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Wang Y, Kathiresan V, Chen Y, Hu Y, Jiang W, Bai G, Liu G, Qin PZ, Fang X. Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions. Chem Sci 2020; 11:9655-9664. [PMID: 33224460 PMCID: PMC7667596 DOI: 10.1039/d0sc01717e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/19/2020] [Indexed: 12/25/2022] Open
Abstract
Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date.
Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date. We here demonstrate an efficient and generally applicable posttranscriptional SDSL method for large RNAs using an expanded genetic alphabet containing the NaM-TPT3 unnatural base pair (UBP). An alkyne-modified TPT3 ribonucleotide triphosphate (rTPT3COTP) is synthesized and site-specifically incorporated into large RNAs by in vitro transcription, which allows attachment of the azide-containing nitroxide through click chemistry. We validate this strategy by SDSL of a 419-nucleotide ribonuclease P (RNase P) RNA from Bacillus stearothermophilus under non-denaturing conditions. The effects of site-directed UBP incorporation and subsequent spin labeling on the global structure and function of RNase P are marginal as evaluated by Circular Dichroism spectroscopy, Small Angle X-ray Scattering, Sedimentation Velocity Analytical Ultracentrifugation and enzymatic assay. Continuous-Wave EPR analyses reveal that the labeling reaction is efficient and specific, and Pulsed Electron–Electron Double Resonance measurements yield an inter-spin distance distribution that agrees with the crystal structure. The labeling strategy as presented overcomes the size constraint of RNA labeling, opening new avenues of spin labeling and EPR spectroscopy for investigating the structure and dynamics of large RNAs.
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Affiliation(s)
- Yan Wang
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Venkatesan Kathiresan
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Yaoyi Chen
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Yanping Hu
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Wei Jiang
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Guangcan Bai
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Peter Z Qin
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
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Uroda T, Chillón I, Annibale P, Teulon JM, Pessey O, Karuppasamy M, Pellequer JL, Marcia M. Visualizing the functional 3D shape and topography of long noncoding RNAs by single-particle atomic force microscopy and in-solution hydrodynamic techniques. Nat Protoc 2020; 15:2107-2139. [PMID: 32451442 DOI: 10.1038/s41596-020-0323-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/24/2020] [Indexed: 11/09/2022]
Abstract
Long noncoding RNAs (lncRNAs) are recently discovered transcripts that regulate vital cellular processes, such as cellular differentiation and DNA replication, and are crucially connected to diseases. Although the 3D structures of lncRNAs are key determinants of their function, the unprecedented molecular complexity of lncRNAs has so far precluded their 3D structural characterization at high resolution. It is thus paramount to develop novel approaches for biochemical and biophysical characterization of these challenging targets. Here, we present a protocol that integrates non-denaturing lncRNA purification with in-solution hydrodynamic analysis and single-particle atomic force microscopy (AFM) imaging to produce highly homogeneous lncRNA preparations and visualize their 3D topology at ~15-Å resolution. Our protocol is suitable for imaging lncRNAs in biologically active conformations and for measuring structural defects of functionally inactive mutants that have been identified by cell-based functional assays. Once optimized for the specific target lncRNA of choice, our protocol leads from cloning to AFM imaging within 3-4 weeks and can be implemented using state-of-the-art biochemical and biophysical instrumentation by trained researchers familiar with RNA handling and supported by AFM and small-angle X-ray scattering (SAXS) experts.
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Affiliation(s)
- Tina Uroda
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France.,Department of BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Isabel Chillón
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | | | - Jean-Marie Teulon
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Ombeline Pessey
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | | | - Jean-Luc Pellequer
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France.
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Mitra S, Demeler B. Probing RNA-Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation. Methods Mol Biol 2020; 2113:281-317. [PMID: 32006321 PMCID: PMC10958623 DOI: 10.1007/978-1-0716-0278-2_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recent advances in multi-wavelength analytical ultracentrifugation (MWL-AUC) combine the power of an exquisitely sensitive hydrodynamic-based separation technique with the added dimension of spectral separation. This added dimension has opened up new doors to much improved characterization of multiple, interacting species in solution. When applied to structural investigations of RNA, MWL-AUC can precisely report on the hydrodynamic radius and the overall shape of an RNA molecule by enabling precise measurements of its sedimentation and diffusion coefficients and identify the stoichiometry of interacting components based on spectral decomposition. Information provided in this chapter will allow an investigator to design experiments for probing ion and/or protein-induced global conformational changes of an RNA molecule and exploit spectral differences between proteins and RNA to characterize their interactions in a physiological solution environment.
