1
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Bertran A, De Zotti M, Timmel CR, Di Valentin M, Bowen AM. Determining and controlling conformational information from orientationally selective light-induced triplet-triplet electron resonance spectroscopy for a set of bis-porphyrin rulers. Phys Chem Chem Phys 2024; 26:2589-2602. [PMID: 38170870 PMCID: PMC10793979 DOI: 10.1039/d3cp03454b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/31/2023] [Indexed: 01/05/2024]
Abstract
We recently reported a new technique, light-induced triplet-triplet electron resonance (LITTER) spectroscopy, which allows quantification of the dipolar interaction between the photogenerated triplet states of two chromophores. Here we carry out a systematic LITTER study, considering orientation selection by the detection pulses, of a series of bis-porphyrin model peptides with different porphyrin-porphyrin distances and relative orientations. Orientation-dependent analysis of the dipolar datasets yields conformational information of the molecules in frozen solution which is in good agreement with density functional theory predictions. Additionally, a fast partial orientational-averaging treatment produces distance distributions with minimized orientational artefacts. Finally, by direct comparison of LITTER data to double electron-electron resonance (DEER) measured on a system with Cu(II) coordinated into the porphyrins, we demonstrate the advantages of the LITTER technique over the standard DEER methodology. This is due to the remarkable spectroscopic properties of the photogenerated porphyrin triplet state. This work sets the basis for the use of LITTER in structural investigations of unmodified complex biological macromolecules, which could be combined with Förster resonance energy transfer and microscopy inside cells.
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Affiliation(s)
- Arnau Bertran
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- Centro Interdipartimentale di Ricerca "Centro Studi di Economia e Tecnica dell'energia Giorgio Levi Cases", 35131 Padova, Italy.
| | - Christiane R Timmel
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- Centro Interdipartimentale di Ricerca "Centro Studi di Economia e Tecnica dell'energia Giorgio Levi Cases", 35131 Padova, Italy.
| | - Alice M Bowen
- The National Research Facility for Electron Paramagnetic Resonance, Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
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2
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Sannikova NE, Kolokolov MI, Khlynova TA, Chubarov AS, Polienko YF, Fedin MV, Krumkacheva OA. Revealing light-induced structural shifts in G-quadruplex-porphyrin complexes: a pulsed dipolar EPR study. Phys Chem Chem Phys 2023; 25:22455-22466. [PMID: 37581249 DOI: 10.1039/d3cp01775c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
The binding of G-quadruplex structures (G4s) with photosensitizers is of considerable importance in medicinal chemistry and drug discovery due to their promising potential in photodynamic therapy applications. G4s can experience structural changes as a result of ligand interactions and light exposure. Understanding these modifications is essential to uncover the fundamental biological roles of the complexes and optimize their therapeutic potential. The structural diversity of G4s makes it challenging to study their complexes with ligands, necessitating the use of various complementary methods to fully understand these interactions. In this study, we introduce, for the first time, the application of laser-induced dipolar EPR as a method to characterize G-quadruplex DNA complexes containing photosensitizers and to investigate light-induced structural modifications in these systems. To demonstrate the feasibility of this approach, we studied complexes of the human telomeric G-quadruplex (HTel-22) with cationic 5,10,15,20-tetrakis(1-methyl-4-pyridinio) porphyrin tetra(p-toluenesulfonate) (TMPyP4). In addition to showcasing a new methodology, we also aimed to provide insights into the mechanisms underlying photoinduced HTel-22/TMPyP4 structural changes, thereby aiding in the advancement of approaches targeting G4s in photodynamic therapy. EPR revealed G-quadruplex unfolding and dimer formation upon light exposure. Our findings demonstrate the potential of EPR spectroscopy for examining G4 complexes with photosensitizers and contribute to a better understanding of G4s' interactions with ligands under light.
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Affiliation(s)
- Natalya E Sannikova
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Mikhail I Kolokolov
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Tamara A Khlynova
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Alexey S Chubarov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Yuliya F Polienko
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia
| | - Matvey V Fedin
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Olesya A Krumkacheva
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
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3
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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4
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Bertran A, Barbon A, Bowen AM, Di Valentin M. Light-induced pulsed dipolar EPR spectroscopy for distance and orientation analysis. Methods Enzymol 2022; 666:171-231. [PMID: 35465920 DOI: 10.1016/bs.mie.2022.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Measuring distances in biology at the molecular level is of great importance for understanding the structure and function of proteins, nucleic acids and other biological molecules and their complexes. Pulsed Dipolar Spectroscopy (PDS) offers advantages with respect to other methods as it is uniquely sensitive and specific to electronic spin centers and allows measurements in near-native conditions, comprising the in-cell environment. PDS methods measure the electron spin-spin dipolar interaction, therefore they require the presence of at least two paramagnetic centers, which are often stable radicals. Recent developments have introduced transient triplet states, photo-activated by a laser pulse, as spin labels and probes, thereby establishing a new family of techniques-Light-induced PDS (LiPDS). In this chapter, an overview of these methods is provided, looking at the chromophores that can be used for LiPDS and some of the technical aspects of the experiments. A guide to the choice of technique that can yield the best results, depending on the type of system studied and the information required, is provided. Examples of previous LiPDS studies of model systems and proteins are given. Characterization data for the chromophores used in these studies is tabulated to help selection of appropriate triplet state probes in future studies.
