1
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Hetzke T, Vogel M, Halbritter ALJ, Saha S, Suess B, Sigurdsson ST, Prisner TF. Simultaneous Localization of Two High Affinity Divalent Metal Ion Binding Sites in the Tetracycline RNA Aptamer with Mn 2+-Based Pulsed Dipolar EPR Spectroscopy. J Phys Chem Lett 2023; 14:11421-11428. [PMID: 38084602 DOI: 10.1021/acs.jpclett.3c02566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Mg2+ ions play an essential part in stabilizing the tertiary structure of nucleic acids. While the importance of these ions is well documented, their localization and elucidation of their role in the structure and dynamics of nucleic acids are often challenging. In this work, pulsed electron-electron double resonance spectroscopy (PELDOR, also known as DEER) was used to localize two high affinity divalent metal ion binding sites in the tetracycline RNA aptamer with high accuracy. For this purpose, the aptamer was labeled at different positions with a semirigid nitroxide spin label and diamagnetic Mg2+ was replaced with paramagnetic Mn2+, which did not alter the folding process or ligand binding. Out of the several divalent metal ion binding sites that are known from the crystal structure, two binding sites with high affinity were detected: one that is located at the ligand binding center and another at the J1/2 junction of the RNA.
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Affiliation(s)
- Thilo Hetzke
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Marc Vogel
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | | | - Subham Saha
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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2
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Huang K, Fang X. A review on recent advances in methods for site-directed spin labeling of long RNAs. Int J Biol Macromol 2023; 239:124244. [PMID: 37001783 DOI: 10.1016/j.ijbiomac.2023.124244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/12/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
RNAs are important biomolecules that play essential roles in various cellular processes and are crucially linked with many human diseases. The key to elucidate the mechanisms underlying their biological functions and develop RNA-based therapeutics is to investigate RNA structure and dynamics and their connections to function in detail using a variety of approaches. Magnetic resonance techniques including paramagnetic nuclear magnetic resonance (NMR) and electron magnetic resonance (EPR) spectroscopies have proved to be powerful tools to gain insights into such properties. The prerequisites for paramagnetic NMR and EPR studies on RNAs are to achieve site-specific spin labeling of the intrinsically diamagnetic RNAs, which however is not trivial, especially for long ones. In this review, we present some covalent labeling strategies that allow site-specific introduction of electron spins to long RNAs. Generally, these strategies include assembly of long RNAs via enzymatic ligation of short oligonucleotides, co- and post-transcriptional site-specific labeling empowered with the unnatural base pair system, and direct enzymatic functionalization of natural RNAs. We introduce a few case studies to discuss the advantages and limitations of each strategy, and to provide a vision for the future development.
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3
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Kaiser F, Endeward B, Collauto A, Scheffer U, Prisner TF, Göbel MW. Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block. Chemistry 2022; 28:e202201822. [PMID: 35903916 PMCID: PMC9804336 DOI: 10.1002/chem.202201822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Indexed: 01/05/2023]
Abstract
The nitroxide TPA (2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene) is an excellent spin label for EPR studies of RNA. Previous synthetic methods, however, are complicated and require special equipment. Herein, we describe a uridine derived phosphoramidite with a photocaged TPA unit attached. The light sensitive 2-nitrobenzyloxymethyl group can be removed in high yield by short irradiation at 365 nm. Based on this approach, a doubly spin-labeled 27mer neomycin sensing riboswitch was synthesized and studied by PELDOR. The overall thermal stability of the fold is not much reduced by TPA. In-line probing nevertheless detected changes in local mobility.
