, 91190 Gif-sur-Yvette France
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22
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Phelps SS, Gaudin C, Yoshizawa S, Benitez C, Fourmy D, Joseph S. Translocation of a tRNA with an extended anticodon through the ribosome. J Mol Biol 2006; 360:610-22. [PMID: 16787653 DOI: 10.1016/j.jmb.2006.05.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 05/04/2006] [Accepted: 05/04/2006] [Indexed: 11/18/2022]
Abstract
Coordinated translocation of the tRNA-mRNA complex by the ribosome occurs in a precise, stepwise movement corresponding to a distance of three nucleotides along the mRNA. Frameshift suppressor tRNAs generally contain an extra nucleotide in the anticodon loop and they subvert the normal mechanisms used by the ribosome for frame maintenance. The mechanism by which suppressor tRNAs traverse the ribosome during translocation is poorly understood. Here, we demonstrate translocation of a tRNA by four nucleotides from the A site to the P site, and from the P site to the E site. We show that translocation of a punctuated mRNA is possible with an extra, unpaired nucleotide between codons. Interestingly, the NMR structure of the four nucleotide anticodon stem-loop reveals a conformation different from the canonical tRNA structure. Flexibility within the loop may allow conformational adjustment upon A site binding and for interacting with the four nucleotide codon in order to shift the mRNA reading frame.
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MESH Headings
- Anticodon/genetics
- Anticodon/metabolism
- Base Sequence
- Escherichia coli
- Hydrogen-Ion Concentration
- Molecular Sequence Data
- Nuclear Magnetic Resonance, Biomolecular
- Nucleic Acid Conformation/drug effects
- Pliability/drug effects
- Protein Biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/genetics
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/genetics
- RNA, Transfer, Val/metabolism
- Reading Frames/genetics
- Ribosomes/genetics
- Ribosomes/metabolism
- Salts/pharmacology
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Affiliation(s)
- Steven S Phelps
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0314, USA
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23
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Gaudin C, Mazauric MH, Traïkia M, Guittet E, Yoshizawa S, Fourmy D. Structure of the RNA signal essential for translational frameshifting in HIV-1. J Mol Biol 2005; 349:1024-35. [PMID: 15907937 DOI: 10.1016/j.jmb.2005.04.045] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Revised: 04/15/2005] [Accepted: 04/20/2005] [Indexed: 11/18/2022]
Abstract
Many pathogenic viruses use a programmed -1 translational frameshifting mechanism to regulate synthesis of their structural and enzymatic proteins. Frameshifting is vital for viral replication. A slippery sequence bound at the ribosomal A and P sites as well as a downstream stimulatory RNA structure are essential for frameshifting. Conflicting data have been reported concerning the structure of the downstream RNA signal in human immunodeficiency virus type 1 (HIV-1). Here, the solution structure of the HIV-1 frameshifting RNA signal was solved by heteronuclear NMR spectroscopy. This structure reveals a long hairpin fold with an internal three-nucleotide bulge. The internal loop introduces a bend between the lower and upper helical regions, a structural feature often seen in frameshifting pseudoknots. The NMR structure correlates with chemical probing data. The upper stem rich in conserved G-C Watson-Crick base-pairs is highly stable, whereas the bulge region and the lower stem are more flexible.
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Affiliation(s)
- Cyril Gaudin
- Laboratoire de RMN, ICSN-CNRS 1 ave de la terrasse, 91190 Gif-sur-Yvette, France
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24
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Ihle Y, Ohlenschläger O, Häfner S, Duchardt E, Zacharias M, Seitz S, Zell R, Ramachandran R, Görlach M. A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA. Nucleic Acids Res 2005; 33:2003-11. [PMID: 15814817 PMCID: PMC1074726 DOI: 10.1093/nar/gki501] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 03/07/2005] [Accepted: 03/21/2005] [Indexed: 11/24/2022] Open
Abstract
The 5'-terminal cloverleaf (CL)-like RNA structures are essential for the initiation of positive- and negative-strand RNA synthesis of entero- and rhinoviruses. SLD is the cognate RNA ligand of the viral proteinase 3C (3C(pro)), which is an indispensable component of the viral replication initiation complex. The structure of an 18mer RNA representing the apical stem and the cGUUAg D-loop of SLD from the first 5'-CL of BEV1 was determined in solution to a root-mean-square deviation (r.m.s.d.) (all heavy atoms) of 0.59 A (PDB 1Z30). The first (antiG) and last (synA) nucleotide of the D-loop forms a novel 'pseudo base pair' without direct hydrogen bonds. The backbone conformation and the base-stacking pattern of the cGUUAg-loop, however, are highly similar to that of the coxsackieviral uCACGg D-loop (PDB 1RFR) and of the stable cUUCGg tetraloop (PDB 1F7Y) but surprisingly dissimilar to the structure of a cGUAAg stable tetraloop (PDB 1MSY), even though the cGUUAg BEV D-loop and the cGUAAg tetraloop differ by 1 nt only. Together with the presented binding data, these findings provide independent experimental evidence for our model [O. Ohlenschlager, J. Wohnert, E. Bucci, S. Seitz, S. Hafner, R. Ramachandran, R. Zell and M. Gorlach (2004) Structure, 12, 237-248] that the proteinase 3C(pro) recognizes structure rather than sequence.
