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Chadda R, Kaushik V, Ahmad IM, Deveryshetty J, Holehouse AS, Sigurdsson ST, Biswas G, Levy Y, Bothner B, Cooley RB, Mehl RA, Dastvan R, Origanti S, Antony E. Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation. Nucleic Acids Res 2024:gkae584. [PMID: 38989614 DOI: 10.1093/nar/gkae584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/30/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024] Open
Abstract
Single-stranded DNA (ssDNA) intermediates which emerge during DNA metabolic processes are shielded by replication protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper to direct the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent functional specificity requires knowledge of the structural conformation of ssDNA when RPA-bound. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA-ssDNA complexes using single-molecule FRET and double electron-electron resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.
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Affiliation(s)
- Rahul Chadda
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Iram Munir Ahmad
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Jaigeeth Deveryshetty
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Gargi Biswas
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Reza Dastvan
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Sofia Origanti
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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2
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Chadda R, Kaushik V, Ahmad IM, Deveryshetty J, Holehouse A, Sigurdsson ST, Bothner B, Dastvan R, Origanti S, Antony E. Wrapping of single-stranded DNA by Replication Protein A and modulation through phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587234. [PMID: 38585962 PMCID: PMC10996701 DOI: 10.1101/2024.03.28.587234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Single-stranded DNA (ssDNA) intermediates, which emerge during DNA metabolic processes are shielded by Replication Protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper, directing the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent specificity requires a comprehensive understanding of the structural conformation of ssDNA when bound to RPA. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA-ssDNA complexes using single-molecule FRET and Double Electron-Electron Resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.
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Affiliation(s)
- Rahul Chadda
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Iram Munir Ahmad
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Jaigeeth Deveryshetty
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Alex Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in Saint Louis School of Medicine, St. Louis, MO, 63110, USA
| | - Snorri Th.d Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Reza Dastvan
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Sofia Origanti
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
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3
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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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Khoroshunova YV, Morozov DA, Kuznetsov DA, Rybalova TV, Glazachev YI, Bagryanskaya EG, Kirilyuk IA. Synthesis and Properties of (1 R( S),5 R( S),7 R( S),8 R( S))-1,8-Bis(hydroxymethyl)-6-azadispiro[4.1.4.2]tridecane-6-oxyl: Reduction-Resistant Spin Labels with High Spin Relaxation Times. Int J Mol Sci 2023; 24:11498. [PMID: 37511257 PMCID: PMC10380268 DOI: 10.3390/ijms241411498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Site-directed spin labeling followed by investigation using Electron Paramagnetic Resonance spectroscopy is a rapidly expanding powerful biophysical technique to study structure, local dynamics and functions of biomolecules using pulsed EPR techniques and nitroxides are the most widely used spin labels. Modern trends of this method include measurements directly inside a living cell, as well as measurements without deep freezing (below 70 K), which provide information that is more consistent with the behavior of the molecules under study in natural conditions. Such studies require nitroxides, which are resistant to the action of biogenic reductants and have high spin relaxation (dephasing) times, Tm. (1R(S),5R(S),7R(S),8R(S))-1,8-bis(hydroxymethyl)-6-azadispiro[4.1.4.2]tridecane-6-oxyl is a unique nitroxide that combines these features. We have developed a convenient method for the synthesis of this radical and studied the ways of its functionalization. Promising spin labels have been obtained, the parameters of their spin relaxation T1 and Tm have been measured, and the kinetics of reduction with ascorbate have been studied.
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Affiliation(s)
- Yulia V Khoroshunova
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia
| | - Denis A Morozov
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Danil A Kuznetsov
- Department of Physics, Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia
| | - Tatyana V Rybalova
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Yurii I Glazachev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3, 630090 Novosibirsk, Russia
| | - Elena G Bagryanskaya
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Igor A Kirilyuk
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
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5
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Jana S, Evans EGB, Jang HS, Zhang S, Zhang H, Rajca A, Gordon SE, Zagotta WN, Stoll S, Mehl RA. Ultrafast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids. J Am Chem Soc 2023; 145:14608-14620. [PMID: 37364003 PMCID: PMC10440187 DOI: 10.1021/jacs.3c00967] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Site-directed spin-labeling (SDSL)─in combination with double electron-electron resonance (DEER) spectroscopy─has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolecules. DEER combined with in situ SDSL in live cells is challenging since current bioorthogonal labeling approaches are too slow to allow for complete labeling with low concentrations of spin label prior to loss of signal from cellular reduction. Here, we overcome this limitation by genetically encoding a novel family of small, tetrazine-bearing noncanonical amino acids (Tet-v4.0) at multiple sites in proteins expressed in Escherichia coli and in human HEK293T cells. We achieved specific and quantitative spin-labeling of Tet-v4.0-containing proteins by developing a series of strained trans-cyclooctene (sTCO)-functionalized nitroxides─including a gem-diethyl-substituted nitroxide with enhanced stability in cells─with rate constants that can exceed 106 M-1 s-1. The remarkable speed of the Tet-v4.0/sTCO reaction allowed efficient spin-labeling of proteins in live cells within minutes, requiring only sub-micromolar concentrations of sTCO-nitroxide. DEER recorded from intact cells revealed distance distributions in good agreement with those measured from proteins purified and labeled in vitro. Furthermore, DEER was able to resolve the maltose-dependent conformational change of Tet-v4.0-incorporated and spin-labeled MBP in vitro and support assignment of the conformational state of an MBP mutant within HEK293T cells. We anticipate the exceptional reaction rates of this system, combined with the relatively short and rigid side chains of the resulting spin labels, will enable structure/function studies of proteins directly in cells, without any requirements for protein purification.