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Affiliation(s)
- Frank Kaiser
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Burkhard Endeward
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Alberto Collauto
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Ute Scheffer
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Thomas F. Prisner
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Michael W. Göbel
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
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4
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Xu B, Zhu Y, Cao C, Chen H, Jin Q, Li G, Ma J, Yang SL, Zhao J, Zhu J, Ding Y, Fang X, Jin Y, Kwok CK, Ren A, Wan Y, Wang Z, Xue Y, Zhang H, Zhang QC, Zhou Y. Recent advances in RNA structurome. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1285-1324. [PMID: 35717434 PMCID: PMC9206424 DOI: 10.1007/s11427-021-2116-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 12/27/2022]
Abstract
RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers-including RNA processing, transport, localization, and mRNA translation-across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes (e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanda Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qiongli Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangnan Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Junfeng Ma
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Siwy Ling Yang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Jieyu Zhao
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Jianghui Zhu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chun Kit Kwok
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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5
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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6
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Endeward B, Hu Y, Bai G, Liu G, Prisner TF, Fang X. Long-range distance determination in fully deuterated RNA with pulsed EPR spectroscopy. Biophys J 2022; 121:37-43. [PMID: 34896070 PMCID: PMC8758415 DOI: 10.1016/j.bpj.2021.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/23/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
Pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy is powerful in structure and dynamics study of biological macromolecules by providing distance distribution information ranging from 1.8 to 6 nm, providing that the biomolecules are site-specifically labeled with paramagnetic tags. However, long distances up to 16 nm have been measured on perdeuterated and spin-labeled proteins in deuterated solvent by PELDOR. Here we demonstrate long-range distance measurement on a large RNA, the 97-nucleotide 3'SL RNA element of the Dengue virus 2 genome, by combining a posttranscriptional site-directed spin labeling method using an unnatural basepair system with RNA perdeuteration by enzymatic synthesis using deuterated nucleotides. The perdeuteration removes the coupling of the electron spins of the nitroxide spin labels from the proton nuclear spin system of the RNA and does extend the observation time windows of PELDOR up to 50 μs. This enables one to determine long distances up to 14 nm for large RNAs and their conformational flexibility.
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Affiliation(s)
- Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Yanping Hu
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 10086, China
| | - Guangcan Bai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 10019, China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 10019, China
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt, Germany,Corresponding author
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 10086, China,Corresponding author
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7
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Vicino MF, Wuebben C, Kerzhner M, Famulok M, Schiemann O. Spin Labeling of Long RNAs Via Click Reaction and Enzymatic Ligation. Methods Mol Biol 2022; 2439:205-221. [PMID: 35226324 DOI: 10.1007/978-1-0716-2047-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Electron paramagnetic resonance (EPR) is a spectroscopic method for investigating structures, conformational changes, and dynamics of biomacromolecules, for example, oligonucleotides. In order to be applicable, the oligonucleotide has to be labeled site-specifically with paramagnetic tags, the so-called spin labels. Here, we provide a protocol for spin labeling of long oligonucleotides with nitroxides. In the first step, a short and commercially available RNA strand is labeled with a nitroxide via a copper-(I)-catalyzed azide-alkyne cycloaddition (CuAAC), also referred to as "click" reaction. In the second step, the labeled RNA strand is fused to another RNA sequence by means of enzymatic ligation to obtain the labeled full-length construct. The protocol is robust and has been shown experimentally to deliver high yields for RNA sequences up to 81 nucleotides, but longer strands are in principle also feasible. Moreover, it sets the path to label, for example, long riboswitches, ribozymes, and DNAzymes for coarse-grained structure determination and enables to investigate mechanistical features of these systems.
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Affiliation(s)
- Maria Francesca Vicino
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich Wilhelms University, Bonn, Germany
| | - Christine Wuebben
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich Wilhelms University, Bonn, Germany
| | - Mark Kerzhner
- Life & Medical Sciences Institute (LIMES), Chemische Biologie, c/o Kekulé-Institut für organische Chemie, Bonn, Germany
| | - Michael Famulok
- Life & Medical Sciences Institute (LIMES), Chemische Biologie, c/o Kekulé-Institut für organische Chemie, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich Wilhelms University, Bonn, Germany.
