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Zhou A, Sun Z, Sun L. Stable organic radical qubits and their applications in quantum information science. Innovation (N Y) 2024; 5:100662. [PMID: 39091459 PMCID: PMC11292369 DOI: 10.1016/j.xinn.2024.100662] [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: 03/06/2024] [Accepted: 06/20/2024] [Indexed: 08/04/2024] Open
Abstract
The past century has witnessed the flourishing of organic radical chemistry. Stable organic radicals are highly valuable for quantum technologies thanks to their inherent room temperature quantum coherence, atomic-level designability, and fine tunability. In this comprehensive review, we highlight the potential of stable organic radicals as high-temperature qubits and explore their applications in quantum information science, which remain largely underexplored. Firstly, we summarize known spin dynamic properties of stable organic radicals and examine factors that influence their electron spin relaxation and decoherence times. This examination reveals their design principles and optimal operating conditions. We further discuss their integration in solid-state materials and surface structures, and present their state-of-the-art applications in quantum computing, quantum memory, and quantum sensing. Finally, we analyze the primary challenges associated with stable organic radical qubits and provide tentative insights to future research directions.
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Affiliation(s)
- Aimei Zhou
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Zhecheng Sun
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Lei Sun
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Key Laboratory for Quantum Materials of Zhejiang Province, Department of Physics, School of Science, Westlake University, Hangzhou 310030, China
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2
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Martin RM, Diaz S, Poncelet M, Driesschaert B, Barth E, Kotecha M, Epel B, Eaton GR, Biller JR. Toward a Nanoencapsulated EPR Imaging Agent for Clinical Use. Mol Imaging Biol 2024; 26:525-541. [PMID: 37870648 PMCID: PMC11035482 DOI: 10.1007/s11307-023-01863-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023]
Abstract
PURPOSE Progress toward developing a novel radiocontrast agent for determining pO2 in tumors in a clinical setting is described. The imaging agent is designed for use with electron paramagnetic resonance imaging (EPRI), in which the collision of a paramagnetic probe molecule with molecular oxygen causes a spectroscopic change which can be calibrated to give the real oxygen concentration in the tumor tissue. PROCEDURES The imaging agent is based on a nanoscaffold of aluminum hydroxide (boehmite) with sizes from 100 to 200 nm, paramagnetic probe molecule, and encapsulation with a gas permeable, thin (10-20 nm) polymer layer to separate the imaging agent and body environment while still allowing O2 to interact with the paramagnetic probe. A specially designed deuterated Finland trityl (dFT) is covalently attached on the surface of the nanoparticle through 1,3-dipolar addition of the alkyne on the dFT with an azide on the surface of the nanoscaffold. This click-chemistry reaction affords 100% efficiency of the trityl attachment as followed by the complete disappearance of the azide peak in the infrared spectrum. The fully encapsulated, dFT-functionalized nanoparticle is referred to as RADI-Sense. RESULTS Side-by-side in vivo imaging comparisons made in a mouse model made between RADI-Sense and free paramagnetic probe (OX-071) showed oxygen sensitivity is retained and RADI-Sense can create 3D pO2 maps of solid tumors CONCLUSIONS: A novel encapsulated nanoparticle EPR imaging agent has been described which could be used in the future to bring EPR imaging for guidance of radiotherapy into clinical reality.
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Affiliation(s)
| | | | - Martin Poncelet
- Department of Pharmaceutical Sciences, School of Pharmacy & In-Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In-Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA
| | - Eugene Barth
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, 60637, USA
| | | | - Boris Epel
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, 60637, USA
- Oxygen Measurement Core, O2M Technologies, Chicago, IL, 60612, USA
| | - Gareth R Eaton
- Department of Chemistry, University of Denver, Denver, CO, 80210, USA
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Shu C, Yang Z, Rajca A. From Stable Radicals to Thermally Robust High-Spin Diradicals and Triradicals. Chem Rev 2023; 123:11954-12003. [PMID: 37831948 DOI: 10.1021/acs.chemrev.3c00406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Stable radicals and thermally robust high-spin di- and triradicals have emerged as important organic materials due to their promising applications in diverse fields. New fundamental properties, such as SOMO/HOMO inversion of orbital energies, are explored for the design of new stable radicals, including highly luminescent ones with good photostability. A relation with the singlet-triplet energy gap in the corresponding diradicals is proposed. Thermally robust high-spin di- and triradicals, with energy gaps that are comparable to or greater than a thermal energy at room temperature, are more challenging to synthesize but more rewarding. We summarize a number of high-spin di- and triradicals, based on nitronyl nitroxides that provide a relation between the experimental pairwise exchange coupling constant J/k in the high-spin species vs experimental hyperfine coupling constants in the corresponding monoradicals. This relation allows us to identify outliers, which may correspond to radicals where J/k is not measured with sufficient accuracy. Double helical high-spin diradicals, in which spin density is delocalized over the chiral π-system, have been barely explored, with the sole example of such high-spin diradical possessing alternant π-system with Kekulé resonance form. Finally, we discuss a high-spin diradical with electrical conductivity and derivatives of triangulene diradicals.
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Affiliation(s)
- Chan Shu
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Zhimin Yang
- 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
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4
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Grazia Concilio M, Frydman L. Steady state effects introduced by local relaxation modes on J-driven DNP-enhanced NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 355:107542. [PMID: 37672989 DOI: 10.1016/j.jmr.2023.107542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/03/2023] [Accepted: 08/26/2023] [Indexed: 09/08/2023]
Abstract
One of solution-state Nuclear Magnetic Resonance (NMR)'s main weaknesses, is its relative insensitivity. J-driven Dynamic Nuclear Polarization (JDNP) was recently proposed for enhancing solution-state NMR's sensitivity, by bypassing the limitations faced by conventional Overhauser DNP (ODNP), at the high magnetic fields where most analytical research is performed. By relying on biradicals with inter-electron exchange couplings Jex on the order of the electron Larmor frequency ωE, JDNP was predicted to introduce a transient enhancement in NMR's nuclear polarization at high magnetic fields, and for a wide range of rotational correlation times of medium-sized molecules in conventional solvents. This communication revisits the JDNP proposal, including additional effects and conditions that were not considered in the original treatment. These include relaxation mechanisms arising from local vibrational modes that often dominate electron relaxation in organic radicals, as well as the possibility of using biradicals with Jex of the order of the nuclear Larmor frequency ωN as potential polarizing agents. The presence of these new relaxation effects lead to variations in the JDNP polarization mechanism originally proposed, and indicate that triplet-to-singlet cross-relaxation processes may lead to a nuclear polarization enhancement that persists even at steady states. The physics and potential limitations of the ensuing theoretical derivations, are briefly discussed.
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Affiliation(s)
- Maria Grazia Concilio
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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5
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Concilio MG, Frydman L. Microwave-free J-driven dynamic nuclear polarization: A proposal for enhancing the sensitivity of solution-state NMR. Phys Rev E 2023; 107:035303. [PMID: 37073023 DOI: 10.1103/physreve.107.035303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 02/16/2023] [Indexed: 04/20/2023]
Abstract
J-driven dynamic nuclear polarization (JDNP) was recently proposed for enhancing the sensitivity of solution-state nuclear magnetic resonance (NMR), while bypassing the limitations faced by conventional (Overhauser) DNP at magnetic fields of interest in analytical applications. Like Overhauser DNP, JDNP also requires saturating the electronic polarization using high-frequency microwaves known to have poor penetration and associated heating effects in most liquids. The present microwave-free JDNP (MF-JDNP) proposal seeks to enhance solution NMR's sensitivity by shuttling the sample between higher and lower magnetic fields, with one of these fields providing an electron Larmor frequency that matches the interelectron exchange coupling J_{ex}. If spins cross this so-called JDNP condition sufficiently fast, we predict that a sizable nuclear polarization will be created without microwave irradiation. This MF-JDNP proposal requires radicals whose singlet-triplet self-relaxation rates are dominated by dipolar hyperfine relaxation, and shuttling times that can compete with these electron relaxation processes. This paper discusses the theory behind the MF-JDNP, as well as proposals for radicals and conditions that could enable this new approach to NMR sensitivity enhancement.
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Affiliation(s)
- Maria Grazia Concilio
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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Koyama S, Sato K, Yamashita M, Sakamoto R, Iguchi H. Observation of slow magnetic relaxation phenomena in spatially isolated π-radical ions. Phys Chem Chem Phys 2023; 25:5459-5467. [PMID: 36748343 DOI: 10.1039/d2cp06026d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The use of molecular spins as quantum bits is fascinating because it offers a wide range of strategies through chemical modifications. In this regard, it is very interesting to search for organic radical ions that have small spin-orbit coupling values. On the other hand, the feature of the magnetic relaxation of π-organic radical ions is rarely exploited due to the difficulty of spin dilution, and π-stacking interaction. In this study, we focus on N,N',N''-tris(2,6-dimethylphenyl)benzenetriimide (BTI-xy), where three xylene moieties connected to the imide groups cover the π-plane of the BTI core. As a result, BTI-xy radical anions without π-stacking interaction were obtained. This led to the slow magnetization relaxation, which is reported for the first time in organic radicals. Furthermore, the relaxation times in a solution state revealed the importance of spin interaction.