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Affiliation(s)
- Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Eric G B Evans
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - Hyo Sang Jang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shuyang Zhang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Hui Zhang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Sharona E Gordon
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - William N Zagotta
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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6
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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: 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.
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7
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Jana S, Evans EGB, Jang HS, Zhang S, Zhang H, Rajca A, Gordon SE, Zagotta WN, Stoll S, Mehl RA. Ultra-Fast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525763. [PMID: 36747808 PMCID: PMC9901033 DOI: 10.1101/2023.01.26.525763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Studying protein structures and dynamics directly in the cellular environments in which they function is essential to fully understand the molecular mechanisms underlying cellular processes. Site-directed spin-labeling (SDSL)-in combination with double electron-electron resonance (DEER) spectroscopy-has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolecules. In-cell DEER spectroscopy on proteins in mammalian cells has thus far not been possible due to the notable challenges of spin-labeling in live cells. In-cell SDSL requires exquisite biorthogonality, high labeling reaction rates and low background signal from unreacted residual spin label. While the bioorthogonal reaction must be highly specific and proceed under physiological conditions, many spin labels display time-dependent instability in the reducing cellular environment. Additionally, high concentrations of spin label can be toxic. Thus, an exceptionally fast bioorthogonal reaction is required that can allow for complete labeling with low concentrations of spin-label prior to loss of signal. Here we utilized genetic code expansion to site-specifically encode a novel family of small, tetrazine-bearing non-canonical amino acids (Tet-v4.0) at multiple sites in green fluorescent protein (GFP) and maltose binding protein (MBP) expressed both in E. coli and in human HEK293T cells. We achieved specific and quantitative spin-labeling of Tet-v4.0-containing proteins by developing a series of strained trans -cyclooctene (sTCO)-functionalized nitroxides-including a gem -diethyl-substituted nitroxide with enhanced stability in cells-with rate constants that can exceed 10 6 M -1 s -1 . The remarkable speed of the Tet-v4.0/sTCO reaction allowed efficient spin-labeling of proteins in live HEK293T cells within minutes, requiring only sub-micromolar concentrations of sTCO-nitroxide added directly to the culture medium. DEER recorded from intact cells revealed distance distributions in good agreement with those measured from proteins purified and labeled in vitro . Furthermore, DEER was able to resolve the maltose-dependent conformational change of Tet-v4.0-incorporated and spin-labeled MBP in vitro and successfully discerned the conformational state of MBP within HEK293T cells. We anticipate the exceptional reaction rates of this system, combined with the relatively short and rigid side chains of the resulting spin labels, will enable structure/function studies of proteins directly in cells, without any requirements for protein purification. TOC
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Affiliation(s)
- Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
- Equal contributors
| | - Eric G B Evans
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
- Equal contributors
| | - Hyo Sang Jang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shuyang Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Hui Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Sharona E Gordon
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
| | - William N Zagotta
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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8
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Dobrynin SA, Gulman MM, Morozov DA, Zhurko IF, Taratayko AI, Sotnikova YS, Glazachev YI, Gatilov YV, Kirilyuk IA. Synthesis of Sterically Shielded Nitroxides Using the Reaction of Nitrones with Alkynylmagnesium Bromides. Molecules 2022; 27:molecules27217626. [PMID: 36364453 PMCID: PMC9654931 DOI: 10.3390/molecules27217626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Sterically shielded nitroxides, which demonstrate high resistance to bioreduction, are the spin labels of choice for structural studies inside living cells using pulsed EPR and functional MRI and EPRI in vivo. To prepare new sterically shielded nitroxides, a reaction of cyclic nitrones, including various 1-pyrroline-1-oxides, 2,5-dihydroimidazole-3-oxide and 4H-imidazole-3-oxide with alkynylmagnesium bromide wereused. The reaction gave corresponding nitroxides with an alkynyl group adjacent to the N-O moiety. The hydrogenation of resulting 2-ethynyl-substituted nitroxides with subsequent re-oxidation of the N-OH group produced the corresponding sterically shielded tetraalkylnitroxides of pyrrolidine, imidazolidine and 2,5-dihydroimidazole series. EPR studies revealed large additional couplings up to 4 G in the spectra of pyrrolidine and imidazolidine nitroxides with substituents in 3- and/or 4-positions of the ring.