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8
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Vicino MF, Hett T, Schiemann O. Spin Labeling of RNA Using "Click" Chemistry for Coarse-grained Structure Determination via Pulsed Electron-electron Double Resonance Spectroscopy. Bio Protoc 2021; 11:e4004. [PMID: 34150941 PMCID: PMC8187847 DOI: 10.21769/bioprotoc.4004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 11/02/2022] Open
Abstract
Understanding the function of oligonucleotides on a molecular level requires methods for studying their structure, conformational changes, and internal dynamics. Various biophysical methods exist to achieve this, including the whole toolbox of Electron Paramagnetic Resonance (EPR or ESR) spectroscopy. An EPR method widely used in this regard is Pulsed Electron-Electron Double Resonance (PELDOR or DEER), which provides distances in the nanometer range between electron spins in biomolecules with Angstrom precision, without restriction to the size of the biomolecule, and in solution. Since oligonucleotides inherently do not contain unpaired electrons, these have to be introduced in the form of so-called spin labels. Firstly, this protocol describes how nitroxide spin labels can be site-specifically attached to oligonucleotides using "Click" chemistry. The reaction provides little byproducts, high yields, and is conveniently performed in aqueous solution. Secondly, the protocol details how to run the PELDOR experiment, analyze the data, and derive a coarse-grained structure. Here, emphasis is placed on the pitfalls, requirements for a good dataset, and limits of interpretation; thus, the protocol gives the user a guideline for the whole experiment i.e., from spin labeling, via the PELDOR measurement and data analysis, to the final coarse-grained structure. Graphical abstract: Schematic overview of the workflow described in this protocol: First, the spin-labeling of RNA is described, which is performed as a "Click"-reaction between the alkyne-functionalized RNA strand and the azide group of the spin label. Next, step-by-step instructions are given for setting up PELDOR/DEER distance measurements on the labeled RNA, and for data analysis. Finally, guidelines are provided for building a structural model from the previously analyzed data.
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Affiliation(s)
- Maria F. Vicino
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Tobias Hett
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
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9
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Abdullin D, Schiemann O. Localization of metal ions in biomolecules by means of pulsed dipolar EPR spectroscopy. Dalton Trans 2021; 50:808-815. [PMID: 33416053 DOI: 10.1039/d0dt03596c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal ions are important for the folding, structure, and function of biomolecules. Thus, knowing where their binding sites are located in proteins or oligonucleotides is a critical objective. X-ray crystallography and nuclear magnetic resonance are powerful methods in this respect, but both have their limitations. Here, a complementary method is highlighted in which paramagnetic metal ions are localized by means of trilateration using a combination of site-directed spin labeling and pulsed dipolar electron paramagnetic resonance spectroscopy. The working principle, the requirements, and the limitations of the method are critically discussed. Several applications of the method are outlined and compared with each other.
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Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany.
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10
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Wuebben C, Vicino MF, Mueller M, Schiemann O. Do the P1 and P2 hairpins of the Guanidine-II riboswitch interact? Nucleic Acids Res 2020; 48:10518-10526. [PMID: 32857846 PMCID: PMC7544219 DOI: 10.1093/nar/gkaa703] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 01/09/2023] Open
Abstract
Riboswitches regulate genes by adopting different structures in responds to metabolite binding. The guanidine-II riboswitch is the smallest representative of the ykkC class with the mechanism of its function being centred on the idea that its two stem loops P1 and P2 form a kissing hairpin interaction upon binding of guanidinium (Gdm+). This mechanism is based on in-line probing experiments with the full-length riboswitch and crystal structures of the truncated stem loops P1 and P2. However, the crystal structures reveal only the formation of the homodimers P1 | P1 and P2 | P2 but not of the proposed heterodimer P1 | P2. Here, site-directed spin labeling (SDSL) in combination with Pulsed Electron–Electron Double Resonance (PELDOR or DEER) is used to study their structures in solution and how they change upon binding of Gdm+. It is found that both hairpins adopt different structures in solution and that binding of Gdm+ does indeed lead to the formation of the heterodimer but alongside the homodimers in a statistical 1:2:1 fashion. These results do thus support the proposed switching mechanism.
