1
|
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.
Collapse
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
| |
Collapse
|
2
|
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: 1] [Impact Index Per Article: 1.0] [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.
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Synthesis of Spin-Labeled Ibuprofen and Its Interaction with Lipid Membranes. Molecules 2022; 27:molecules27134127. [PMID: 35807376 PMCID: PMC9268589 DOI: 10.3390/molecules27134127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Ibuprofen is a non-steroidal anti-inflammatory drug possessing analgesic and antipyretic activity. Electron paramagnetic resonance (EPR) spectroscopy could be applied to study its interaction with biological membranes and proteins if its spin-labeled analogs were synthesized. Here, a simple sequence of ibuprofen transformations—nitration, esterification, reduction, Sandmeyer reaction, Sonogashira cross-coupling, oxidation and saponification—was developed to attain this goal. The synthesis resulted in spin-labeled ibuprofen (ibuprofen-SL) in which the spin label TEMPOL is attached to the benzene ring. EPR spectra confirmed interaction of ibuprofen-SL with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. Using 2H electron spin echo envelope modulation (ESEEM) spectroscopy, ibuprofen-SL was found to be embedded into the hydrophobic bilayer interior.
Collapse
|
5
|
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: 35] [Impact Index Per Article: 17.5] [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.
Collapse
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
| |
Collapse
|
6
|
Juliusson HY, Sigurdsson ST. Nitroxide-Derived N-Oxide Phenazines for Noncovalent Spin-Labeling of DNA. Chembiochem 2020; 21:2635-2642. [PMID: 32353177 DOI: 10.1002/cbic.202000128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/28/2020] [Indexed: 12/11/2022]
Abstract
Two o-benzoquinone derivatives of isoindoline were synthesized for use as building blocks to incorporate isoindoline nitroxides into different compounds and materials. These o-quinones were condensed with a number of o-phenylenediamines to form isoindoline-phenazines in high yields. Subsequent oxidation gave phenazine-di-N-oxide isoindoline nitroxides that were evaluated for noncovalent and site-directed spin-labeling of duplex DNA and RNA that contained abasic sites. Although only minor binding was observed for RNA, the unsubstituted phenazine-N,N-dioxide tetramethyl isoindoline nitroxide showed high binding affinity and selectivity towards abasic sites in duplex DNA that contained cytosine as the orphan base.
Collapse
Affiliation(s)
- Haraldur Y Juliusson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland
| |
Collapse
|
7
|
Site-Specific Spin Labeling of RNA for NMR and EPR Structural Studies. Methods Mol Biol 2020. [PMID: 32006317 DOI: 10.1007/978-1-0716-0278-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Many RNA architectures were discovered to be involved in essential biological pathways acting as catalysts and/or regulators of gene expression, transcription, translation, splicing, or viral infection. The key to understand their diverse biological functions is to investigate their structure and dynamic. Nuclear Magnetic Resonance (NMR) is a powerful method to gain insight into these properties. However, the study of high-molecular-weight RNAs by NMR remains challenging. Advances in biochemical and NMR methods over the recent years allow to overcome the limitation of NMR. In particular, the incorporation of paramagnetic probes, coupled to the measurement of the induced effects on nuclear spins, has become an efficient tool providing long-range distance restraints and information on dynamic in solution. At the same time, the use of spin label enabled the application of Electron Paramagnetic Resonance (EPR) to study biological macromolecules. Combining NMR and EPR is emerging as a new approach to investigate the architecture of biological systems.Here, we describe an efficient protocol to introduce a paramagnetic probe into a RNA at a specific position. This method enables various combinations of isotopic labeling for NMR and is also of interest for EPR studies.
Collapse
|
8
|
Kamble N, Wolfrum M, Halbritter T, Sigurdsson ST, Richert C. Noncovalent Spin-Labeling of DNA and RNA Triplexes. Chem Biodivers 2019; 17:e1900676. [PMID: 31872549 DOI: 10.1002/cbdv.201900676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/23/2019] [Indexed: 11/07/2022]
Abstract
Studying nucleic acids often requires labeling. Many labeling approaches require covalent bonds between the nucleic acid and the label, which complicates experimental procedures. Noncovalent labeling avoids the need for highly specific reagents and reaction conditions, and the effort of purifying bioconjugates. Among the least invasive techniques for studying biomacromolecules are NMR and EPR. Here, we report noncovalent labeling of DNA and RNA triplexes with spin labels that are nucleobase derivatives. Spectroscopic signals indicating strong binding were detected in EPR experiments in the cold, and filtration assays showed micromolar dissociation constants for complexes between a guanine-derived label and triplex motifs containing a single-nucleotide gap in the oligopurine strand. The advantages and challenges of noncovalent labeling via this approach that complements techniques relying on covalent links are discussed.