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Affiliation(s)
- Sergey A. Dobrynin
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
- Correspondence: (S.A.D.); (D.A.M.)
| | - Mark M. Gulman
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, 630090 Novosibirsk, Russia
| | - Denis A. Morozov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
- Correspondence: (S.A.D.); (D.A.M.)
| | - Irina F. Zhurko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Andrey I. Taratayko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, 630090 Novosibirsk, Russia
| | - Yulia S. Sotnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Yurii I. Glazachev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3, 630090 Novosibirsk, Russia
| | - Yuri V. Gatilov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Igor A. Kirilyuk
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
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9
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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: 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.
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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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10
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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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11
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Collauto A, Bülow S, Gophane DB, Saha S, Stelzl LS, Hummer G, Sigurdsson ST, Prisner TF. Compaction of RNA Duplexes in the Cell**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alberto Collauto
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Sören Bülow
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
| | - Dnyaneshwar B. Gophane
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Subham Saha
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Lukas S. Stelzl
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
- Institute for Biophysics Goethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
| | - Snorri T. Sigurdsson
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
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12
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Collauto A, von Bülow S, Gophane DB, Saha S, Stelzl LS, Hummer G, Sigurdsson ST, Prisner TF. Compaction of RNA Duplexes in the Cell*. Angew Chem Int Ed Engl 2020; 59:23025-23029. [PMID: 32804430 PMCID: PMC7756485 DOI: 10.1002/anie.202009800] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Indexed: 11/15/2022]
Abstract
The structure and flexibility of RNA depends sensitively on the microenvironment. Using pulsed electron-electron double-resonance (PELDOR)/double electron-electron resonance (DEER) spectroscopy combined with advanced labeling techniques, we show that the structure of double-stranded RNA (dsRNA) changes upon internalization into Xenopus laevis oocytes. Compared to dilute solution, the dsRNA A-helix is more compact in cells. We recapitulate this compaction in a densely crowded protein solution. Atomic-resolution molecular dynamics simulations of dsRNA semi-quantitatively capture the compaction, and identify non-specific electrostatic interactions between proteins and dsRNA as a possible driver of this effect.
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Affiliation(s)
- Alberto Collauto
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Str. 760438Frankfurt am MainGermany
| | - Sören von Bülow
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
| | - Dnyaneshwar B. Gophane
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Subham Saha
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Lukas S. Stelzl
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
| | - Gerhard Hummer
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
- Institute for BiophysicsGoethe University FrankfurtMax-von-Laue-Str. 960438Frankfurt am MainGermany
| | - Snorri T. Sigurdsson
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Str. 760438Frankfurt am MainGermany
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13
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Ghosh S, Casto J, Bogetti X, Arora C, Wang J, Saxena S. Orientation and dynamics of Cu 2+ based DNA labels from force field parameterized MD elucidates the relationship between EPR distance constraints and DNA backbone distances. Phys Chem Chem Phys 2020; 22:26707-26719. [PMID: 33159779 PMCID: PMC10521111 DOI: 10.1039/d0cp05016d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Pulsed electron paramagnetic resonance (EPR) based distance measurements using the recently developed Cu2+-DPA label present a promising strategy for measuring DNA backbone distance constraints. Herein we develop force field parameters for Cu2+-DPA in order to understand the features of this label at an atomic level. We perform molecular dynamics (MD) simulations using the force field parameters of Cu2+-DPA on four different DNA duplexes. The distance between the Cu2+ centers, extracted from the 2 μs MD trajectories, agrees well with the experimental distance for all the duplexes. Further analyses of the trajectory provide insight into the orientation of the Cu2+-DPA inside the duplex that leads to such agreement with experiments. The MD results also illustrate the ability of the Cu2+-DPA to report on the DNA backbone distance constraints. Furthermore, measurement of fluctuations of individual residues showed that the flexibility of Cu2+-DPA in a DNA depends on the position of the label in the duplex, and a 2 μs MD simulation is not sufficient to fully capture the experimental distribution in some cases. Finally, the MD trajectories were utilized to understand the key aspects of the double electron electron resonance (DEER) results. The lack of orientational selectivity effects of the Cu2+-DPA at Q-band frequency is rationalized in terms of fluctuations in the Cu2+ coordination environment and rotameric fluctuations of the label linker. Overall, a combination of EPR and MD simulations based on the Cu2+-DPA labelling strategy can contribute towards understanding changes in DNA backbone conformations during protein-DNA interactions.