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Affiliation(s)
- Yvonne Ihle
- Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V.Beutenbergstraße 11, D-07745 Jena, Germany
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Oliver Ohlenschläger
- Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V.Beutenbergstraße 11, D-07745 Jena, Germany
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Sabine Häfner
- Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V.Beutenbergstraße 11, D-07745 Jena, Germany
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Elke Duchardt
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
| | - Martin Zacharias
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
| | - Simone Seitz
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Roland Zell
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Ramadurai Ramachandran
- Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V.Beutenbergstraße 11, D-07745 Jena, Germany
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Matthias Görlach
- To whom correspondence should be addressed. Tel: +49 3641 656220; Fax: +49 3641 656225;
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Abstract
NMR spectroscopy is a powerful tool for studying proteins and nucleic acids in solution. This is illustrated by the fact that nearly half of all current RNA structures were determined by using NMR techniques. Information about the structure, dynamics, and interactions with other RNA molecules, proteins, ions, and small ligands can be obtained for RNA molecules up to 100 nucleotides. This review provides insight into the resonance assignment methods that are the first and crucial step of all NMR studies, into the determination of base-pair geometry, into the examination of local and global RNA conformation, and into the detection of interaction sites of RNA. Examples of NMR investigations of RNA are given by using several different RNA molecules to illustrate the information content obtainable by NMR spectroscopy and the applicability of NMR techniques to a wide range of biologically interesting RNA molecules.
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Affiliation(s)
- Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany
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Cabello-Villegas J, Giles KE, Soto AM, Yu P, Mougin A, Beemon KL, Wang YX. Solution structure of the pseudo-5' splice site of a retroviral splicing suppressor. RNA (NEW YORK, N.Y.) 2004; 10:1388-1398. [PMID: 15317975 PMCID: PMC1370626 DOI: 10.1261/rna.7020804] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2004] [Accepted: 06/09/2004] [Indexed: 05/24/2023]
Abstract
Control of Rous sarcoma virus RNA splicing depends in part on the interaction of U1 and U11 snRNPs with an intronic RNA element called the negative regulator of splicing (NRS). A 23mer RNA hairpin (NRS23) of the NRS directly binds U1 and U11 snRNPs. Mutations that disrupt base-pairing between the loop of NRS23 and U1 snRNA abolish its negative control of splicing. We have determined the solution structure of NRS23 using NOEs, torsion angles, and residual dipolar couplings that were extracted from multidimensional heteronuclear NMR spectra. Our structure showed that the 6-bp stem of NRS23 adopts a nearly A-form duplex conformation. The loop, which consists of 11 residues according to secondary structure probing, was in a closed conformation. U913, the first residue in the loop, was bulged out or dynamic, and loop residues G914-C923, G915-U922, and U916-A921 were base-paired. The remaining UUGU tetraloop sequence did not adopt a stable structure and appears flexible in solution. This tetraloop differs from the well-known classes of tetraloops (GNRA, CUYG, UNCG) in terms of its stability, structure, and function. Deletion of the bulged U913, which is not complementary to U1 snRNA, increased the melting temperature of the RNA hairpin. This hyperstable hairpin exhibited a significant decrease in binding to U1 snRNP. Thus, the structure of the NRS RNA, as well as its sequence, is important for interaction with U1 snRNP and for splicing suppression.