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Affiliation(s)
- Shohei Koyama
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan.
| | - Kazunobu Sato
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Masahiro Yamashita
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan. .,School of Materials Science and Engineering, Nankai University, Tianjin 300350, P. R. China
| | - Ryota Sakamoto
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan.
| | - Hiroaki Iguchi
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
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Hasanbasri Z, Poncelet M, Hunter H, Driesschaert B, Saxena S. A new 13C trityl-based spin label enables the use of DEER for distance measurements. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 347:107363. [PMID: 36620971 PMCID: PMC9928843 DOI: 10.1016/j.jmr.2022.107363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Triarylmethyl (TAM)-based labels, while still underutilized, are a powerful class of labels for pulsed-Electron Spin Resonance (ESR) distance measurements. They feature slow relaxation rates for long-lasting signals, high stability for cellular experiments, and narrow spectral features for efficient excitation of the spins. However, the typical narrow line shape limits the available distance measurements to only single-frequency experiments, such as Double Quantum Coherence (DQC) and Relaxation Induced Dipolar Modulation Enhancement (RIDME), which can be complicated to perform or hard to process. Therefore, widespread usage of TAM labels can be enhanced by the use of Double Electron-Electron Resonance (DEER) distance measurements. In this work, we developed a new spin label, 13C1-mOX063-d24, with a 13C isotope as the radical center. Due to the resolved hyperfine splitting, the spectrum is sufficiently broadened to permit DEER-based experiments at Q-band spectrometers. Additionally, this new label can be incorporated orthogonally with Cu(II)-based protein label. The orthogonal labeling scheme enables DEER distance measurement at X-band frequencies. Overall, the new trityl label allows for DEER-based distance measurements that complement existing TAM-label DQC and RIDME experiments.
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Affiliation(s)
- Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Martin Poncelet
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, WV 26506, United States
| | - Hannah Hunter
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, WV 26506, United States; C. Eugene Bennett Department of Chemistry West Virginia University, Morgantown, WV 26506, United States.
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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8
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Moore W, Huffman JL, Driesschaert B, Eaton SS, Eaton GR. Impact of Chlorine Substitution on Electron Spin Relaxation of a Trityl Radical. APPLIED MAGNETIC RESONANCE 2022; 53:797-808. [PMID: 35601029 PMCID: PMC9122340 DOI: 10.1007/s00723-021-01405-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A perchlorotriarylmethyl tricarboxylic acid radical 99% enriched in 13C at the central carbon (13C1-PTMTC) was characterized in phosphate buffered saline solution (pH = 7.2) (PBS) at ambient temperature. Samples immobilized in 1:1 PBS:glycerol or in 9:1 trehalose:sucrose were studied as a function of temperature. Isotope enrichment at C1 creates a trityl that can be used to accurately measure microscopic viscosity. Understanding of the impact of the 13C hyperfine interaction on electron spin relaxation is important for application of this trityl in oximetry and distance measurements. The anisotropic 13C1 hyperfine couplings (Ax = Ay = 24 ± 2 MHz, Az = 200 ± 1 MHz) are larger than for the related 13C1-perdeuterated Finland trityl (13C1-dFT) and the g anisotropy (gx = 2.0013, gy = 2.0016, gz = 2.0042) is slightly larger than for 13C1-dFT. The tumbling correlation times (τR) for 13C1-PTMTC are 0.20 ± 0.02 ns in PBS and 0.40 ± 0.05 ns in 3:1 PBS:glycerol, which are shorter than for 13C1-dFT in the same solutions. T1 for 13C1-PTMTC is 3.5 ± 0.5 μs in PBS and 5.3 ± 0.4 μs in 3:1 PBS:glycerol, which are shorter than for 13C1-dFT due to faster tumbling, larger anisotropy of the 13C1 hyperfine, and about 30% larger contribution from the local mode. In immobilized samples T1 for 13C1-PTMTC is similar to that for 13C1-dFT and other trityls without chlorine or 13C1 substituents, indicating that the 13C1 and Cl substituents on the phenyl rings have little impact on T1. The temperature dependence of T1 was modeled with contributions from the direct, Raman, and local mode processes. Broadening of CW linewidths of about 0.6 G in fluid solution and about 2 G in rigid lattice is attributed to unresolved 35,37Cl hyperfine couplings.
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Affiliation(s)
- Whylder Moore
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Justin L. Huffman
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance Center, West Virginia University, Morgantown, WV 26506, USA
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance Center, West Virginia University, Morgantown, WV 26506, USA
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
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9
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Abstract
Different types of spin labels are currently available for structural studies of biomolecules both in vitro and in cells using Electron Paramagnetic Resonance (EPR) and pulse dipolar spectroscopy (PDS). Each type of label has its own advantages and disadvantages, that will be addressed in this chapter. The spectroscopically distinct properties of the labels have fostered new applications of PDS aimed to simultaneously extract multiple inter-label distances on the same sample. In fact, combining different labels and choosing the optimal strategy to address their inter-label distances can increase the information content per sample, and this is pivotal to better characterize complex multi-component biomolecular systems. In this review, we provide a brief background of the spectroscopic properties of the four most common orthogonal spin labels for PDS measurements and focus on the various methods at disposal to extract homo- and hetero-label distances in proteins. We also devote a section to possible artifacts arising from channel crosstalk and provide few examples of applications in structural biology.
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10
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Biondi B, Syryamina VN, Rocchio G, Barbon A, Formaggio F, Toniolo C, Raap J, Dzuba SA. Is Cys(MTSL) the Best α-Amino Acid Residue to Electron Spin Labeling of Synthetically Accessible Peptide Molecules with Nitroxides? ACS OMEGA 2022; 7:5154-5165. [PMID: 35187331 PMCID: PMC8851612 DOI: 10.1021/acsomega.1c06227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Electron paramagnetic resonance spectroscopy, particularly its pulse technique double electron-electron resonance (DEER) (also termed PELDOR), is rapidly becoming an extremely useful tool for the experimental determination of side chain-to-side chain distances between free radicals in molecules fundamental for life, such as polypeptides. Among appropriate probes, the most popular are undoubtedly nitroxide electron spin labels. In this context, suitable biosynthetically derived, helical regions of proteins, along with synthetic peptides with amphiphilic properties and antibacterial activities, are the most extensively investigated compounds. A strict requirement for a precise distance measurement has been identified in a minimal dynamic flexibility of the two nitroxide-bearing α-amino acid side chains. To this end, in this study, we have experimentally compared in detail the side-chain mobility properties of the two currently most widely utilized residues, namely, Cys(MTSL) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, two double-labeled, chemically synthesized 20-mer peptide molecules have been adopted as appropriate templates for our investigation on the determination of the model intramolecular separations. These double-Cys(MTSL) and double-TOAC compounds are both analogues of the almost completely rigid backbone peptide ruler which we have envisaged and 3D structurally analyzed as our original, unlabeled compound. Here, we have clearly found that the TOAC side-chain labels are largely more 3D structurally restricted than the MTSL labels. From this result, we conclude that the TOAC residue offers more precise information than the Cys(MTSL) residue on the side chain-to-side chain distance distribution in synthetically accessible peptide molecules.
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Affiliation(s)
- Barbara Biondi
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Victoria N. Syryamina
- Institute
of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
| | - Gabriele Rocchio
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Antonio Barbon
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Claudio Toniolo
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Jan Raap
- Leiden
Institute of Chemistry, Gorlaeus Laboratories,
Leiden University, 2300 RA Leiden, The Netherlands
| | - Sergei A. Dzuba
- Institute
of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
- Department
of Physics, Novosibirsk State University, 630090 Novosibirsk, Russian Federation
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11
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Concilio MG, Kuprov I, Frydman L. J-Driven dynamic nuclear polarization for sensitizing high field solution state NMR. Phys Chem Chem Phys 2022; 24:2118-2125. [PMID: 35024715 DOI: 10.1039/d1cp04186j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Dynamic nuclear polarization (DNP) is widely used to enhance solid state nuclear magnetic resonance (NMR) sensitivity. Its efficiency as a generic signal-enhancing approach for liquid state NMR, however, decays rapidly with magnetic field B0, unless mediated by scalar interactions arising only in exceptional cases. This has prevented a more widespread use of DNP in structural and dynamical solution NMR analyses. This study introduces a potential solution to this problem, relying on biradicals with exchange couplings Jex of the order of the electron Larmor frequency ωE. Numerical and analytical calculations show that in such Jex ≈ ±ωE cases a phenomenon akin to that occurring in chemically induced DNP (CIDNP) happens, leading to different relaxation rates for the biradical singlet and triplet states which are hyperfine-coupled to the nuclear α or β states. Microwave irradiation can then generate a transient nuclear polarization build-up with high efficiency, at all magnetic fields that are relevant in contemporary NMR, and for all rotational diffusion correlation times that occur in small- and medium-sized molecules in conventional solvents.
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Affiliation(s)
- Maria Grazia Concilio
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton, UK
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel. .,National High Magnetic Field Laboratory, Tallahassee, Florida, USA
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12
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Ivanov MY, Surovtsev NV, Fedin MV. Ionic liquid glasses: properties and applications. RUSSIAN CHEMICAL REVIEWS 2022. [DOI: 10.1070/rcr5031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Moore W, Yao R, Liu Y, Eaton SS, Eaton GR. Spin-spin interaction and relaxation in two trityl-nitroxide diradicals. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 332:107078. [PMID: 34649176 PMCID: PMC8592039 DOI: 10.1016/j.jmr.2021.107078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 05/11/2023]
Abstract
Trityl-nitroxides show substantial promise as polarizing agents in solid state dynamic nuclear polarization. To optimize performance it is important to understand the impact of spin-spin interactions on relaxation times of the diradicals. CW spectra and electron spin relaxation were measured for two trityl-nitroxides that differ in the substituents on the amide linker and have different strengths of the exchange interaction J. Analysis of the EPR spectra in terms of overlapping AB spin-spin splitting patterns explains the impact of J on various regions of the spectra. Even modest values of J are large relative to the separation between trityl and nitroxide resonances for some nitrogen nuclear spin state. Two conformations for each diradical were observed in CW spectra in fluid solution at X-band and Q-band. For one diradical J = 15 G (83%) and 5 G (17%) at 293 K, and J = 27 G (67%) and 3 G (33%) with interspin distances of 16 Å and 12 Å, respectively, at 80 K. For the second diradical the exchange interaction is stronger: the two conformations in fluid solution at 293 K had J = 113 G (67%) and 59 G (33%) and at 80 K the value of J was 43 G and there were two conformations with interspin distances of 13 and 11.5 Å. The observation of two conformations for each diradical, with different values of J, demonstrates the dependence of their exchange interactions on through-bond orbital interactions. X-band values of spin relaxation rates 1/T1 and 1/Tm at 80 to 120 K for the trityl-nitroxides are similar to values for nitroxide mono-radicals, and faster than for trityl radicals. These observations show that even for a relatively small value of J, the nitroxide is very effective in enhancing the relaxation of the more slowly relaxing trityl.