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Affiliation(s)
- Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
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14
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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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15
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Ghosh S, Lawless MJ, Brubaker HJ, Singewald K, Kurpiewski MR, Jen-Jacobson L, Saxena S. Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution. Nucleic Acids Res 2020; 48:e49. [PMID: 32095832 PMCID: PMC7229862 DOI: 10.1093/nar/gkaa133] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/24/2020] [Accepted: 02/17/2020] [Indexed: 11/12/2022] Open
Abstract
Electron paramagnetic resonance (EPR) has become an important tool to probe conformational changes in nucleic acids. An array of EPR labels for nucleic acids are available, but they often come at the cost of long tethers, are dependent on the presence of a particular nucleotide or can be placed only at the termini. Site directed incorporation of Cu2+-chelated to a ligand, 2,2'dipicolylamine (DPA) is potentially an attractive strategy for site-specific, nucleotide independent Cu2+-labelling in DNA. To fully understand the potential of this label, we undertook a systematic and detailed analysis of the Cu2+-DPA motif using EPR and molecular dynamics (MD) simulations. We used continuous wave EPR experiments to characterize Cu2+ binding to DPA as well as optimize Cu2+ loading conditions. We performed double electron-electron resonance (DEER) experiments at two frequencies to elucidate orientational selectivity effects. Furthermore, comparison of DEER and MD simulated distance distributions reveal a remarkable agreement in the most probable distances. The results illustrate the efficacy of the Cu2+-DPA in reporting on DNA backbone conformations for sufficiently long base pair separations. This labelling strategy can serve as an important tool for probing conformational changes in DNA upon interaction with other macromolecules.
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Affiliation(s)
- Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Matthew J Lawless
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Hanna J Brubaker
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Michael R Kurpiewski
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Linda Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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16
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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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17
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Braun TS, Widder P, Osswald U, Groß L, Williams L, Schmidt M, Helmle I, Summerer D, Drescher M. Isoindoline-Based Nitroxides as Bioresistant Spin Labels for Protein Labeling through Cysteines and Alkyne-Bearing Noncanonical Amino Acids. Chembiochem 2020; 21:958-962. [PMID: 31657498 PMCID: PMC7187341 DOI: 10.1002/cbic.201900537] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/18/2019] [Indexed: 12/15/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) is a powerful tool in protein structural research. Nitroxides are highly suitable spin labeling reagents, but suffer from limited stability, particularly in the cellular environment. Herein we present the synthesis of a maleimide- and an azide-modified tetraethyl-shielded isoindoline-based nitroxide (M- and Az-TEIO) for labeling of cysteines or the noncanonical amino acid para-ethynyl-l-phenylalanine (pENF). We demonstrate the high stability of TEIO site-specifically attached to the protein thioredoxin (TRX) against reduction in prokaryotic and eukaryotic environments, and conduct double electron-electron resonance (DEER) measurements. We further generate a rotamer library for the new residue pENF-Az-TEIO that affords a distance distribution that is in agreement with the measured distribution.
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Affiliation(s)
- Theresa Sophie Braun
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Konstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Pia Widder
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Konstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Uwe Osswald
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Lina Groß
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Lara Williams
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Moritz Schmidt
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Irina Helmle
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Present address: Faculty of ScienceDepartment of Pharmaceutical BiologyUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical BiologyTU DortmundOtto-Hahn-Strasse 4a44227DortmundGermany
| | - Malte Drescher
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Konstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
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18
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Juliusson HY, Sigurdsson ST. Reduction Resistant and Rigid Nitroxide Spin-Labels for DNA and RNA. J Org Chem 2020; 85:4036-4046. [PMID: 32103670 DOI: 10.1021/acs.joc.9b02988] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy, coupled with site-directed spin labeling (SDSL), is a useful method for studying conformational changes of biomolecules in cells. To employ in-cell EPR using nitroxide-based spin labels, the structure of the nitroxides must confer reduction resistance to withstand the reductive environment within cells. Here, we report the synthesis of two new spin labels, EÇ and EÇm, both of which possess the rigidity and the reduction resistance needed for extracting detailed structural information by EPR spectroscopy. EÇ and EÇm were incorporated into DNA and RNA, respectively, by oligonucleotide synthesis. Both labels were shown to be nonperturbing of the duplex structure. The partial reduction of EÇm during RNA synthesis was circumvented by the protection of the nitroxide as a benzoylated hydroxylamine.