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Affiliation(s)
- Javier Cabello-Villegas
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, CCR, National Cancer Institute-Frederick, National Institutes of Health, MD 21702, USA
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27
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Lebars I, Yoshizawa S, Stenholm AR, Guittet E, Douthwaite S, Fourmy D. Structure of 23S rRNA hairpin 35 and its interaction with the tylosin-resistance methyltransferase RlmAII. EMBO J 2003; 22:183-92. [PMID: 12514124 PMCID: PMC140097 DOI: 10.1093/emboj/cdg022] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The bacterial rRNA methyltransferase RlmAII (formerly TlrB) contributes to resistance against tylosin-like 16-membered ring macrolide antibiotics. RlmAII was originally discovered in the tylosin-producer Streptomyces fradiae, and members of this subclass of methyltransferases have subsequently been found in other Gram-positive bacteria, including Streptococcus pneumoniae. In all cases, RlmAII methylates 23S rRNA at nucleotide G748, which is situated in a stem-loop (hairpin 35) at the macrolide binding site of the ribosome. The conformation of hairpin 35 recognized by RlmAII is shown here by NMR spectroscopy to resemble the anticodon loop of tRNA. The loop folds independently of the rest of the 23S rRNA, and is stabilized by a non-canonical G-A pair and a U-turn motif, rendering G748 accessible. Binding of S.pneumoniae RlmAII induces changes in NMR signals at specific nucleotides that are involved in the methyltransferase-RNA interaction. The conformation of hairpin 35 that interacts with RlmAII is radically different from the structure this hairpin adopts within the 50S subunit. This indicates that the hairpin undergoes major structural rearrangement upon interaction with ribosomal proteins during 50S assembly.
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Affiliation(s)
- Isabelle Lebars
- Laboratoire de RMN, ICSN-CNRS, 1 ave de la terrasse, 91190 Gif-sur-Yvette, France and Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark Corresponding authors e-mail: or
| | - Satoko Yoshizawa
- Laboratoire de RMN, ICSN-CNRS, 1 ave de la terrasse, 91190 Gif-sur-Yvette, France and Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark Corresponding authors e-mail: or
| | - Anne R. Stenholm
- Laboratoire de RMN, ICSN-CNRS, 1 ave de la terrasse, 91190 Gif-sur-Yvette, France and Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark Corresponding authors e-mail: or
| | - Eric Guittet
- Laboratoire de RMN, ICSN-CNRS, 1 ave de la terrasse, 91190 Gif-sur-Yvette, France and Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark Corresponding authors e-mail: or
| | - Stephen Douthwaite
- Laboratoire de RMN, ICSN-CNRS, 1 ave de la terrasse, 91190 Gif-sur-Yvette, France and Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark Corresponding authors e-mail: or
| | - Dominique Fourmy
- Laboratoire de RMN, ICSN-CNRS, 1 ave de la terrasse, 91190 Gif-sur-Yvette, France and Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark Corresponding authors e-mail: or
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28
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Fourmy D, Guittet E, Yoshizawa S. Structure of prokaryotic SECIS mRNA hairpin and its interaction with elongation factor SelB. J Mol Biol 2002; 324:137-50. [PMID: 12421564 DOI: 10.1016/s0022-2836(02)01030-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In prokaryotes, the recoding of a UGA stop codon as a selenocysteine codon requires a special elongation factor (EF) SelB and a stem-loop structure within the mRNA called a selenocysteine insertion sequence (SECIS). Here, we used NMR spectroscopy to determine the solution structure of the SECIS mRNA hairpin and characterized its interaction with the mRNA-binding domain of SelB. Our structural and biochemical data identified the conserved structural features important for binding to EF SelB within different SECIS RNA sequences. In the free SECIS mRNA structure, conserved nucleotides are strongly exposed for recognition by SelB. Binding of the C-terminal domain of SelB stabilizes the RNA secondary structure. In the protein-RNA complex, a Watson-Crick loop base-pair leaves a GpU sequence accessible for SelB recognition. This GpU sequence at the tip of the capping tetraloop and a bulge uracil five Watson-Crick base-pairs apart from the GpU are essential for interaction with SelB.