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Affiliation(s)
- Whylder Moore
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, United States
| | - Ru Yao
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, PR China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, PR China.
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, United States
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, United States.
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14
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Casto J, Mandato A, Saxena S. dHis-troying Barriers: Deuteration Provides a Pathway to Increase Sensitivity and Accessible Distances for Cu 2+ Labels. J Phys Chem Lett 2021; 12:4681-4685. [PMID: 33979151 DOI: 10.1021/acs.jpclett.1c01002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recently, site-directed Cu2+ labeling has emerged as an incisive biophysical tool to directly report on distance constraints that pertain to the structure, conformational transitions, and dynamics of proteins and nucleic acids. However, short phase memory times inherent to the Cu2+ labels limit measurable distances to 4-5 nm. In this work we systematically examine different methods to dampen electron-nuclear and electron-electron coupled interactions to decrease rapid relaxation. We show that using Cu2+ spin concentrations up to ca. 800 μM has an invariant effect on relaxation and that increasing the cryoprotectant concentration reduces contributions of solvent protons to relaxation. On the other hand, the deuteration of protein and solvent dramatically increases the duration of the dipolar modulated signal by over 6-fold to 32 μs. Based on this increase in signal longevity, distances up to 9 nm and beyond can potentially be measured with Cu2+ labels.
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Affiliation(s)
- Joshua Casto
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alysia Mandato
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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15
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Gizatullin B, Mattea C, Stapf S. Molecular Dynamics in Ionic Liquid/Radical Systems. J Phys Chem B 2021; 125:4850-4862. [PMID: 33930266 DOI: 10.1021/acs.jpcb.1c02118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular dynamics of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethyl sulfonyl)imide (Emim-Tf2N) with either of the four organic stable radicals, TEMPO, 4-benzoyloxy-TEMPO, BDPA, and DPPH, is studied by using Nuclear Magnetic Resonance (NMR) and Dynamic Nuclear Polarization (DNP). In complex fluids at ambient temperature, NMR signal enhancement by DNP is frequently obtained by a combination of several mechanisms, where the Overhauser effect and solid effect are the most common. Understanding the interactions of free radicals with ionic liquid molecules is of particular significance due to their complex dynamics in these systems, influencing the properties of the ion-radical interaction. A combined analysis of EPR, DNP, and NMR relaxation dispersion is carried out for cations and anions containing, respectively, the NMR active nuclei 1H or 19F. Depending on the size and the chemical properties of the radical, different interaction processes are distinguished, namely, the Overhauser effect and solid effect, driven by dominating dipolar or scalar interactions. The resulting NMR relaxation dispersion is decomposed into rotational and translational contributions, allowing the identification of the corresponding correlation times of motion and interactions. The influence of electron relaxation time and electron-nuclear spin hyperfine coupling is discussed.
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Affiliation(s)
- Bulat Gizatullin
- FG Technische Physik II/Polymerphysik, Technische Universität Ilmenau, D-98684 Ilmenau, Germany
| | - Carlos Mattea
- FG Technische Physik II/Polymerphysik, Technische Universität Ilmenau, D-98684 Ilmenau, Germany
| | - Siegfried Stapf
- FG Technische Physik II/Polymerphysik, Technische Universität Ilmenau, D-98684 Ilmenau, Germany
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16
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Hasanbasri Z, Singewald K, Gluth TD, Driesschaert B, Saxena S. Cleavage-Resistant Protein Labeling With Hydrophilic Trityl Enables Distance Measurements In-Cell. J Phys Chem B 2021; 125:5265-5274. [PMID: 33983738 DOI: 10.1021/acs.jpcb.1c02371] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sensitive in-cell distance measurements in proteins using pulsed-electron spin resonance (ESR) require reduction-resistant and cleavage-resistant spin labels. Among the reduction-resistant moieties, the hydrophilic trityl core known as OX063 is promising due to its long phase-memory relaxation time (Tm). This property leads to a sufficiently intense ESR signal for reliable distance measurements. Furthermore, the Tm of OX063 remains sufficiently long at higher temperatures, opening the possibility for measurements at temperatures above 50 K. In this work, we synthesized deuterated OX063 with a maleimide linker (mOX063-d24). We show that the combination of the hydrophilicity of the label and the maleimide linker enables high protein labeling that is cleavage-resistant in-cells. Distance measurements performed at 150 K using this label are more sensitive than the measurements at 80 K. The sensitivity gain is due to the significantly short longitudinal relaxation time (T1) at higher temperatures, which enables more data collection per unit of time. In addition to in vitro experiments, we perform distance measurements in Xenopus laevis oocytes. Interestingly, the Tm of mOX063-d24 is sufficiently long even in the crowded environment of the cell, leading to signals of appreciable intensity. Overall, mOX063-d24 provides highly sensitive distance measurements both in vitro and in-cells.
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Affiliation(s)
- Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Teresa D Gluth
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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17
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Ketter S, Gopinath A, Rogozhnikova O, Trukhin D, Tormyshev VM, Bagryanskaya EG, Joseph B. In Situ Labeling and Distance Measurements of Membrane Proteins in E. coli Using Finland and OX063 Trityl Labels. Chemistry 2021; 27:2299-2304. [PMID: 33197077 PMCID: PMC7898545 DOI: 10.1002/chem.202004606] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/13/2020] [Indexed: 01/03/2023]
Abstract
In situ investigation of membrane proteins is a challenging task. Previously we demonstrated that nitroxide labels combined with pulsed ESR spectroscopy is a promising tool for this purpose. However, the nitroxide labels suffer from poor stability, high background labeling, and low sensitivity. Here we show that Finland (FTAM) and OX063 based labels enable labeling of the cobalamin transporter BtuB and BamA, the central component of the β-barrel assembly machinery (BAM) complex, in E coli. Compared to the methanethiosulfonate spin label (MTSL), trityl labels eliminated the background signals and enabled specific in situ labeling of the proteins with high efficiency. The OX063 labels show a long phase memory time (TM ) of ≈5 μs. All the trityls enabled distance measurements between BtuB and an orthogonally labeled substrate with high selectivity and sensitivity down to a few μm concentration. Our data corroborate the BtuB and BamA conformations in the cellular environment of E. coli.
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Affiliation(s)
- Sophie Ketter
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
| | - Aathira Gopinath
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
| | - Olga Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Dmitrii Trukhin
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Victor M. Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Elena G. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Benesh Joseph
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
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18
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Poncelet M, Driesschaert B. A 13 C-Labeled Triarylmethyl Radical as an EPR Spin Probe Highly Sensitive to Molecular Tumbling. Angew Chem Int Ed Engl 2020; 59:16451-16454. [PMID: 32542924 PMCID: PMC7901239 DOI: 10.1002/anie.202006591] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 12/21/2022]
Abstract
A stable triarylmethyl spin probe whose electron paramagnetic resonance (EPR) spectrum is highly sensitive to molecular tumbling is reported. The strong anisotropy of the hyperfine coupling tensor with the central carbon of a 13 C1 -labeled triarylmethyl radical enables the measurement of the probe rotational correlation time with applications to measure microviscosity and molecular dynamics.
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Affiliation(s)
- Martin Poncelet
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown WV, 26506, USA
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown WV, 26506, USA
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown WV, 26506, USA
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown WV, 26506, USA
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19
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Moore W, McPeak JE, Poncelet M, Driesschaert B, Eaton SS, Eaton GR. 13C isotope enrichment of the central trityl carbon decreases fluid solution electron spin relaxation times. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 318:106797. [PMID: 32769018 PMCID: PMC7492462 DOI: 10.1016/j.jmr.2020.106797] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 05/19/2023]
Abstract
Electron spin relaxation times for perdeuterated Finland trityl 99% enriched in 13C at the central carbon (13C1-dFT) were measured in phosphate buffered saline (pH = 7.2) (PBS) solution at X-band. The anisotropic 13C1 hyperfine (Ax = Ay = 18 ± 2, Az = 162 ± 1 MHz) and g values (2.0033, 2.0032, 2.00275) in a 9:1 trehalose:sucrose glass at 293 K and in 1:1 PBS:glycerol at 160 K were determined by simulation of spectra at X-band and Q-band. In PBS at room temperature the tumbling correlation time, τR, is 0.29 ± 0.02 ns. The linewidths are broadened by incomplete motional averaging of the hyperfine anisotropy and T2 is 0.13 ± 0.02 µs, which is shorter than the T2 ~ 3.8 µs for natural abundance dFT at low concentration in PBS. T1 for 13C1-dFT in deoxygenated PBS is 5.9 ± 0.5 µs, which is shorter than for natural abundance dFT in PBS (16 µs) but much longer than in air-saturated solution (0.48 ± 0.04 µs). The tumbling dependence of T1 in PBS, 3:1 PBS:glycerol (τR = 0.80 ± 0.05 ns, T1 = 9.7 ± 0.7 µs) and 1:1 PBS:glycerol (τR = 3.4 ± 0.3 ns, T1 = 12.0 ± 1.0 µs) was modeled with contributions to the relaxation predominantly from modulation of hyperfine anisotropy and a local mode. The 1/T1 rate for the 1% 12C1-dFT in the predominantly 13C labeled sample is about a factor of 6 more strongly concentration dependent than for natural abundance 12C1-trityl, which reflects the importance of Heisenberg exchange with molecules with different resonance frequencies and faster relaxation rates. In glassy matrices at 160 K, T1 and Tm for 13C1-dFT are in good agreement with previously reported values for 12C1-dFT consistent with the expectation that modulation of nuclear hyperfine does not contribute to electron spin relaxation in a rigid lattice.