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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
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19
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Tapmeyer L, Beske M, Plackmeyer J. 1,1,3,3-Tetraethyl-5-nitroisoindoline. IUCRDATA 2019. [DOI: 10.1107/s2414314619016298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The title compound, C16H24N2O2, previously obtained as a yellow oil, exhibits a rather low melting point close to room temperature 297–298 K). In the molecule, the isoindoline ring system is approximately planar and coplanar to the nitro group, forming a dihedral angle of 5.63 (15)°. In the crystal, only weak N—H...O and C—H...π interactions are observed, linking molecules into chains parallel to the [101] direction.
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20
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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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21
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Sameach H, Ruthstein S. EPR Distance Measurements as a Tool to Characterize Protein‐DNA Interactions. Isr J Chem 2019. [DOI: 10.1002/ijch.201900091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hila Sameach
- The Department of Chemistry, Faculty of Exact SciencesBar Ilan University Ramat Gan Israel 5290002
| | - Sharon Ruthstein
- The Department of Chemistry, Faculty of Exact SciencesBar Ilan University Ramat Gan Israel 5290002
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22
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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
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23
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Akakuru OU, Iqbal MZ, Saeed M, Liu C, Paunesku T, Woloschak G, Hosmane NS, Wu A. The Transition from Metal-Based to Metal-Free Contrast Agents for T1 Magnetic Resonance Imaging Enhancement. Bioconjug Chem 2019; 30:2264-2286. [PMID: 31380621 DOI: 10.1021/acs.bioconjchem.9b00499] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Magnetic resonance imaging (MRI) has received significant attention as the noninvasive diagnostic technique for complex diseases. Image-guided therapeutic strategy for diseases such as cancer has also been at the front line of biomedical research, thanks to the innovative MRI, enhanced by the prior delivery of contrast agents (CAs) into patients' bodies through injection. These CAs have contributed a great deal to the clinical utility of MRI but have been based on metal-containing compounds such as gadolinium, manganese, and iron oxide. Some of these CAs have led to cytotoxicities such as the incurable Nephrogenic Systemic Fibrosis (NSF), resulting in their removal from the market. On the other hand, CAs based on organic nitroxide radicals, by virtue of their structural composition, are metal free and without the aforementioned drawbacks. They also have improved biocompatibility, ease of functionalization, and long blood circulation times, and have been proven to offer tissue contrast enhancement with longitudinal relaxivities comparable with those for the metal-containing CAs. Thus, this Review highlights the recent progress in metal-based CAs and their shortcomings. In addition, the remarkable goals achieved by the organic nitroxide radical CAs in the enhancement of MR images have also been discussed extensively. The focal point of this Review is to emphasize or demonstrate the crucial need for transition into the use of organic nitroxide radicals-metal-free CAs-as against the metal-containing CAs, with the aim of achieving safer application of MRI for early disease diagnosis and image-guided therapy.
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Affiliation(s)
- Ozioma Udochukwu Akakuru
- Cixi Institute of Biomedical Engineering, CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province , Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , Ningbo 315201 , P.R. China.,University of Chinese Academy of Sciences , No. 19(A) Yuquan Road , Shijingshan District, Beijing 100049 , P.R. China
| | - M Zubair Iqbal
- Cixi Institute of Biomedical Engineering, CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province , Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , Ningbo 315201 , P.R. China.,Department of Materials Engineering, College of Materials and Textiles , Zhejiang Sci-Tech University , No. 2 Road of Xiasha , Hangzhou 310018 , P.R. China
| | - Madiha Saeed
- Cixi Institute of Biomedical Engineering, CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province , Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , Ningbo 315201 , P.R. China.,University of Chinese Academy of Sciences , No. 19(A) Yuquan Road , Shijingshan District, Beijing 100049 , P.R. China
| | - Chuang Liu
- Cixi Institute of Biomedical Engineering, CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province , Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , Ningbo 315201 , P.R. China.,University of Chinese Academy of Sciences , No. 19(A) Yuquan Road , Shijingshan District, Beijing 100049 , P.R. China
| | - Tatjana Paunesku
- Department of Radiation Oncology , Northwestern University , Chicago , Illinois 60611 , United States
| | - Gayle Woloschak
- Department of Radiation Oncology , Northwestern University , Chicago , Illinois 60611 , United States
| | - Narayan S Hosmane
- Department of Chemistry and Biochemistry , Northern Illinois University , DeKalb , Illinois 60115 , United States
| | - Aiguo Wu
- Cixi Institute of Biomedical Engineering, CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province , Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , Ningbo 315201 , P.R. China
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24
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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.