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Affiliation(s)
- Christine Wuebben
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Maria F Vicino
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Marcel Mueller
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
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11
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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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12
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Bartosik K, Debiec K, Czarnecka A, Sochacka E, Leszczynska G. Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post-Synthetic Approach. Molecules 2020; 25:E3344. [PMID: 32717917 PMCID: PMC7436257 DOI: 10.3390/molecules25153344] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
The chemical synthesis of modified oligoribonucleotides represents a powerful approach to study the structure, stability, and biological activity of RNAs. Selected RNA modifications have been proven to enhance the drug-like properties of RNA oligomers providing the oligonucleotide-based therapeutic agents in the antisense and siRNA technologies. The important sites of RNA modification/functionalization are the nucleobase residues. Standard phosphoramidite RNA chemistry allows the site-specific incorporation of a large number of functional groups to the nucleobase structure if the building blocks are synthetically obtainable and stable under the conditions of oligonucleotide chemistry and work-up. Otherwise, the chemically modified RNAs are produced by post-synthetic oligoribonucleotide functionalization. This review highlights the post-synthetic RNA modification approach as a convenient and valuable method to introduce a wide variety of nucleobase modifications, including recently discovered native hypermodified functional groups, fluorescent dyes, photoreactive groups, disulfide crosslinks, and nitroxide spin labels.
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Affiliation(s)
| | | | | | | | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.B.); (K.D.); (A.C.); (E.S.)
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13
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Kamiya Y, Takeyama Y, Mizuno T, Satoh F, Asanuma H. Investigation of Strand-Selective Interaction of SNA-Modified siRNA with AGO2-MID. Int J Mol Sci 2020; 21:ijms21155218. [PMID: 32717920 PMCID: PMC7432901 DOI: 10.3390/ijms21155218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/22/2022] Open
Abstract
Small interfering RNA (siRNA) has been recognized as a powerful gene-silencing tool. For therapeutic application, chemical modification is often required to improve the properties of siRNA, including its nuclease resistance, activity, off-target effects, and tissue distribution. Careful siRNA guide strand selection in the RNA-induced silencing complex (RISC) is important to increase the RNA interference (RNAi) activity as well as to reduce off-target effects. The passenger strand-mediated off-target activity was previously reduced and on-target activity was enhanced by substitution with acyclic artificial nucleic acid, namely serinol nucleic acid (SNA). In the present study, the reduction of off-target activity caused by the passenger strand was investigated by modifying siRNAs with SNA. The interactions of SNA-substituted mononucleotides, dinucleotides, and (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO)-labeled double-stranded RNA (dsRNA) with the MID domain of the Argonaute 2 (AGO2) protein, which plays a pivotal role in strand selection by accommodation of the 5’-terminus of siRNA, were comprehensively analyzed. The obtained nuclear magnetic resonance (NMR) data revealed that AGO2-MID selectively bound to the guide strand of siRNA due to the inhibitory effect of the SNA backbone located at the 5’ end of the passenger strand.
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Affiliation(s)
- Yukiko Kamiya
- Correspondence: (Y.K.); (H.A.); Tel.: +81-52-789-2552 (Y.K.); +81-52-789-2488 (H.A.)
| | | | | | | | - Hiroyuki Asanuma
- Correspondence: (Y.K.); (H.A.); Tel.: +81-52-789-2552 (Y.K.); +81-52-789-2488 (H.A.)
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14
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Hardwick JS, Haugland MM, El-Sagheer AH, Ptchelkine D, Beierlein FR, Lane AN, Brown T, Lovett JE, Anderson EA. 2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis. Nucleic Acids Res 2020; 48:2830-2840. [PMID: 32052020 PMCID: PMC7102949 DOI: 10.1093/nar/gkaa086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 01/28/2020] [Accepted: 02/10/2020] [Indexed: 02/06/2023] Open
Abstract
The determination of distances between specific points in nucleic acids is essential to understanding their behaviour at the molecular level. The ability to measure distances of 2-10 nm is particularly important: deformations arising from protein binding commonly fall within this range, but the reliable measurement of such distances for a conformational ensemble remains a significant challenge. Using several techniques, we show that electron paramagnetic resonance (EPR) spectroscopy of oligonucleotides spin-labelled with triazole-appended nitroxides at the 2' position offers a robust and minimally perturbing tool for obtaining such measurements. For two nitroxides, we present results from EPR spectroscopy, X-ray crystal structures of B-form spin-labelled DNA duplexes, molecular dynamics simulations and nuclear magnetic resonance spectroscopy. These four methods are mutually supportive, and pinpoint the locations of the spin labels on the duplexes. In doing so, this work establishes 2'-alkynyl nitroxide spin-labelling as a minimally perturbing method for probing DNA conformation.