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Affiliation(s)
- Whylder Moore
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Joseph E McPeak
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Martin Poncelet
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance Center, West Virginia University, Morgantown, WV 26506, USA
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance Center, West Virginia University, Morgantown, WV 26506, USA
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA.
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20
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Poncelet M, Driesschaert B. A
13
C‐Labeled Triarylmethyl Radical as an EPR Spin Probe Highly Sensitive to Molecular Tumbling. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Martin Poncelet
- Department of Pharmaceutical SciencesSchool of PharmacyWest Virginia University Morgantown WV 26506 USA
- In Vivo Multifunctional Magnetic Resonance CenterRobert C. Byrd Health Sciences CenterWest Virginia University Morgantown WV 26506 USA
| | - Benoit Driesschaert
- Department of Pharmaceutical SciencesSchool of PharmacyWest Virginia University Morgantown WV 26506 USA
- In Vivo Multifunctional Magnetic Resonance CenterRobert C. Byrd Health Sciences CenterWest Virginia University Morgantown WV 26506 USA
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21
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Tormyshev VM, Chubarov AS, Krumkacheva OA, Trukhin DV, Rogozhnikova OY, Spitsyna AS, Kuzhelev AA, Koval VV, Fedin MV, Godovikova TS, Bowman MK, Bagryanskaya EG. Methanethiosulfonate Derivative of OX063 Trityl: A Promising and Efficient Reagent for Side-Directed Spin Labeling of Proteins. Chemistry 2020; 26:2705-2712. [PMID: 31851392 DOI: 10.1002/chem.201904587] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/30/2019] [Indexed: 12/20/2022]
Abstract
Trityl radicals (TAMs) have recently appeared as an alternative source of spin labels for measuring long distances in biological systems. Finland trityl radical (FTAM) served as the basis for this new generation of spin labels, but FTAM is rather lipophilic and susceptible to self-aggregation, noncovalent binding with lipophilic sites of proteins, and noncovalent docking at the termini of duplex DNA. In this paper the very hydrophilic OX063 TAM with very low toxicity and little tendency for aggregation is used as the basis for a spin label. Human serum albumin (HSA) labeled with OX063 has an intense narrow line typical of TAM radicals in solution, whereas HSA labeled with FTAM shows broad lines and extensive aggregation. In pulse EPR measurements, the measured phase memory time TM for HSA labeled with OX063 is 6.3 μs at 50 K, the longest yet obtained with a TAM-based spin label. The lowered lipophilicity also decreases side products in the labeling reaction.
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Affiliation(s)
- Victor M Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Alexey S Chubarov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Pr. Lavrentjeva 8, Novosibirsk, 630090, Russia
| | - Olesya A Krumkacheva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk, 630090, Russia
| | - Dmitry V Trukhin
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Olga Yu Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Anna S Spitsyna
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Andrey A Kuzhelev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Vladimir V Koval
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Pr. Lavrentjeva 8, Novosibirsk, 630090, Russia
| | - Matvey V Fedin
- International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk, 630090, Russia
| | - Tatyana S Godovikova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Pr. Lavrentjeva 8, Novosibirsk, 630090, Russia
| | - Michael K Bowman
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama, 35487-0336, USA
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
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22
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Kuzhelev AA, Tormyshev VM, Plyusnin VF, Rogozhnikova OY, Edeleva MV, Veber SL, Bagryanskaya EG. Photochemistry of tris(2,3,5,6-tetrathiaaryl)methyl radicals in various solutions. Phys Chem Chem Phys 2020; 22:1019-1026. [DOI: 10.1039/c9cp06213k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A detailed mechanism of TAM photolysis was studied and includes photoionization of the TAM radical with the formation of carbocation and further conversion of the carbocation under aerobic conditions into quinone-methide and under anaerobic conditions supposedly into an aromatic carbene.
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Affiliation(s)
- Andrey A. Kuzhelev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- Novosibirsk 630090
- Russia
| | - Victor M. Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- Novosibirsk 630090
- Russia
- Novosibirsk State University
- Novosibirsk 630090
| | - Victor F. Plyusnin
- Novosibirsk State University
- Novosibirsk 630090
- Russia
- Voevodsky Institute of Chemical Kinetics and Combustion
- SB RAS
| | - Olga Yu. Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- Novosibirsk 630090
- Russia
| | - Mariya V. Edeleva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- Novosibirsk 630090
- Russia
- Novosibirsk State University
- Novosibirsk 630090
| | - Sergey L. Veber
- Novosibirsk State University
- Novosibirsk 630090
- Russia
- International Tomography Center SB RAS
- Novosibirsk 630090
| | - Elena G. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- Novosibirsk 630090
- Russia
- Novosibirsk State University
- Novosibirsk 630090
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23
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Shi Y, Eaton SS, Eaton GR. Rapid-scan EPR imaging of a phantom comprised of species with different linewidths and relaxation times. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 308:106593. [PMID: 31520789 PMCID: PMC6829054 DOI: 10.1016/j.jmr.2019.106593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
As a demonstration of the application of rapid-scan EPR to imaging at low frequency and magnetic field, a multi-compartment phantom containing six different samples was imaged. The samples were nitroxide radicals, trityl (substituted triarylmethyl) radicals, and the oxygen-sensitive solid lithium phthalocyanine (LiPc), all of which are useful for in vivo imaging. The 2D spectral-spatial image demonstration was performed at 250 MHz, with samples in sealed tubes of various sizes arranged in a 3D-printed plastic holder. Maximum gradients of 10 G/cm gave a spatial resolution of about 0.1 mm for the narrow trityl and LiPc signals and about 1 mm for the nitroxide. The importance of proper selection of resonator bandwidth and scan rate for obtaining accurate linewidth information is demonstrated for a case in which the phantom is composed of species with signal linewidths and relaxation times that differ by more than a factor of 10.
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Affiliation(s)
- Yilin Shi
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA.
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24
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Site Selective and Efficient Spin Labeling of Proteins with a Maleimide-Functionalized Trityl Radical for Pulsed Dipolar EPR Spectroscopy. Molecules 2019; 24:molecules24152735. [PMID: 31357628 PMCID: PMC6696014 DOI: 10.3390/molecules24152735] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 01/18/2023] Open
Abstract
Pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) in combination with site-directed spin labeling (SDSL) of proteins and oligonucleotides is a powerful tool in structural biology. Instead of using the commonly employed gem-dimethyl-nitroxide labels, triarylmethyl (trityl) spin labels enable such studies at room temperature, within the cells and with single-frequency electron paramagnetic resonance (EPR) experiments. However, it has been repeatedly reported that labeling of proteins with trityl radicals led to low labeling efficiencies, unspecific labeling and label aggregation. Therefore, this work introduces the synthesis and characterization of a maleimide-functionalized trityl spin label and its corresponding labeling protocol for cysteine residues in proteins. The label is highly cysteine-selective, provides high labeling efficiencies and outperforms the previously employed methanethiosulfonate-functionalized trityl label. Finally, the new label is successfully tested in PDS measurements on a set of doubly labeled Yersinia outer protein O (YopO) mutants.
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25
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Qu Y, Li Y, Tan X, Zhai W, Han G, Hou J, Liu G, Song Y, Liu Y. Synthesis and Characterization of Hydrophilic Trityl Radical TFO for Biomedical and Biophysical Applications. Chemistry 2019; 25:7888-7895. [PMID: 30972843 DOI: 10.1002/chem.201900262] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Indexed: 12/18/2022]
Abstract
Tetrathiatriarylmethyl (TAM, trityl) radicals have found wide applications as spin probes/labels for EPR spectroscopy and imaging, and as polarizing agents for dynamic nuclear polarization. The high hydrophilicity of TAM radicals is essential for their biomedical applications. However, the synthesis of hydrophilic TAM radicals (e.g., OX063) is extremely challenging and has only been reported in the patent literature, to date. Herein, an efficient synthesis of a highly water-soluble TAM radical bis(8-carboxyl-2,2,6,6-tetramethylbenzo[1,2-d:4,5-d']bis([1,3]dithiol-4-yl)-mono-(8-carboxyl-2,2,6,6-tetrakis(2-hydroxyethyl)benzo[1,2-d:4,5-d']bis([1,3]dithiol-4-yl)methyl (TFO), which contains four additional hydroxylethyl groups, relative to the Finland trityl radical CT-03, is reported. Similar to OX063, TFO exhibits excellent properties, including high water solubility in phosphate buffer, low log P, low pKa , long relaxation times, and negligible binding with bovine serum albumin. On the other hand, TFO has a sharper EPR line and higher O2 sensitivity than those of OX063. Therefore, in combination with its facile synthesis, TFO should find wide applications in magnetic resonance related fields and this synthetic approach would shed new light on the synthesis of other hydrophilic TAM radicals.