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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
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25
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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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26
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Kamble NR, Gränz M, Prisner TF, Sigurdsson ST. Noncovalent and site-directed spin labeling of duplex RNA. Chem Commun (Camb) 2018; 52:14442-14445. [PMID: 27901530 DOI: 10.1039/c6cc08387k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An isoindoline-nitroxide derivative of guanine (Ǵ, "G-spin") was shown to bind specifically and effectively to abasic sites in duplex RNAs. Distance measurements on a Ǵ-labeled duplex RNA with PELDOR (DEER) showed a strong orientation dependence. Thus, Ǵ is a readily synthesized, orientation-selective spin label for "mix and measure" PELDOR experiments.
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Affiliation(s)
- Nilesh R Kamble
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland.
| | - Markus Gränz
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Hessen, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Hessen, Germany
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland.
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27
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Weinrich T, Jaumann EA, Scheffer UM, Prisner TF, Göbel MW. Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA. Beilstein J Org Chem 2018; 14:1563-1569. [PMID: 30013683 PMCID: PMC6036967 DOI: 10.3762/bjoc.14.133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/14/2018] [Indexed: 12/23/2022] Open
Abstract
TEMPO spin labels protected with 2-nitrobenzyloxymethyl groups were attached to the amino residues of three different nucleosides: deoxycytidine, deoxyadenosine, and adenosine. The corresponding phosphoramidites could be incorporated by unmodified standard procedures into four different self-complementary DNA and two RNA oligonucleotides. After photochemical removal of the protective group, elimination of formic aldehyde and spontaneous air oxidation, the nitroxide radicals were regenerated in high yield. The resulting spin-labeled palindromic duplexes could be directly investigated by PELDOR spectroscopy without further purification steps. Spin–spin distances measured by PELDOR correspond well to the values obtained from molecular models.
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Affiliation(s)
- Timo Weinrich
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Eva A Jaumann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Ute M Scheffer
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Michael W Göbel
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
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28
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Kerzhner M, Matsuoka H, Wuebben C, Famulok M, Schiemann O. High-Yield Spin Labeling of Long RNAs for Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2018; 57:2923-2931. [PMID: 29715006 DOI: 10.1021/acs.biochem.8b00040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Site-directed spin labeling is a powerful tool for investigating the conformation and dynamics of biomacromolecules such as RNA. Here we introduce a spin labeling strategy based on click chemistry in solution that, in combination with enzymatic ligation, allows highly efficient labeling of complex and long RNAs with short reaction times and suppressed RNA degradation. With this approach, a 34-nucleotide aptamer domain of the preQ1 riboswitch and an 81-nucleotide TPP riboswitch aptamer could be labeled with two labels in several positions. We then show that conformations of the preQ1 aptamer and its dynamics can be monitored in the absence and presence of Mg2+ and a preQ1 ligand by continuous wave electron paramagnetic resonance spectroscopy at room temperature and pulsed electron-electron double resonance spectroscopy (PELDOR or DEER) in the frozen state.
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Affiliation(s)
- Mark Kerzhner
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie University of Bonn , Gerhard-Domagk-Strasse 1 , 53121 Bonn , Germany
| | - Hideto Matsuoka
- Institute of Physical and Theoretical Chemistry , University of Bonn , Wegelerstrasse 12 , 53115 Bonn , Germany
| | - Christine Wuebben
- Institute of Physical and Theoretical Chemistry , University of Bonn , Wegelerstrasse 12 , 53115 Bonn , Germany
| | - Michael Famulok
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie University of Bonn , Gerhard-Domagk-Strasse 1 , 53121 Bonn , Germany.,Max Planck Fellowship Chemical Biology Group , Stiftung caesar , Ludwig-Erhard-Allee 2 , 53175 Bonn , Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry , University of Bonn , Wegelerstrasse 12 , 53115 Bonn , Germany
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29
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Weinrich T, Jaumann EA, Scheffer U, Prisner TF, Göbel MW. A Cytidine Phosphoramidite with Protected Nitroxide Spin Label: Synthesis of a Full-Length TAR RNA and Investigation by In-Line Probing and EPR Spectroscopy. Chemistry 2018; 24:6202-6207. [PMID: 29485736 DOI: 10.1002/chem.201800167] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/23/2018] [Indexed: 01/20/2023]
Abstract
EPR studies on RNA are complicated by three major obstacles related to the chemical nature of nitroxide spin labels: Decomposition while oligonucleotides are chemically synthesized, further decay during enzymatic strand ligation, and undetected changes in conformational equilibria due to the steric demand of the label. Herein possible solutions for all three problems are presented: A 2-nitrobenzyloxymethyl protective group for nitroxides that is stable under all conditions of chemical RNA synthesis and can be removed photochemically. By careful selection of ligation sites and splint oligonucleotides, high yields were achieved in the assembly of a full-length HIV-1 TAR RNA labeled with two protected nitroxide groups. PELDOR measurements on spin-labeled TAR in the absence and presence of arginine amide indicated arrest of interhelical motions on ligand binding. Finally, even minor changes in conformation due to the presence of spin labels are detected with high sensitivity by in-line probing.