Collapse
Affiliation(s)
- Nilesh Kamble
- Science Institute, University of Iceland, Dunhaga 3, 107 R, eykjavik, Iceland
| | - Manpreet Wolfrum
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Thomas Halbritter
- Science Institute, University of Iceland, Dunhaga 3, 107 R, eykjavik, Iceland
| | - Snorri T Sigurdsson
- Science Institute, University of Iceland, Dunhaga 3, 107 R, eykjavik, Iceland
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| |
Collapse
|
9
|
Bonucci A, Ouari O, Guigliarelli B, Belle V, Mileo E. In‐Cell EPR: Progress towards Structural Studies Inside Cells. Chembiochem 2019; 21:451-460. [DOI: 10.1002/cbic.201900291] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Alessio Bonucci
- Magnetic Resonance CenterCERMUniversity of Florence 50019 Sesto Fiorentino Italy
| | - Olivier Ouari
- Aix Marseille UnivCNRSICRInstitut de Chimie Radicalaire 13013 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Juliusson HY, Segler ALJ, Sigurdsson ST. Benzoyl-Protected Hydroxylamines for Improved Chemical Synthesis of Oligonucleotides Containing Nitroxide Spin Labels. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900553] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Haraldur Y. Juliusson
- Department of Chemistry; Science Institute; University of Iceland; Dunhaga 3 107 Reykjavik Iceland
| | - Anna-Lena J. Segler
- Department of Chemistry; Science Institute; University of Iceland; Dunhaga 3 107 Reykjavik Iceland
| | - Snorri Th. Sigurdsson
- Department of Chemistry; Science Institute; University of Iceland; Dunhaga 3 107 Reykjavik Iceland
| |
Collapse
|
12
|
Bognár B, Úr G, Sár C, Hankovszky OH, Hideg K, Kálai T. Synthesis and Application of Stable Nitroxide Free Radicals Fused with Carbocycles and Heterocycles. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190318163321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Stable nitroxide free radicals have traditionally been associated with 2,2,6,6-
tetramethylpiperidine-1-oxyl (TEMPO) or its 4-substituted derivatives as relatively inexpensive
and readily accessible compounds with limited possibilities for further chemical
modification. Over the past two decades, there has been a resurgence of interest in stable
free radicals with proper functionalization tuned for various applications. The objective of
this review is to present recent results with synthetic methodologies to achieve stable nitroxide
free radicals fused with aromatic carbocycles and heterocycles. There are two
main approaches for accessing stable nitroxide free radicals fused with arenes, e.g., isoindoline-
like nitroxides: further functionalization and oxidation of phthalimide or inventive
functionalization of pyrroline nitroxide key compounds. The latter also offers the constructions
of versatile heterocyclic scaffolds (furan, pyrrole, thiophene, 1,2-thiazole, selenophene, pyrazole,
pyrimidine, pyridine, pyridazine, 1,5-benzothiazepine) that are fused with pyrroline or tetrahydropyridine nitroxide
rings. The possible applications of these new stable nitroxide free radicals, such as covalent spin labels
and noncovalent spin probes of proteins and nucleic acids, profluorescent probes, building blocks for construction
of dual active drugs and electroactive materials, and substances for controlled free radical polymerization,
are discussed.
Collapse
Affiliation(s)
- Balázs Bognár
- Institute of Organic and Medicinal Chemistry, Medical School, University of Pecs, Szigeti st. 12, H-7624 Pecs, Hungary
| | - Györgyi Úr
- Institute of Organic and Medicinal Chemistry, Medical School, University of Pecs, Szigeti st. 12, H-7624 Pecs, Hungary
| | - Cecília Sár
- Institute of Organic and Medicinal Chemistry, Medical School, University of Pecs, Szigeti st. 12, H-7624 Pecs, Hungary
| | - Olga H. Hankovszky
- Institute of Organic and Medicinal Chemistry, Medical School, University of Pecs, Szigeti st. 12, H-7624 Pecs, Hungary
| | - Kálmán Hideg
- Institute of Organic and Medicinal Chemistry, Medical School, University of Pecs, Szigeti st. 12, H-7624 Pecs, Hungary
| | - Tamás Kálai
- Institute of Organic and Medicinal Chemistry, Medical School, University of Pecs, Szigeti st. 12, H-7624 Pecs, Hungary
| |
Collapse
|