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Affiliation(s)
- Dominique Fourmy
- Laboratoire de RMN, ICSN-CNRS, 1 ave de la terrasse, 91190 Gif-sur-Yvette, France
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29
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Lebars I, Lamontagne B, Yoshizawa S, Abou Elela S, Fourmy D. Solution structure of conserved AGNN tetraloops: insights into Rnt1p RNA processing. EMBO J 2001; 20:7250-8. [PMID: 11743001 PMCID: PMC125334 DOI: 10.1093/emboj/20.24.7250] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Rnt1p, the yeast orthologue of RNase III, cleaves rRNAs, snRNAs and snoRNAs at a stem capped with conserved AGNN tetraloop. Here we show that 9 bp long stems ending with AGAA or AGUC tetraloops bind to Rnt1p and direct specific but sequence-independent RNA cleavage when provided with stems longer than 13 bp. The solution structures of these two tetraloops reveal a common fold for the terminal loop stabilized by non-canonical A-A or A-C pairs and extensive base stacking. The conserved nucleotides are stacked at the 5' side of the loop, exposing their Watson-Crick and Hoogsteen faces for recognition by Rnt1p. These results indicate that yeast RNase III recognizes the fold of a conserved single-stranded tetraloop to direct specific dsRNA cleavage.
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Affiliation(s)
| | - Bruno Lamontagne
- Laboratoire de RMN, ICSN-CNRS, 1 ave de la terrasse, F-91190 Gif-sur-Yvette, France and
Groupe ARN/RNA Group, Département de Microbiologie et d’Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4 Corresponding authors e-mail: or I.Lebars and B.Lamontagne contributed equally to this work
| | | | - Sherif Abou Elela
- Laboratoire de RMN, ICSN-CNRS, 1 ave de la terrasse, F-91190 Gif-sur-Yvette, France and
Groupe ARN/RNA Group, Département de Microbiologie et d’Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4 Corresponding authors e-mail: or I.Lebars and B.Lamontagne contributed equally to this work
| | - Dominique Fourmy
- Laboratoire de RMN, ICSN-CNRS, 1 ave de la terrasse, F-91190 Gif-sur-Yvette, France and
Groupe ARN/RNA Group, Département de Microbiologie et d’Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4 Corresponding authors e-mail: or I.Lebars and B.Lamontagne contributed equally to this work
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30
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Wu H, Yang PK, Butcher SE, Kang S, Chanfreau G, Feigon J. A novel family of RNA tetraloop structure forms the recognition site for Saccharomyces cerevisiae RNase III. EMBO J 2001; 20:7240-9. [PMID: 11743000 PMCID: PMC125782 DOI: 10.1093/emboj/20.24.7240] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RNases III are a family of double-stranded RNA (dsRNA) endoribonucleases involved in the processing and decay of a large number of cellular RNAs as well as in RNA interference. The dsRNA substrates of Saccharomyces cerevisiae RNase III (Rnt1p) are capped by tetraloops with the consensus sequence AGNN, which act as the primary docking site for the RNase. We have solved the solution structures of two RNA hairpins capped by AGNN tetraloops, AGAA and AGUU, using NMR spectroscopy. Both tetraloops have the same overall structure, in which the backbone turn occurs on the 3' side of the syn G residue in the loop, with the first A and G in a 5' stack and the last two residues in a 3' stack. A non-bridging phosphate oxygen and the universal G which are essential for Rnt1p binding are strongly exposed. The compared biochemical and structural analysis of various tetraloop sequences defines a novel family of RNA tetraloop fold with the consensus (U/A)GNN and implicates this conserved structure as the primary determinant for specific recognition of Rnt1p substrates.