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Affiliation(s)
- Timo Weinrich
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Eva A Jaumann
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Ute Scheffer
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Michael W Göbel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
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30
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Haugland MM, Lovett JE, Anderson EA. Advances in the synthesis of nitroxide radicals for use in biomolecule spin labelling. Chem Soc Rev 2018; 47:668-680. [PMID: 29192696 DOI: 10.1039/c6cs00550k] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
EPR spectroscopy is an increasingly useful analytical tool to probe biomolecule structure, dynamic behaviour, and interactions. Nitroxide radicals are the most commonly used radical probe in EPR experiments, and many methods have been developed for their synthesis, as well as incorporation into biomolecules using site-directed spin labelling. In this Tutorial Review, we discuss the most practical methods for the synthesis of nitroxides, focusing on the tunability of their structures, the manipulation of their sidechains into spin labelling handles, and their installation into biomolecules.
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Affiliation(s)
- Marius M Haugland
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford, OX1 3TA, UK.
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31
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Kamble NR, Sigurdsson ST. Purine-Derived Nitroxides for Noncovalent Spin-Labeling of Abasic Sites in Duplex Nucleic Acids. Chemistry 2018; 24:4157-4164. [DOI: 10.1002/chem.201705410] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Nilesh R. Kamble
- University of Iceland; Department of Chemistry; Science Institute; Dunhaga 3 107 Reykjavik Iceland
| | - Snorri Th. Sigurdsson
- University of Iceland; Department of Chemistry; Science Institute; Dunhaga 3 107 Reykjavik Iceland
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32
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Schnorr KA, Gophane DB, Helmling C, Cetiner E, Pasemann K, Fürtig B, Wacker A, Qureshi NS, Gränz M, Barthelmes D, Jonker HRA, Stirnal E, Sigurdsson ST, Schwalbe H. Impact of spin label rigidity on extent and accuracy of distance information from PRE data. JOURNAL OF BIOMOLECULAR NMR 2017; 68:53-63. [PMID: 28500543 DOI: 10.1007/s10858-017-0114-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Paramagnetic relaxation enhancement (PRE) is a versatile tool for NMR spectroscopic structural and kinetic studies in biological macromolecules. Here, we compare the quality of PRE data derived from two spin labels with markedly different dynamic properties for large RNAs using the I-A riboswitch aptamer domain (78 nt) from Mesoplamsa florum as model system. We designed two I-A aptamer constructs that were spin-labeled by noncovalent hybridization of short spin-labeled oligomer fragments. As an example of a flexible spin label, UreidoU-TEMPO was incorporated into the 3' terminal end of helix P1 while, the recently developed rigid spin-label Çm was incorporated in the 5' terminal end of helix P1. We determined PRE rates obtained from aromatic 13C bound proton intensities and compared these rates to PREs derived from imino proton intensities in this sizeable RNA (~78 nt). PRE restraints derived from both imino and aromatic protons yielded similar data quality, and hence can both be reliably used for PRE determination. For NMR, the data quality derived from the rigid spin label Çm is slightly better than the data quality for the flexible UreidoTEMPO as judged by comparison of the structural agreement with the I-A aptamer crystal structure (3SKI).
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Affiliation(s)
- K A Schnorr
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - D B Gophane
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland
| | - C Helmling
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - E Cetiner
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - K Pasemann
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - B Fürtig
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - A Wacker
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - N S Qureshi
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - M Gränz
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - D Barthelmes
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - H R A Jonker
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - E Stirnal
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - S Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland
| | - H Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany.
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33
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Lawless MJ, Sarver JL, Saxena S. Nucleotide-Independent Copper(II)-Based Distance Measurements in DNA by Pulsed ESR Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Matthew J. Lawless
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| | - Jessica L. Sarver
- Division of Biological, Chemical, and Environmental Sciences; Westminster College; 319 S Market St. New Wilmington PA 16172 USA
| | - Sunil Saxena
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
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34
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Lawless MJ, Sarver JL, Saxena S. Nucleotide-Independent Copper(II)-Based Distance Measurements in DNA by Pulsed ESR Spectroscopy. Angew Chem Int Ed Engl 2017; 56:2115-2117. [PMID: 28090713 DOI: 10.1002/anie.201611197] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/14/2016] [Indexed: 01/05/2023]
Abstract
A site-specific Cu2+ binding motif within a DNA duplex for distance measurements by ESR spectroscopy is reported. This motif utilizes a commercially available 2,2'-dipicolylamine (DPA) phosphormadite easily incorporated into any DNA oligonucleotide during initial DNA synthesis. The method only requires the simple post-synthetic addition of Cu2+ without the need for further chemical modification. Notably, the label is positioned within the DNA duplex, as opposed to outside the helical perimeter, for an accurate measurement of duplex distance. A distance of 2.7 nm was measured on a doubly Cu2+ -labeled DNA sequence, which is in exact agreement with the expected distance from both DNA modeling and molecular dynamic simulations. This result suggests that with this labeling strategy the ESR measured distance directly reports on backbone DNA distance, without the need for further modeling. Furthermore, the labeling strategy is structure- and nucleotide-independent.