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Affiliation(s)
- Jack S Hardwick
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Marius M Haugland
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Denis Ptchelkine
- Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Frank R Beierlein
- Computer-Chemistry-Center and Interdisciplinary Center for Molecular Materials, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry and Department of Toxicology & Cancer Biology, The University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, USA
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Janet E Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, UK
| | - Edward A Anderson
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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15
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Wuebben C, Blume S, Abdullin D, Brajtenbach D, Haege F, Kath-Schorr S, Schiemann O. Site-Directed Spin Labeling of RNA with a Gem-Diethylisoindoline Spin Label: PELDOR, Relaxation, and Reduction Stability. Molecules 2019; 24:E4482. [PMID: 31817785 PMCID: PMC6943706 DOI: 10.3390/molecules24244482] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 01/08/2023] Open
Abstract
Ribonucleic acid function is governed by its structure, dynamics, and interaction with other biomolecules and influenced by the local environment. Thus, methods are needed that enable one to study RNA under conditions as natural as possible, possibly within cells. Site-directed spin-labeling of RNA with nitroxides in combination with, for example, pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy has been shown to provide such information. However, for in-cell measurements, the usually used gem-dimethyl nitroxides are less suited, because they are quickly reduced under in-cell conditions. In contrast, gem-diethyl nitroxides turned out to be more stable, but labeling protocols for binding these to RNA have been sparsely reported. Therefore, we describe here the bioconjugation of an azide functionalized gem-diethyl isoindoline nitroxide to RNA using a copper (I)-catalyzed azide-alkyne cycloaddition ("click"-chemistry). The labeling protocol provides high yields and site selectivity. The analysis of the orientation selective PELDOR data show that the gem-diethyl and gem-dimethyl labels adopt similar conformations. Interestingly, in deuterated buffer, both labels attached to RNA yield TM relaxation times that are considerably longer than observed for the same type of label attached to proteins, enabling PELDOR time windows of up to 20 microseconds. Together with the increased stability in reducing environments, this label is very promising for in-cell Electron Paramagnetic Resonance (EPR) studies.
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Affiliation(s)
- Christine Wuebben
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany; (C.W.); (S.B.); (D.A.); (D.B.); (F.H.)
| | - Simon Blume
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany; (C.W.); (S.B.); (D.A.); (D.B.); (F.H.)
| | - Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany; (C.W.); (S.B.); (D.A.); (D.B.); (F.H.)
| | - Dominik Brajtenbach
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany; (C.W.); (S.B.); (D.A.); (D.B.); (F.H.)
| | - Florian Haege
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany; (C.W.); (S.B.); (D.A.); (D.B.); (F.H.)
| | - Stephanie Kath-Schorr
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany;
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany; (C.W.); (S.B.); (D.A.); (D.B.); (F.H.)
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16
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Site Selective and Efficient Spin Labeling of Proteins with a Maleimide-Functionalized Trityl Radical for Pulsed Dipolar EPR Spectroscopy. Molecules 2019; 24:molecules24152735. [PMID: 31357628 PMCID: PMC6696014 DOI: 10.3390/molecules24152735] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 01/18/2023] Open
Abstract
Pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) in combination with site-directed spin labeling (SDSL) of proteins and oligonucleotides is a powerful tool in structural biology. Instead of using the commonly employed gem-dimethyl-nitroxide labels, triarylmethyl (trityl) spin labels enable such studies at room temperature, within the cells and with single-frequency electron paramagnetic resonance (EPR) experiments. However, it has been repeatedly reported that labeling of proteins with trityl radicals led to low labeling efficiencies, unspecific labeling and label aggregation. Therefore, this work introduces the synthesis and characterization of a maleimide-functionalized trityl spin label and its corresponding labeling protocol for cysteine residues in proteins. The label is highly cysteine-selective, provides high labeling efficiencies and outperforms the previously employed methanethiosulfonate-functionalized trityl label. Finally, the new label is successfully tested in PDS measurements on a set of doubly labeled Yersinia outer protein O (YopO) mutants.