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Affiliation(s)
| | | | - Samuel E. Butcher
- Department of Chemistry and Biochemistry, 405 Hilgard Avenue, PO Box 951569, University of California, Los Angeles, CA 90095-1569, USA
Present address: Department of Biochemistry, 433 Babcock Drive, University of Wisconsin, Madison, WI 53706, USA Corresponding authors e-mail: or
| | | | - Guillaume Chanfreau
- Department of Chemistry and Biochemistry, 405 Hilgard Avenue, PO Box 951569, University of California, Los Angeles, CA 90095-1569, USA
Present address: Department of Biochemistry, 433 Babcock Drive, University of Wisconsin, Madison, WI 53706, USA Corresponding authors e-mail: or
| | - Juli Feigon
- Department of Chemistry and Biochemistry, 405 Hilgard Avenue, PO Box 951569, University of California, Los Angeles, CA 90095-1569, USA
Present address: Department of Biochemistry, 433 Babcock Drive, University of Wisconsin, Madison, WI 53706, USA Corresponding authors e-mail: or
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31
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Puglisi EV, Puglisi JD. HIV-1 A-rich RNA loop mimics the tRNA anticodon structure. NATURE STRUCTURAL BIOLOGY 1998; 5:1033-6. [PMID: 9846871 DOI: 10.1038/4141] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Interaction of HIV-1 genomic RNA and human tRNA(Lys)3 initiates viral reverse transcription. An adenosine-rich (A-rich) loop in HIV RNA mediates complex formation between tRNA and viral RNA. We have determined the structure of an A-rich loop oligonucleotide using nuclear magnetic resonance spectroscopy. The loop structure is stabilized by a noncanonical G-A pair and a U-turn motif, which leads to stacking of the conserved adenosines. The structure has similarity to the tRNA anticodon structure, and suggests possible mechanisms for its role in initiation of reverse transcription.
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Affiliation(s)
- E V Puglisi
- Department of Structural Biology, Stanford University School of Medicine, California 94305-5400, USA
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32
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Brutscher B, Boisbouvier J, Pardi A, Marion D, Simorre JP. Improved Sensitivity and Resolution in 1H−13C NMR Experiments of RNA. J Am Chem Soc 1998. [DOI: 10.1021/ja982853l] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bernhard Brutscher
- Contribution from the Institut de Biologie Structurale, Jean-Pierre Ebel C.N.R.S.-C.E.A. 41, Avenue des Martyrs, 38027 Grenoble Cedex, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, 80309-0215
| | - Jérôme Boisbouvier
- Contribution from the Institut de Biologie Structurale, Jean-Pierre Ebel C.N.R.S.-C.E.A. 41, Avenue des Martyrs, 38027 Grenoble Cedex, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, 80309-0215
| | - Arthur Pardi
- Contribution from the Institut de Biologie Structurale, Jean-Pierre Ebel C.N.R.S.-C.E.A. 41, Avenue des Martyrs, 38027 Grenoble Cedex, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, 80309-0215
| | - Dominique Marion
- Contribution from the Institut de Biologie Structurale, Jean-Pierre Ebel C.N.R.S.-C.E.A. 41, Avenue des Martyrs, 38027 Grenoble Cedex, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, 80309-0215
| | - Jean-Pierre Simorre
- Contribution from the Institut de Biologie Structurale, Jean-Pierre Ebel C.N.R.S.-C.E.A. 41, Avenue des Martyrs, 38027 Grenoble Cedex, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, 80309-0215
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33
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Sich C, Ohlenschläger O, Ramachandran R, Görlach M, Brown LR. Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry. Biochemistry 1997; 36:13989-4002. [PMID: 9369470 DOI: 10.1021/bi971207g] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Structural features of a 19-nucleotide RNA hairpin loop (5'-GGCGUACGUUUCGUACGCC-3'), a loop motif which occurs in eukaryotic 18S rRNA, have been derived using multidimensional heteronuclear NMR spectroscopy in combination with local conformational analysis and torsion angle distance geometry followed by restrained energy minimization. A method to obtain both the 3JC4'P3' and 3JC4'P5' coupling constants from a set of spin-echo difference constant time HSQC spectra is introduced, and it is shown how these couplings can be assigned to the backbone angles beta and epsilon. A total of 280 distance constraints as well as 132 homo- and heteronuclear three-bond scalar coupling constants were derived from the NMR data. The structure which has been determined is a pentaloop rather than a triloop with no base pairing between G8 and C12. G8 is pointed to the minor groove where it forms a base triplet with C7-G13 that is further stabilized by hydrogen bonding to the 2'-hydroxyl group of C7. C12 is directed to the major groove where its conformation is stabilized by hydrogen bonding between O2 and HO2'. The NMR data suggest two possible, interconverting conformations with stacking of bases U10-G8 or U11-C7. Overall, the loop provides a variety of interaction sites for RNA or protein interactions.