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Affiliation(s)
- Matthew J Lawless
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Jessica L Sarver
- Division of Biological, Chemical, and Environmental Sciences, Westminster College, 319 S Market St., New Wilmington, PA, 16172, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
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35
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Weinrich T, Gränz M, Grünewald C, Prisner TF, Göbel MW. Synthesis of a Cytidine Phosphoramidite with Protected Nitroxide Spin Label for EPR Experiments with RNA. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601174] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Timo Weinrich
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Markus Gränz
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Michael W. Göbel
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
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36
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Haugland MM, El-Sagheer AH, Porter RJ, Peña J, Brown T, Anderson EA, Lovett JE. 2'-Alkynylnucleotides: A Sequence- and Spin Label-Flexible Strategy for EPR Spectroscopy in DNA. J Am Chem Soc 2016; 138:9069-72. [PMID: 27409454 DOI: 10.1021/jacs.6b05421] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a powerful method to elucidate molecular structure through the measurement of distances between conformationally well-defined spin labels. Here we report a sequence-flexible approach to the synthesis of double spin-labeled DNA duplexes, where 2'-alkynylnucleosides are incorporated at terminal and internal positions on complementary strands. Post-DNA synthesis copper-catalyzed azide-alkyne cycloaddition (CuAAC) reactions with a variety of spin labels enable the use of double electron-electron resonance experiments to measure a number of distances on the duplex, affording a high level of detailed structural information.
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Affiliation(s)
- Marius M Haugland
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford, OX1 3TA, U.K
| | - Afaf H El-Sagheer
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford, OX1 3TA, U.K.,Chemistry Branch, Faculty of Petroleum and Mining Engineering, Suez University , Suez 43721, Egypt
| | - Rachel J Porter
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford, OX1 3TA, U.K
| | - Javier Peña
- Departamento de Química Orgánica, Universidad de Salamanca , Plaza de los Caídos 1-5, 37008 Salamanca, Spain
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford, OX1 3TA, U.K
| | - Edward A Anderson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford, OX1 3TA, U.K
| | - Janet E Lovett
- SUPA, School of Physics and Astronomy, University of St Andrews , North Haugh, St Andrews, KY16 9SS, U.K
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37
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Saha S, Jagtap AP, Sigurdsson ST. Site-Directed Spin Labeling of RNA by Postsynthetic Modification of 2'-Amino Groups. Methods Enzymol 2015; 563:397-414. [PMID: 26478493 DOI: 10.1016/bs.mie.2015.07.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To elucidate mechanisms that govern functions of nucleic acids, it is essential to understand their structure and dynamics. Electron paramagnetic resonance (EPR) spectroscopy is a valuable technique that is routinely used to study those aspects of nucleic acids. A prerequisite for most EPR studies of nucleic acids is incorporation of spin labels at specific sites, known as site-directed spin labeling (SDSL). There are two main strategies for SDSL through formation of covalent bonds, i.e., the phosphoramidite approach and postsynthetic spin-labeling. After describing briefly the advantages and disadvantages of these two strategies, postsynthetic labeling of 2'-amino groups in RNA is delineated. Postsynthetic labeling of 2'-amino groups in RNA using 4-isocyanato-TEMPO has long been established as a useful approach. However, this method has some drawbacks, both with regard to the spin-labeling protocol and the flexibility of the spin label itself. Recently reported isothiocyanate-substituted aromatic isoindoline-derived nitroxides can be used to quantitatively and selectively modify 2'-amino groups in RNA and do not have the drawbacks associated with 4-isocyanato-TEMPO. This chapter provides a detailed description of the postsynthetic spin-labeling methods of 2'-amino groups in RNA with a special focus on using the aromatic isothiocyanate spin labels.
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Affiliation(s)
- Subham Saha
- Department of Chemistry, Science Institute, University of Iceland, Reykjavik, Iceland
| | - Anil P Jagtap
- Department of Chemistry, Science Institute, University of Iceland, Reykjavik, Iceland
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Reykjavik, Iceland.
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