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Affiliation(s)
- Yuying Qu
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Yingchun Li
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Xiaoli Tan
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Weixiang Zhai
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Guifang Han
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Jingli Hou
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, P.R. China
| | - Yuguang Song
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
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26
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Fleck N, Hett T, Brode J, Meyer A, Richert S, Schiemann O. C–C Cross-Coupling Reactions of Trityl Radicals: Spin Density Delocalization, Exchange Coupling, and a Spin Label. J Org Chem 2019; 84:3293-3303. [DOI: 10.1021/acs.joc.8b03229] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Nico Fleck
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Tobias Hett
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Jonas Brode
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Andreas Meyer
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Sabine Richert
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegelerstr. 12, 53115 Bonn, Germany
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27
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McPeak JE, Quine RW, Eaton SS, Eaton GR. An x-band continuous wave saturation recovery electron paramagnetic resonance spectrometer based on an arbitrary waveform generator. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:024102. [PMID: 30831717 PMCID: PMC6364795 DOI: 10.1063/1.5043316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 12/20/2018] [Indexed: 05/29/2023]
Abstract
An X-band (ca. 9-10 GHz) continuous wave saturation recovery spectrometer to measure electron spin-lattice relaxation (T1) was designed around an arbitrary waveform generator (AWG). The AWG is the microwave source and is used for timing of microwave pulses, generation of control signals, and digitizer triggering. Use of the AWG substantially simplifies the hardware in the bridge relative to that in conventional spectrometers and decreases the footprint. The bridge includes selectable paths with different power amplifications to permit experiments requiring hundreds of milliwatts to fractions of nanowatts for the pump and observe periods. The signal is detected with either a single or quadrature-output double balanced mixer. The system can operate with reflection or crossed-loop resonators. The source noise from the AWG was decreased by addition of a Wenzel high-stability clock. The source is sufficiently stable that automatic frequency control is not needed. The spectrometer was tested with samples that contained 1 × 1015 to 8 × 1017 spins and have T1 between a few hundred ns and hundreds of μs. Excellent signal-to-noise ratio was obtained with acquisition times of 2-90 s. Signal-to-noise performance is similar to that of a conventional saturation recovery spectrometer with a solid-state source. The stability and data reproducibility are better than with conventional sources. With replacement of frequency-sensitive components, this spectrometer can be used to perform saturation recovery measurements at any frequency within the range of the AWG.
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Affiliation(s)
- Joseph E. McPeak
- Department of Chemistry and Biochemistry,
University of Denver, Denver, Colorado 80210, USA
| | - Richard W. Quine
- Ritchie School of Engineering and Computer
Science, University of Denver, Denver, Colorado 80210,
USA
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry,
University of Denver, Denver, Colorado 80210, USA
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry,
University of Denver, Denver, Colorado 80210, USA
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28
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Wu Y, Zhou J, Nelson JN, Young RM, Krzyaniak MD, Wasielewski MR. Covalent Radical Pairs as Spin Qubits: Influence of Rapid Electron Motion between Two Equivalent Sites on Spin Coherence. J Am Chem Soc 2018; 140:13011-13021. [DOI: 10.1021/jacs.8b08105] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yilei Wu
- Department of Chemistry and Institute for Sustainability and Energy, Northwestern Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Jiawang Zhou
- Department of Chemistry and Institute for Sustainability and Energy, Northwestern Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Jordan N. Nelson
- Department of Chemistry and Institute for Sustainability and Energy, Northwestern Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department of Chemistry and Institute for Sustainability and Energy, Northwestern Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Matthew D. Krzyaniak
- Department of Chemistry and Institute for Sustainability and Energy, Northwestern Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry and Institute for Sustainability and Energy, Northwestern Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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29
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Kuzhelev AA, Krumkacheva OA, Ivanov MY, Prikhod'ko SA, Adonin NY, Tormyshev VM, Bowman MK, Fedin MV, Bagryanskaya EG. Pulse EPR of Triarylmethyl Probes: A New Approach for the Investigation of Molecular Motions in Soft Matter. J Phys Chem B 2018; 122:8624-8630. [PMID: 30137993 DOI: 10.1021/acs.jpcb.8b07714] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triarylmethyl (TAM) radicals have become widely used free radicals in the past few years. Their electron spins have long relaxation times and narrow electron paramagnetic resonance (EPR) lines, which make them an important class of probes and tags in biological applications and materials science. In this work, we propose a new approach to characterize librations by means of TAM radicals. The temperature dependence of motional parameter ⟨α2⟩τc, where ⟨α2⟩ is the mean-squared amplitude of librations and τc is their characteristic time, is obtained by comparison of the 1/ Tm phase-relaxation rates at X- and Q-band EPR frequencies. We study three soft matrixes, viz., glassy trehalose and two ionic liquids, using TAMs with optimized relaxation properties OX063D and a dodeca- n-butyl homologue of Finland trityl (DBT). The motional parameters ⟨α2⟩τc obtained using TAMs are in excellent agreement with those obtained by means of nitroxide radicals. At the same time, the new TAM-based approach has (1) greater sensitivity due to the narrower EPR spectrum and (2) greater measuring accuracy and broader temperature range due to longer relaxation times. The developed approach may be fruitfully implemented to probe low-temperature molecular motions of TAM-labeled biopolymers, membrane systems, polymers, molecules in glassy media, and ionic liquids.
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Affiliation(s)
- Andrey A Kuzhelev
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS , Novosibirsk 630090 , Russia.,International Tomography Center SB RAS , Novosibirsk 630090 , Russia.,Novosibirsk State University , Novosibirsk 630090 , Russia
| | - Olesya A Krumkacheva
- International Tomography Center SB RAS , Novosibirsk 630090 , Russia.,Novosibirsk State University , Novosibirsk 630090 , Russia
| | - Mikhail Yu Ivanov
- International Tomography Center SB RAS , Novosibirsk 630090 , Russia.,Novosibirsk State University , Novosibirsk 630090 , Russia
| | | | - Nicolay Yu Adonin
- Boreskov Institute of Catalysis SB RAS , Novosibirsk 630090 , Russia
| | - Victor M Tormyshev
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS , Novosibirsk 630090 , Russia.,Novosibirsk State University , Novosibirsk 630090 , Russia
| | - Michael K Bowman
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS , Novosibirsk 630090 , Russia.,University of Alabama , Tuscaloosa , Alabama 35487-0336 , United States
| | - Matvey V Fedin
- International Tomography Center SB RAS , Novosibirsk 630090 , Russia.,Novosibirsk State University , Novosibirsk 630090 , Russia
| | - Elena G Bagryanskaya
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS , Novosibirsk 630090 , Russia.,Novosibirsk State University , Novosibirsk 630090 , Russia
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30
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Wilson CB, Aronson S, Clayton JA, Glaser SJ, Han S, Sherwin MS. Multi-step phase-cycling in a free-electron laser-powered pulsed electron paramagnetic resonance spectrometer. Phys Chem Chem Phys 2018; 20:18097-18109. [PMID: 29938285 DOI: 10.1039/c8cp01876f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance (EPR) is a powerful tool for research in chemistry, biology, physics and materials science, which can benefit significantly from moving to frequencies above 100 GHz. In pulsed EPR spectrometers driven by powerful sub-THz oscillators, such as the free electron laser (FEL)-powered EPR spectrometer at UCSB, control of the duration, power and relative phases of the pulses in a sequence must be performed at the frequency and power level of the oscillator. Here we report on the implementation of an all-quasioptical four-step phase cycling procedure carried out directly at the kW power level of the 240 GHz pulses used in the FEL-powered EPR spectrometer. Phase shifts are introduced by modifying the optical path length of a 240 GHz pulse with precision-machined dielectric plates in a procedure we call phase cycling with optomechanical phase shifters (POPS), while numerical receiver phase cycling is implemented in post-processing. The POPS scheme was successfully used to reduce experimental dead times, enabling pulsed EPR of fast-relaxing spin systems such as gadolinium complexes at temperatures above 190 K. Coherence transfer pathway selection with POPS was used to perform spin echo relaxation experiments to measure the phase memory time of P1 centers in diamond in the presence of a strong unwanted FID signal in the background. The large excitation bandwidth of FEL-EPR, together with phase cycling, enabled the quantitative measurement of instantaneous electron spectral diffusion, from which the P1 center concentration was estimated to within 10%. Finally, phase cycling enabled saturation-recovery measurements of T1 in a trityl-water solution at room temperature - the first FEL-EPR measurement of electron T1.
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Affiliation(s)
- C Blake Wilson
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California, USA.
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31
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Kuzhelev AA, Krumkacheva OA, Shevelev GY, Yulikov M, Fedin MV, Bagryanskaya EG. Room-temperature distance measurements using RIDME and the orthogonal spin labels trityl/nitroxide. Phys Chem Chem Phys 2018; 20:10224-10230. [PMID: 29594278 DOI: 10.1039/c8cp01093e] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance (EPR) based nanometer distance measurements at ambient temperatures are of particular interest for structural biology applications. The nitroxide spin labels commonly used in EPR reveal relatively short transverse relaxation under these conditions, which limits their use for detecting static dipolar interactions. At the same time, the longitudinal relaxation of nitroxide spin labels is still long enough to allow using them as 'pumped' species in the relaxation induced dipolar modulation enhancement (RIDME) experiment where the detection is carried out on the slower relaxing triarylmethyl (TAM) spin labels. In the present study, we report the first demonstration of room-temperature RIDME distance measurements in nucleic acids using TAM as the slow-relaxing detected species and traditional nitroxide as the fast-relaxing partner spin. Two types of immobilizers, glassy trehalose and the modified silica gel Nucleosil, were used for immobilization of the spin-labeled biomolecules. The room-temperature RIDME-based distance distributions are in good agreement with those measured at 80 K by other techniques. Room-temperature RIDME on the spin pairs trityl/nitroxide may become a useful method for the structural characterization of biomacromolecules and biomolecular complexes at near physiological temperatures.
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Affiliation(s)
- Andrey A Kuzhelev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.
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32
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Buchanan LA, Rinard GA, Quine RW, Eaton SS, Eaton GR. Tabletop 700 MHz electron paramagnetic resonance imaging spectrometer. CONCEPTS IN MAGNETIC RESONANCE. PART B, MAGNETIC RESONANCE ENGINEERING 2018; 48B:e21384. [PMID: 30804714 PMCID: PMC6386469 DOI: 10.1002/cmr.b.21384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/11/2018] [Indexed: 06/05/2023]
Abstract
Low frequency electron paramagnetic resonance imaging is a powerful tool to non-invasively measure the physiological status of tumors. Here, we report on the design and functionality of a rapid scan and pulse table-top imaging spectrometer based around an arbitrary waveform generator and 25mm cross-loop resonator operating at 700 MHz. Two and four-dimensional rapid scan spectral-spatial images are presented. This table-top imager is a prototype for future pre-clinical imagers.