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Affiliation(s)
- C Sich
- Institut für Molekulare Biotechnologie eV, Abteilung für Molekulare Biophysik/NMR Spektroskopie, Postfach 100 813, D-07708 Jena, Germany
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34
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Marino JP, Diener JL, Moore PB, Griesinger C. Multiple-Quantum Coherence Dramatically Enhances the Sensitivity of CH and CH2 Correlations in Uniformly 13C-Labeled RNA. J Am Chem Soc 1997. [DOI: 10.1021/ja964379u] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. P. Marino
- Contribution from the Institut für Organische Chemie, Universität Frankfurt, Marie Curie Strasse 11, D-60439 Frankfurt, Germany, and Department of Chemistry, Yale University, 225 Prospect Street, P.O. Box 208107, New Haven, Connecticut 06520-208107
| | - J. L. Diener
- Contribution from the Institut für Organische Chemie, Universität Frankfurt, Marie Curie Strasse 11, D-60439 Frankfurt, Germany, and Department of Chemistry, Yale University, 225 Prospect Street, P.O. Box 208107, New Haven, Connecticut 06520-208107
| | - P. B. Moore
- Contribution from the Institut für Organische Chemie, Universität Frankfurt, Marie Curie Strasse 11, D-60439 Frankfurt, Germany, and Department of Chemistry, Yale University, 225 Prospect Street, P.O. Box 208107, New Haven, Connecticut 06520-208107
| | - C. Griesinger
- Contribution from the Institut für Organische Chemie, Universität Frankfurt, Marie Curie Strasse 11, D-60439 Frankfurt, Germany, and Department of Chemistry, Yale University, 225 Prospect Street, P.O. Box 208107, New Haven, Connecticut 06520-208107
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35
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Fiala R, Jiang F, Patel DJ. Direct Correlation of Exchangeable and Nonexchangeable Protons on Purine Bases in 13C,15N-Labeled RNA Using a HCCNH-TOCSY Experiment. J Am Chem Soc 1996. [DOI: 10.1021/ja9533656] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Radovan Fiala
- Cellular Biochemistry & Biophysics Program Memorial Sloan-Kettering Cancer Center 1275 York Avenue, New York, New York 10021
| | - Feng Jiang
- Cellular Biochemistry & Biophysics Program Memorial Sloan-Kettering Cancer Center 1275 York Avenue, New York, New York 10021
| | - Dinshaw J. Patel
- Cellular Biochemistry & Biophysics Program Memorial Sloan-Kettering Cancer Center 1275 York Avenue, New York, New York 10021
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36
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Homonuclear and Heteronuclear Hartmann—Hahn Transfer in Isotropic Liquids. ADVANCES IN MAGNETIC AND OPTICAL RESONANCE 1996. [DOI: 10.1016/s1057-2732(96)80018-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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37
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Simorre JP, Zimmermann GR, Pardi A, Farmer BT, Mueller L. Triple resonance HNCCCH experiments for correlating exchangeable and nonexchangeable cytidine and uridine base protons in RNA. JOURNAL OF BIOMOLECULAR NMR 1995; 6:427-432. [PMID: 8563469 DOI: 10.1007/bf00197641] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A set of triple resonance experiments is presented, providing through-bond H2N/HN to H6 connectivities in uridines and cytidines in 13C-/15N-labeled RNAs. These connectivities provide an important link between the sequential assignment pathways for the exchangeable and nonexchangeable proton resonances in nucleic acids. Both 2D and pseudo-3D HNCCCH experiments were applied to a 30-nucleotide lead-dependent ribozyme, known as the leadzyme. The HN to H6 connectivities for three uridines in the leadzyme were identified from one 2D H(NCCC)H experiment, and the H2N to H6 connectivities were identified for seven of the eight cytidines from the combination of a 2D H(NCCC)H and a pseudo-3D H(NCC)CH experiment.
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Affiliation(s)
- J P Simorre
- Department of Chemistry and Biochemistry, University of Colorado at Boulder 80309-0215, USA
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38
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Pardi A. Multidimensional heteronuclear NMR experiments for structure determination of isotopically labeled RNA. Methods Enzymol 1995; 261:350-80. [PMID: 8569503 DOI: 10.1016/s0076-6879(95)61017-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- A Pardi
- Department of Chemistry and Biochemistry, University of Colorado at Boulder 80309, USA
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39
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Partially-deuterated nucleotide residues in large DNA duplex simplify the spectral overlap and provide both the J-coupling and nOe informations by the “NMR-window” approach. Tetrahedron 1995. [DOI: 10.1016/0040-4020(95)00579-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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