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17
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Ehrenberger MA, Vieyra A, Esquiaqui JM, Fanucci GE. Ion-dependent mobility effects of the Fusobacterium nucleatum glycine riboswitch aptamer II via site-directed spin-labeling (SDSL) electron paramagnetic resonance (EPR). Biochem Biophys Res Commun 2019; 516:839-844. [PMID: 31262445 DOI: 10.1016/j.bbrc.2019.06.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 06/19/2019] [Indexed: 01/31/2023]
Abstract
Site-directed spin-labeling (SDSL) with continuous wave electron paramagnetic resonance (cw-EPR) spectroscopy was utilized to probe site-specific changes in backbone dynamics that accompany folding of the isolated 84 nucleotide aptamer II domain of the Fusobacterium nucleatum (FN) glycine riboswitch. Spin-labels were incorporated using splinted ligation strategies. Results show differential dynamics for spin-labels incorporated into the backbone at a base-paired and loop region. Additionally, the addition of a biologically relevant concentration of 5 mM Mg2+, to an RNA solution with 100 mM K+, folds and compacts the structure, inferred by a reduction in spin-label mobility. Furthermore, when controlling for ionic strength, Mg2+ added to the RNA induces more folding/less flexibility at the two sites than RNA with K+ alone. Addition of glycine does not alter the dynamics of this singlet aptamer II, indicating that the full length riboswitch construct may be needed for glycine binding and induced conformational changes. This work adds to our growing understanding of how splinted-ligation SDSL can be utilized to interrogate differential dynamics in large dynamic RNAs, providing insights into how RNA folding and structure is differentially stabilized by monovalent versus divalent cations.
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Affiliation(s)
- Michelle A Ehrenberger
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, United States
| | - Aleida Vieyra
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, United States
| | - Jackie M Esquiaqui
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, United States.
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18
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Domnick C, Hagelueken G, Eggert F, Schiemann O, Kath-Schorr S. Posttranscriptional spin labeling of RNA by tetrazine-based cycloaddition. Org Biomol Chem 2019; 17:1805-1808. [DOI: 10.1039/c8ob02597e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Spin labeling of in vitro transcribed RNA by iEDDA click chemistry is demonstrated. This allows the determination of distance distributions between two nitroxide spin labels by PELDOR in a self-complementary RNA duplex.
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Affiliation(s)
- Christof Domnick
- Life & Medical Sciences Institute
- Chemical Biology & Medicinal Chemistry Unit
- University of Bonn
- 53121 Bonn
- Germany
| | - Gregor Hagelueken
- Institute for Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Frank Eggert
- Life & Medical Sciences Institute
- Chemical Biology & Medicinal Chemistry Unit
- University of Bonn
- 53121 Bonn
- Germany
| | - Olav Schiemann
- Institute for Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Stephanie Kath-Schorr
- Life & Medical Sciences Institute
- Chemical Biology & Medicinal Chemistry Unit
- University of Bonn
- 53121 Bonn
- Germany
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19
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Saha S, Hetzke T, Prisner TF, Sigurdsson ST. Noncovalent spin-labeling of RNA: the aptamer approach. Chem Commun (Camb) 2018; 54:11749-11752. [PMID: 30276367 DOI: 10.1039/c8cc05597a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the first example of site-directed spin-labeling of unmodified RNA, a pyrrolidine-nitroxide derivative of tetramethylrosamine (TMR) was shown to bind with high affinity to the malachite green (MG) aptamer, as determined by continuous-wave (CW) electron paramagnetic resonance (EPR), pulsed electron-electron double resonance (PELDOR) and fluorescence spectroscopies.
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Affiliation(s)
- Subham Saha
- Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland.
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