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Affiliation(s)
- Laura A. Buchanan
- Department of Chemistry and Biochemistry and Center for EPR Imaging of In Vivo Physiology, University of
Denver, Denver, CO 80210
| | - George A. Rinard
- School of Engineering and Computer Science and Center for EPR Imaging of In Vivo Physiology, University of
Denver, Denver, CO 80210
| | - Richard W. Quine
- School of Engineering and Computer Science and Center for EPR Imaging of In Vivo Physiology, University of
Denver, Denver, CO 80210
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry and Center for EPR Imaging of In Vivo Physiology, University of
Denver, Denver, CO 80210
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry and Center for EPR Imaging of In Vivo Physiology, University of
Denver, Denver, CO 80210
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33
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Jassoy JJ, Meyer A, Spicher S, Wuebben C, Schiemann O. Synthesis of Nanometer Sized Bis- and Tris-trityl Model Compounds with Different Extent of Spin-Spin Coupling. Molecules 2018; 23:E682. [PMID: 29562622 PMCID: PMC6017437 DOI: 10.3390/molecules23030682] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 12/29/2022] Open
Abstract
Tris(2,3,5,6-tetrathiaaryl)methyl radicals, so-called trityl radicals, are emerging as spin labels for distance measurements in biological systems based on Electron Paramagnetic Resonance (EPR). Here, the synthesis and characterization of rigid model systems carrying either two or three trityl moieties is reported. The monofunctionalized trityl radicals are connected to the molecular bridging scaffold via an esterification reaction employing the Mukaiyama reagent 2-chloro-methylpyridinium iodide. The bis- and tris-trityl compounds exhibit different inter-spin distances, strength of electron-electron exchange and dipolar coupling and can give rise to multi-spin effects. They are to serve as benchmark systems in comparing EPR distance measurement methods.
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Affiliation(s)
- J Jacques Jassoy
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Andreas Meyer
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Sebastian Spicher
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Christine Wuebben
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
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34
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Elewa M, Maltar-Strmečki N, Said MM, El Shihawy HA, El-Sadek M, Frank J, Drescher S, Drescher M, Mäder K, Hinderberger D, Imming P. Synthesis and EPR-spectroscopic characterization of the perchlorotriarylmethyl tricarboxylic acid radical (PTMTC) and its 13C labelled analogue (13C-PTMTC). Phys Chem Chem Phys 2018; 19:6688-6697. [PMID: 28210718 DOI: 10.1039/c6cp07200c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A hydrophilic tris(tetrachlorotriaryl)methyl (tetrachloro-TAM) radical labelled 50% with 13C at the central carbon atom was prepared. The mixture of isotopologue radicals was characterised by continuous wave and pulsed X-band electron paramagnetic spectroscopy (EPS). For the pharmaceutical and medical applications planned, the quantitative influence of oxygen, viscosity, temperature and pH on EPR line widths was studied in aqueous buffer, DMSO, water-methanol and water-glycerol mixtures. Under in vivo conditions, pH can be disregarded. There is a clear oxygen dependence of the width of the 12C isotopologue single EPR line in aqueous solutions while changes in rotational motion (viscosity) are observable only in the doublet lines of the central carbon of the 13C isotopologue. The tetrachloro-TAM proved to be very stable as a solid. Its thermal decay was determined quantitatively by thermal annealing. Towards ascorbic acid as a reducing agent and towards an oocyte cell extract it had a half-life of approx. 60 and 10 min. Thus for in vivo applications, 50% 13C tetrachloro-TAMs are suitable for selective and simultaneous oxygen and macroviscosity measurements in a formulation, e.g. nanocapsules.
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Affiliation(s)
- Marwa Elewa
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle, Germany. and Faculty of Pharmacy, Suez Canal University, P.O. 41522, Ismailia, Egypt
| | - Nadica Maltar-Strmečki
- Institut für Chemie, Physikalische Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Germany.
| | - Mohamed M Said
- Faculty of Pharmacy, Suez Canal University, P.O. 41522, Ismailia, Egypt
| | | | | | - Juliane Frank
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle, Germany.
| | - Simon Drescher
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle, Germany.
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Karsten Mäder
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle, Germany.
| | - Dariush Hinderberger
- Institut für Chemie, Physikalische Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Germany.
| | - Peter Imming
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle, Germany.
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35
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Shi Y, Quine RW, Rinard GA, Buchanan L, Eaton SS, Eaton GR, Epel B, Seagle SW, Halpern HJ. Triarylmethyl Radical OX063d24 Oximetry: Electron Spin Relaxation at 250 MHz and RF Frequency Dependence of Relaxation and Signal-to-Noise. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 977:327-334. [PMID: 28685462 DOI: 10.1007/978-3-319-55231-6_43] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
The triarylmethyl radical OX063d24 is currently used for pulsed electron paramagnetic resonance oximetry at 250 MHz. Both 1/T 1 and 1/T 2 increase with increasing oxygen concentration. The dependence of 1/T 1 on probe concentration is smaller than for 1/T 2. To inform the selection of the optimum frequency for in vivo oximetry 1/T 1, 1/T 2 and signal-to-noise were measured as a function of frequency between 400 and 1000 MHz on a variable-frequency spectrometer with an adjustable-frequency cross-loop resonator. 1/T 1 and 1/T 2 decrease with increasing frequency and signal-to-noise increases with increasing frequency, which are all favourable for imaging at higher frequencies. However, depth of penetration of the radio frequency (RF) into an animal decreases with increasing frequency. Assuming that the RF loss in the animal to be studied determines the resonator Q, our results indicate that the optimum frequency for in vivo imaging will be determined by the desired depth of penetration in the tissue.
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Affiliation(s)
- Yilin Shi
- Department of Chemistry and Biochemistry and Center for EPR Imaging In Vivo Physiology, University of Denver, Denver, CO, 80210, USA
| | - Richard W Quine
- School of Engineering and Computer Science and Center for EPR Imaging In Vivo Physiology, University of Denver, Denver, CO, 80210, USA
| | - George A Rinard
- School of Engineering and Computer Science and Center for EPR Imaging In Vivo Physiology, University of Denver, Denver, CO, 80210, USA
| | - Laura Buchanan
- Department of Chemistry and Biochemistry and Center for EPR Imaging In Vivo Physiology, University of Denver, Denver, CO, 80210, USA
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry and Center for EPR Imaging In Vivo Physiology, University of Denver, Denver, CO, 80210, USA
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry and Center for EPR Imaging In Vivo Physiology, University of Denver, Denver, CO, 80210, USA.
| | - Boris Epel
- Department of Radiation and Cellular Oncology and Center for EPR Imaging In Vivo Physiology, University of Chicago, Chicago, IL, 60637, USA
| | - Simone Wanless Seagle
- Department of Radiation and Cellular Oncology and Center for EPR Imaging In Vivo Physiology, University of Chicago, Chicago, IL, 60637, USA
| | - Howard J Halpern
- Department of Radiation and Cellular Oncology and Center for EPR Imaging In Vivo Physiology, University of Chicago, Chicago, IL, 60637, USA
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36
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Kuzhelev A, Akhmetzyanov D, Denysenkov V, Shevelev G, Krumkacheva O, Bagryanskaya E, Prisner T. High-frequency pulsed electron–electron double resonance spectroscopy on DNA duplexes using trityl tags and shaped microwave pulses. Phys Chem Chem Phys 2018; 20:26140-26144. [DOI: 10.1039/c8cp03951h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Distances between trityl spin labels attached to DNA duplexes were determined by 180 GHz and 260 GHz PELDOR spectroscopy applying broadband pump pulse at higher frequency.
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Affiliation(s)
- A. Kuzhelev
- Novosibirsk State University
- 630090 Novosibirsk
- Russia
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- 630090 Novosibirsk
| | - D. Akhmetzyanov
- Goethe University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry
- Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
| | - V. Denysenkov
- Goethe University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry
- Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
| | - G. Shevelev
- Novosibirsk State University
- 630090 Novosibirsk
- Russia
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- 630090 Novosibirsk
| | - O. Krumkacheva
- Novosibirsk State University
- 630090 Novosibirsk
- Russia
- International Tomography Center SB RAS
- Novosibirsk
| | - E. Bagryanskaya
- Novosibirsk State University
- 630090 Novosibirsk
- Russia
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- 630090 Novosibirsk
| | - T. Prisner
- Goethe University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry
- Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
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37
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Meyer A, Jassoy JJ, Spicher S, Berndhäuser A, Schiemann O. Performance of PELDOR, RIDME, SIFTER, and DQC in measuring distances in trityl based bi- and triradicals: exchange coupling, pseudosecular coupling and multi-spin effects. Phys Chem Chem Phys 2018; 20:13858-13869. [DOI: 10.1039/c8cp01276h] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The performance of pulsed EPR methods for distance measurements is evaluated on three different trityl model systems.
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Affiliation(s)
- Andreas Meyer
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Jean Jacques Jassoy
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Sebastian Spicher
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Andreas Berndhäuser
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
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38
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Shevelev GY, Gulyak EL, Lomzov AA, Kuzhelev AA, Krumkacheva OA, Kupryushkin MS, Tormyshev VM, Fedin MV, Bagryanskaya EG, Pyshnyi DV. A Versatile Approach to Attachment of Triarylmethyl Labels to DNA for Nanoscale Structural EPR Studies at Physiological Temperatures. J Phys Chem B 2017; 122:137-143. [PMID: 29206458 DOI: 10.1021/acs.jpcb.7b10689] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Triarylmethyl (trityl, TAM) radicals are a promising class of spin labels for nanometer-scale distance measurements in biomolecules at physiological temperatures. However, to date, existing approaches to site-directed TAM labeling of DNA have been limited to label attachment at the termini of oligonucleotides, thus hindering a majority of demanded applications. Herein, we report a new versatile strategy for TAM attachment at arbitrary sites of nucleic acids. It utilizes an achiral non-nucleoside phosphoramidite monomer for automated solid-phase synthesis of oligonucleotides, which are then postsynthetically functionalized with TAM. We demonstrate a synthesis of a set of oligonucleotide complexes that are TAM-labeled at internal or terminal sites, as well as the possibility of measuring interspin distances up to ∼5-6 nm at 298 K using double quantum coherence electron paramagnetic resonance (EPR). Implementation of the developed approach strongly broadens the scope of nucleic acids and nucleoprotein complexes available for nanoscale structural EPR studies at room temperatures.