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Affiliation(s)
- Somdeb Mitra
- Department of Chemistry, New York University, New York, NY, USA.
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
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Dadonaite B, Gilbertson B, Knight ML, Trifkovic S, Rockman S, Laederach A, Brown LE, Fodor E, Bauer DLV. The structure of the influenza A virus genome. Nat Microbiol 2019; 4:1781-1789. [PMID: 31332385 DOI: 10.1038/s41564-019-0513-7] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/12/2019] [Indexed: 12/19/2022]
Abstract
Influenza A viruses (IAVs) constitute a major threat to human health. The IAV genome consists of eight single-stranded viral RNA segments contained in separate viral ribonucleoprotein (vRNP) complexes that are packaged together into a single virus particle. The structure of viral RNA is believed to play a role in assembling the different vRNPs into budding virions1-8 and in directing reassortment between IAVs9. Reassortment between established human IAVs and IAVs harboured in the animal reservoir can lead to the emergence of pandemic influenza strains to which there is little pre-existing immunity in the human population10,11. While previous studies have revealed the overall organization of the proteins within vRNPs, characterization of viral RNA structure using conventional structural methods is hampered by limited resolution and an inability to resolve dynamic components12,13. Here, we employ multiple high-throughput sequencing approaches to generate a global high-resolution structure of the IAV genome. We show that different IAV genome segments acquire distinct RNA conformations and form both intra- and intersegment RNA interactions inside influenza virions. We use our detailed map of IAV genome structure to provide direct evidence for how intersegment RNA interactions drive vRNP cosegregation during reassortment between different IAV strains. The work presented here is a roadmap both for the development of improved vaccine strains and for the creation of a framework to 'risk assess' reassortment potential to better predict the emergence of new pandemic influenza strains.
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Affiliation(s)
| | - Brad Gilbertson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michael L Knight
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sanja Trifkovic
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Steven Rockman
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Seqirus Ltd, Parkville, Victoria, Australia
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Lorena E Brown
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| | - David L V Bauer
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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Chillón I, Marcia M, Legiewicz M, Liu F, Somarowthu S, Pyle AM. Native Purification and Analysis of Long RNAs. Methods Enzymol 2015; 558:3-37. [PMID: 26068736 PMCID: PMC4477701 DOI: 10.1016/bs.mie.2015.01.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The purification and analysis of long noncoding RNAs (lncRNAs) in vitro is a challenge, particularly if one wants to preserve elements of functional structure. Here, we describe a method for purifying lncRNAs that preserves the cotranscriptionally derived structure. The protocol avoids the misfolding that can occur during denaturation-renaturation protocols, thus facilitating the folding of long RNAs to a native-like state. This method is simple and does not require addition of tags to the RNA or the use of affinity columns. LncRNAs purified using this type of native purification protocol are amenable to biochemical and biophysical analysis. Here, we describe how to study lncRNA global compaction in the presence of divalent ions at equilibrium using sedimentation velocity analytical ultracentrifugation and analytical size-exclusion chromatography as well as how to use these uniform RNA species to determine robust lncRNA secondary structure maps by chemical probing techniques like selective 2'-hydroxyl acylation analyzed by primer extension and dimethyl sulfate probing.
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Affiliation(s)
- Isabel Chillón
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Marco Marcia
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Michal Legiewicz
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Fei Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Srinivas Somarowthu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA; Department of Chemistry, Yale University, New Haven, Connecticut, USA.
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Harding SE, Adams GG, Almutairi F, Alzahrani Q, Erten T, Samil Kök M, Gillis RB. Ultracentrifuge Methods for the Analysis of Polysaccharides, Glycoconjugates, and Lignins. Methods Enzymol 2015; 562:391-439. [DOI: 10.1016/bs.mie.2015.06.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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