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Affiliation(s)
- Georgiy Yu Shevelev
- Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Evgeny L Gulyak
- Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Andrey A Kuzhelev
- Novosibirsk State University , Novosibirsk 630090, Russia.,N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS , Novosibirsk 630090, Russia
| | - Olesya A Krumkacheva
- Novosibirsk State University , Novosibirsk 630090, Russia.,International Tomography Center SB RAS , Novosibirsk 630090, Russia
| | - Maxim S Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- Novosibirsk State University , Novosibirsk 630090, Russia.,N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS , Novosibirsk 630090, Russia
| | - Matvey V Fedin
- Novosibirsk State University , Novosibirsk 630090, Russia.,International Tomography Center SB RAS , Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- Novosibirsk State University , Novosibirsk 630090, Russia.,International Tomography Center SB RAS , Novosibirsk 630090, Russia.,N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS , Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
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39
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Krumkacheva O, Bagryanskaya E. EPR-based distance measurements at ambient temperature. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 280:117-126. [PMID: 28579097 DOI: 10.1016/j.jmr.2017.02.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 05/24/2023]
Abstract
Pulsed dipolar (PD) EPR spectroscopy is a powerful technique allowing for distance measurements between spin labels in the range of 2.5-10.0nm. It was proposed more than 30years ago, and nowadays is widely used in biophysics and materials science. Until recently, PD EPR experiments were limited to cryogenic temperatures (T<80K). Recently, application of spin labels with long electron spin dephasing time at room temperature such as triarylmethyl radicals and nitroxides with bulky substituents at a position close to radical centers enabled measurements at room temperature and even at physiologically relevant temperatures by PD EPR as well as other approaches based on EPR (e.g., relaxation enhancement; RE). In this paper, we review the features of PD EPR and RE at ambient temperatures, in particular, requirements on electron spin phase memory time, ways of immobilization of biomolecules, the influence of a linker between the spin probe and biomolecule, and future opportunities.
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Affiliation(s)
- Olesya Krumkacheva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090, Russian Federation; International Tomography Center SB RAS, Institutskaya 3A, Novosibirsk 630090, Russian Federation.
| | - Elena Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090, Russian Federation.
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40
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Kuzhelev AA, Tormyshev VM, Rogozhnikova OY, Trukhin DV, Troitskaya TI, Strizhakov RK, Krumkacheva OA, Fedin MV, Bagryanskaya EG. Triarylmethyl Radicals: EPR Study of 13C Hyperfine Coupling Constants. Z PHYS CHEM 2017; 231:777-794. [PMID: 28539703 PMCID: PMC5439964 DOI: 10.1515/zpch-2016-0811] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Triarylmethyl (TAM) radicals are widely used in Electron Paramagnetic Resonance (EPR) spectroscopy as spin labels and in EPR imaging as spin probes for in vivo oxymetry. One of the key advantages of TAMs is extremely narrow EPR line, especially in case of deuterated analogues (~5 μT). Another advantage is their slow spin relaxation even at physiological temperatures allowing, in particular, application of pulsed dipolar EPR methods for distance measurements in biomolecules. In this paper a large series of TAM radicals and their deuterated analogues is synthesized, and corresponding spectroscopic parameters including 13C hyperfine constants are obtained for the first time. The negligible dependence of 13C hyperfine constants on solvent, as well as on structure and number of substituents at para-C atoms of aromatic rings, has been found. In addition, we have demonstrated that 13C signals at natural abundance can be employed for successful room-temperature distance measurements using Pulsed Electron Double Resonance (PELDOR or DEER).
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Affiliation(s)
- Andrey A. Kuzhelev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Victor M. Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olga Yu. Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry V. Trukhin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Tatiana I. Troitskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Rodion K. Strizhakov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Olesya A. Krumkacheva
- International Tomography Center SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Matvey V. Fedin
- International Tomography Center SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G. Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
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41
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Legenzov EA, Muralidharan S, Woodcock LB, Eaton GR, Eaton SS, Rosen GM, Kao JPY. Designing Molecular Probes To Prolong Intracellular Retention: Application to Nitroxide Spin Probes. Bioconjug Chem 2016; 27:2923-2930. [PMID: 27998079 DOI: 10.1021/acs.bioconjchem.6b00595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Targeted delivery of molecular probes into cells enables cellular imaging through optical and magnetic modalities. Probe molecules that are well retained by cells can accumulate to higher intracellular concentrations, and thus increase the signal-to-noise ratio of, and widen the temporal window for, imaging. Here we synthesize a paramagnetic spin probe bearing six ionic functional groups and show that it has long intracellular half-life (>12 h) and exceptional biostability in living cells. We demonstrate that judicious incorporation of ionic substituents on probe molecules systematically increases intracellular retention time, and should therefore be beneficial to imaging experiments.
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Affiliation(s)
- Eric A Legenzov
- Center for Biomedical Engineering & Technology, and Department of Physiology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Sukumaran Muralidharan
- Center for Biomedical Engineering & Technology, and Department of Physiology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Lukas B Woodcock
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Gerald M Rosen
- Department of Pharmaceutical Sciences, School of Pharmacy, and Center for Biomedical Engineering & Technology, School of Medicine, University of Maryland , Baltimore, Maryland 21201, United States
| | - Joseph P Y Kao
- Center for Biomedical Engineering & Technology, and Department of Physiology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
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42
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Shi Y, Quine RW, Rinard GA, Buchanan L, Eaton SS, Eaton GR, Epel B, Seagle SW, Halpern HJ. Triarylmethyl Radical: EPR Signal to Noise at Frequencies between 250 MHz and 1.5 GHz and Dependence of Relaxation on Radical and Salt Concentration and on Frequency. ACTA ACUST UNITED AC 2016; 231:923-937. [PMID: 28392627 DOI: 10.1515/zpch-2016-0813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In vivo oximetry by pulsed electron paramagnetic resonance is based on measurements of changes in electron spin relaxation rates of probe molecules, such as the triarylmethyl radicals. A series of experiments was performed at frequencies between 250 MHz and 1.5 GHz to assist in the selection of an optimum frequency for oximetry. Electron spin relaxation rates for the triarylmethyl radical OX063 as a function of radical concentration, salt concentration, and resonance frequency were measured by electron spin echo 2-pulse decay and 3-pulse inversion recovery in the frequency range of 250 MHz-1.5 GHz. At constant OX063 concentration, 1/T1 decreases with increasing frequency because the tumbling dependent processes that dominate relaxation at 250 MHz are less effective at higher frequency. 1/T2 also decreases with increasing frequency because 1/T1 is a significant contribution to 1/T2 for trityl radicals in fluid solution. 1/T2-1/T1, the incomplete motional averaging contribution to 1/T2, increases with increasing frequency. At constant frequency, relaxation rates increase with increasing radical concentration due to contributions from collisions that are more effective for 1/T2 than 1/T1. The collisional contribution to relaxation increases as the concentration of counter-ions in solution increases, which is attributed to interactions of cations with the negatively charged radicals that decrease repulsion between trityl radicals. The Signal-to-Noise ratio (S/N) of field-swept echo-detected spectra of OX063 were measured in the frequency range of 400 MHz-1 GHz. S/N values, normalized by √Q, increase as frequency increases. Adding salt to the radical solution decreased S/N because salt lowers the resonator Q. Changing the temperature from 19 to 37 °C caused little change in S/N at 700 MHz. Both slower relaxation rates and higher S/N at higher frequencies are advantageous for oximetry. The potential disadvantage of higher frequencies is the decreased depth of penetration into tissue.
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Affiliation(s)
- Yilin Shi
- Department of Chemistry and Biochemistry and Center for EPR Imaging In Vivo Physiology, University of Denver, Denver, CO 80210, USA
| | - Richard W Quine
- School of Engineering and Computer Science and Center for EPR Imaging In Vivo Physiology, University of Denver, Denver, CO 80210, USA
| | - George A Rinard
- School of Engineering and Computer Science and Center for EPR Imaging In Vivo Physiology, University of Denver, Denver, CO 80210, USA
| | - Laura Buchanan
- Department of Chemistry and Biochemistry and Center for EPR Imaging In Vivo Physiology, University of Denver, Denver, CO 80210, USA
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry and Center for EPR Imaging In Vivo Physiology, University of Denver, Denver, CO 80210, USA
| | - Gareth R Eaton
- Gareth R. Eaton, Department of Chemistry and Biochemistry and Center for EPR Imaging In Vivo Physiology, University of Denver, Denver, CO 80210, USA
| | - Boris Epel
- Department of Radiation and Cellular Oncology and Center for EPR Imaging In Vivo Physiology, University of Chicago, Chicago, IL 60637, USA
| | - Simone Wanless Seagle
- Department of Radiation and Cellular Oncology and Center for EPR Imaging In Vivo Physiology, University of Chicago, Chicago, IL 60637, USA
| | - Howard J Halpern
- Department of Radiation and Cellular Oncology and Center for EPR Imaging In Vivo Physiology, University of Chicago, Chicago, IL 60637, USA
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43
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Kadtsyn E, Anikeenko A, Medvedev N. Molecular dynamics simulation of a DNA duplex labeled with triarylmethyl spin radicals. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.06.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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44
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Joseph B, Tormyshev VM, Rogozhnikova OY, Akhmetzyanov D, Bagryanskaya EG, Prisner TF. Selective High-Resolution Detection of Membrane Protein-Ligand Interaction in Native Membranes Using Trityl-Nitroxide PELDOR. Angew Chem Int Ed Engl 2016; 55:11538-42. [DOI: 10.1002/anie.201606335] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Benesh Joseph
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum; Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Victor M. Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk 630090 Russia
- Novosibirsk State University; Novosibirsk 630090 Russia
| | - Olga Yu. Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk 630090 Russia
| | - Dmitry Akhmetzyanov
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum; Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Elena G. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk 630090 Russia
| | - Thomas F. Prisner
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum; Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
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45
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Joseph B, Tormyshev VM, Rogozhnikova OY, Akhmetzyanov D, Bagryanskaya EG, Prisner TF. Selective High-Resolution Detection of Membrane Protein-Ligand Interaction in Native Membranes Using Trityl-Nitroxide PELDOR. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606335] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Benesh Joseph
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum; Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Victor M. Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk 630090 Russia
- Novosibirsk State University; Novosibirsk 630090 Russia
| | - Olga Yu. Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk 630090 Russia
| | - Dmitry Akhmetzyanov
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum; Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Elena G. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk 630090 Russia
| | - Thomas F. Prisner
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum; Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
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46
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Yang Z, Bridges MD, López CJ, Rogozhnikova OY, Trukhin DV, Brooks EK, Tormyshev V, Halpern HJ, Hubbell WL. A triarylmethyl spin label for long-range distance measurement at physiological temperatures using T1 relaxation enhancement. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 269:50-54. [PMID: 27214582 PMCID: PMC4958593 DOI: 10.1016/j.jmr.2016.05.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 05/19/2023]
Abstract
Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy has become an important tool for measuring distances in proteins on the order of a few nm. For this purpose pairs of spin labels, most commonly nitroxides, are site-selectively introduced into the protein. Recent efforts to develop new spin labels are focused on tailoring the intrinsic properties of the label to either extend the upper limit of measurable distances at physiological temperature, or to provide a unique spectral lineshape so that selective pairwise distances can be measured in a protein or complex containing multiple spin label species. Triarylmethyl (TAM) radicals are the foundation for a new class of spin labels that promise to provide both capabilities. Here we report a new methanethiosulfonate derivative of a TAM radical that reacts rapidly and selectively with an engineered cysteine residue to generate a TAM containing side chain (TAM1) in high yield. With a TAM1 residue and Cu(2+) bound to an engineered Cu(2+) binding site, enhanced T1 relaxation of TAM should enable measurement of interspin distances up to 50Å at physiological temperature. To achieve favorable TAM1-labeled protein concentrations without aggregation, proteins are tethered to a solid support either site-selectively using an unnatural amino acid or via native lysine residues. The methodology is general and readily extendable to complex systems, including membrane proteins.
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Affiliation(s)
- Zhongyu Yang
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael D Bridges
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Carlos J López
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Olga Yu Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry V Trukhin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Evan K Brooks
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Victor Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Howard J Halpern
- The Center for EPR Imaging in vivo Physiology, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637, USA.
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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47
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Kuzhelev AA, Shevelev GY, Krumkacheva OA, Tormyshev VM, Pyshnyi DV, Fedin MV, Bagryanskaya EG. Saccharides as Prospective Immobilizers of Nucleic Acids for Room-Temperature Structural EPR Studies. J Phys Chem Lett 2016; 7:2544-8. [PMID: 27320083 PMCID: PMC5453311 DOI: 10.1021/acs.jpclett.6b01024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for structural studies of biomolecules and their complexes. This method, whose applicability has been recently extended to room temperatures, requires immobilization of the studied biosystem to prevent averaging of dipolar couplings; at the same time, the modification of native conformations by immobilization must be avoided. In this work, we provide first demonstration of room-temperature EPR distance measurements in nucleic acids using saccharides trehalose, sucrose, and glucose as immobilizing media. We propose an approach that keeps structural conformation and unity of immobilized double-stranded DNA. Remarkably, room-temperature electron spin dephasing time of triarylmethyl-labeled DNA in trehalose is noticeably longer compared to previously used immobilizers, thus providing a broader range of available distances. Therefore, saccharides, and especially trehalose, can be efficiently used as immobilizers of nucleic acids, mimicking native conditions and allowing wide range of structural EPR studies at room temperatures.
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Affiliation(s)
- Andrey A. Kuzhelev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Georgiy Yu. Shevelev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olesya A. Krumkacheva
- International Tomography Center SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Victor M. Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Matvey V. Fedin
- International Tomography Center SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G. Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
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48
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Quine RW, Rinard GA, Shi Y, Buchanan L, Biller JR, Eaton SS, Eaton GR. UHF EPR spectrometer operating at frequencies between 400 MHz and 1 GHz. CONCEPTS IN MAGNETIC RESONANCE. PART B, MAGNETIC RESONANCE ENGINEERING 2016; 46B:123-133. [PMID: 28190987 PMCID: PMC5300075 DOI: 10.1002/cmr.b.21328] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A spectrometer was designed and constructed to facilitate measurements of T1, T2, spin echo signal-to-noise, and resonator quality factor, Q, between about 400 and 1000 MHz. Pulse patterns are generated at 250 MHz and mixed with the output from a second source to perform excitation and detection. A cross-loop resonator was constructed in which the same sample could be measured in the same resonator over the full range of frequencies. An air-core, 4-coil, water-cooled electromagnet with a large experimental volume was built.
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Affiliation(s)
- Richard W. Quine
- Ritchie School of Engineering and Computer Science, University of Denver, Denver, Colorado 80210 USA
| | - George A. Rinard
- Ritchie School of Engineering and Computer Science, University of Denver, Denver, Colorado 80210 USA
| | - Yilin Shi
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, 80210 USA
| | - Laura Buchanan
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, 80210 USA
| | - Joshua R. Biller
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, 80210 USA
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, 80210 USA
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, 80210 USA
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49
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Lomzov AA, Sviridov EA, Shernuykov AV, Shevelev GY, Pyshnyi DV, Bagryanskaya EG. Study of a DNA Duplex by Nuclear Magnetic Resonance and Molecular Dynamics Simulations. Validation of Pulsed Dipolar Electron Paramagnetic Resonance Distance Measurements Using Triarylmethyl-Based Spin Labels. J Phys Chem B 2016; 120:5125-33. [PMID: 27195671 DOI: 10.1021/acs.jpcb.6b03193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pulse dipole-dipole electron paramagnetic resonance (EPR) spectroscopy (double electron-electron resonance [DEER] or pulse electron-electron double resonance [PELDOR] and double quantum coherence [DQC]) allows for measurement of distances in biomolecules and can be used at low temperatures in a frozen solution. Recently, the possibility of distance measurement in a nucleic acid at a physiological temperature using pulse EPR was demonstrated. In these experiments, triarylmethyl (TAM) radicals with long memory time of the electron spin served as a spin label. In addition, the duplex was immobilized on modified silica gel particles (Nucleosil DMA); this approach enables measurement of interspin distances close to 4.5 nm. Nevertheless, the possible influence of TAM on the structure of a biopolymer under study and validity of the data obtained by DQC are debated. In this paper, a combination of molecular dynamics (MD) and nuclear magnetic resonance (NMR) methods was used for verification of interspin distances measured by the X-band DQC method. NMR is widely used for structural analysis of biomolecules under natural conditions (room temperature and an aqueous solution). The ultraviolet (UV) melting method and thermal series (1)H NMR in the range 5-95 °C revealed the presence of only the DNA duplex in solution at oligonucleotide concentrations 1 μM to 1.1 mM at temperatures below 40 °C. The duplex structures and conformation flexibility of native and TAM-labeled DNA complexes obtained by MD simulation were the same as the structure obtained by NMR refinement. Thus, we showed that distance measurements at physiological temperatures by the X-band DQC method allow researchers to obtain valid structural information on an unperturbed DNA duplex using terminal TAM spin labels.
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Affiliation(s)
- Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Eugeniy A Sviridov
- Novosibirsk State University , Novosibirsk 630090, Russia.,N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , 9 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Andrey V Shernuykov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , 9 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Georgiy Yu Shevelev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- Novosibirsk State University , Novosibirsk 630090, Russia.,N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , 9 Lavrentiev Avenue, Novosibirsk 630090, Russia
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50
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Marin-Montesinos I, Paniagua JC, Peman A, Vilaseca M, Luis F, Van Doorslaer S, Pons M. Paramagnetic spherical nanoparticles by the self-assembly of persistent trityl radicals. Phys Chem Chem Phys 2016; 18:3151-8. [DOI: 10.1039/c5cp05767a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The self-association of a water-soluble persistent trityl radical gives rise to paramagnetic nanoparticles: a new class of non-metallic high spin systems.
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Affiliation(s)
- I. Marin-Montesinos
- Biomolecular NMR Laboratory
- Department of Organic Chemistry
- University of Barcelona
- 10-12 08028 Barcelona
- Spain
| | - J. C. Paniagua
- Department of Physical Chemistry
- University of Barcelona
- Martí i Franquès
- 1-11 08028-Barcelona
- Spain
| | - Alejandro Peman
- Biomolecular NMR Laboratory
- Department of Organic Chemistry
- University of Barcelona
- 10-12 08028 Barcelona
- Spain
| | - M. Vilaseca
- Mass Spectrometry Core Facility
- Institute for Research in Biomedicine (IRB Barcelona)
- 10-12 08028 Barcelona
- Spain
| | - F. Luis
- Instituto de Ciencia de Materiales de Aragón
- CSIC-Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | | | - M. Pons
- Biomolecular NMR Laboratory
- Department of Organic Chemistry
- University of Barcelona
- 10-12 08028 Barcelona
- Spain
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