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Affiliation(s)
- Arnau Bertran
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Antonio Barbon
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Alice M Bowen
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom; EPSRC National Research Facility for Electron Paramagnetic Resonance Spectroscopy, Department of Chemistry and Photon Science Institute, The University of Manchester, Manchester, United Kingdom.
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5
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Endeward B, Hu Y, Bai G, Liu G, Prisner TF, Fang X. Long-range distance determination in fully deuterated RNA with pulsed EPR spectroscopy. Biophys J 2022; 121:37-43. [PMID: 34896070 PMCID: PMC8758415 DOI: 10.1016/j.bpj.2021.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/23/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
Pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy is powerful in structure and dynamics study of biological macromolecules by providing distance distribution information ranging from 1.8 to 6 nm, providing that the biomolecules are site-specifically labeled with paramagnetic tags. However, long distances up to 16 nm have been measured on perdeuterated and spin-labeled proteins in deuterated solvent by PELDOR. Here we demonstrate long-range distance measurement on a large RNA, the 97-nucleotide 3'SL RNA element of the Dengue virus 2 genome, by combining a posttranscriptional site-directed spin labeling method using an unnatural basepair system with RNA perdeuteration by enzymatic synthesis using deuterated nucleotides. The perdeuteration removes the coupling of the electron spins of the nitroxide spin labels from the proton nuclear spin system of the RNA and does extend the observation time windows of PELDOR up to 50 μs. This enables one to determine long distances up to 14 nm for large RNAs and their conformational flexibility.
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Affiliation(s)
- Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Yanping Hu
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 10086, China
| | - Guangcan Bai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 10019, China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 10019, China
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt, Germany,Corresponding author
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 10086, China,Corresponding author
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6
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Segler ALJ, Sigurdsson ST. A Carbazole-Derived Nitroxide That Is an Analogue of Cytidine: A Rigid Spin Label for DNA and RNA. J Org Chem 2021; 86:11647-11659. [PMID: 34410721 DOI: 10.1021/acs.joc.1c01176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A variety of semirigid and rigid spin labels comprise a valuable arsenal for measurements of biomolecular structures and dynamics by electron paramagnetic resonance (EPR) spectroscopy. Here, we report the synthesis and characterization of rigid spin labels Ċ and Ċm for DNA and RNA, respectively, that are carbazole-derived nitroxides and analogues of cytidine. Ċ and Ċm were converted to their phosphoramidites and used for their incorporation into oligonucleotides by solid-phase synthesis. Analysis of Ċ and Ċm by single-crystal X-ray crystallography verified their identity and showed little deviation from planarity of the nucleobase. Analysis of the continuous-wave (CW) EPR spectra of the spin-labeled DNA and RNA duplexes confirmed their incorporation into the nucleic acids and the line-shape was characteristic of rigid spin labels. Circular dichroism (CD) and thermal denaturation studies of the Ċ-labeled DNAs and Ċm-labeled RNAs indicated that the labels are nonperturbing of duplex structure.
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Affiliation(s)
- Anna-Lena Johanna Segler
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland
| | - Snorri Th Sigurdsson
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland
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7
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Kozak F, Kurzbach D. How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations. Comput Struct Biotechnol J 2021; 19:2097-2105. [PMID: 33995905 PMCID: PMC8085671 DOI: 10.1016/j.csbj.2021.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
We review recent advances in modeling structural ensembles of transcription factors from nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopic data, integrated with molecular dynamics (MD) simulations. We focus on approaches that confirm computed conformational ensembles by sparse constraints obtained from magnetic resonance. This combination enables the deduction of functional and structural protein models even if nuclear Overhauser effects (NOEs) are too scarce for conventional structure determination. We highlight recent insights into the folding-upon-DNA binding transitions of intrinsically disordered transcription factors that could be assessed using such integrative approaches.
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Affiliation(s)
- Fanny Kozak
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Waehringer Str. 38, 1090 Vienna, Austria
| | - Dennis Kurzbach
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Waehringer Str. 38, 1090 Vienna, Austria
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8
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Scherer A, Tischlik S, Weickert S, Wittmann V, Drescher M. Optimising broadband pulses for DEER depends on concentration and distance range of interest. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:59-74. [PMID: 37904889 PMCID: PMC10500711 DOI: 10.5194/mr-1-59-2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/26/2020] [Indexed: 11/01/2023]
Abstract
EPR distance determination in the nanometre region has become an important tool for studying the structure and interaction of macromolecules. Arbitrary waveform generators (AWGs), which have recently become commercially available for EPR spectrometers, have the potential to increase the sensitivity of the most common technique, double electron-electron resonance (DEER, also called PELDOR), as they allow the generation of broadband pulses. There are several families of broadband pulses, which are different in general pulse shape and the parameters that define them. Here, we compare the most common broadband pulses. When broadband pulses lead to a larger modulation depth, they also increase the background decay of the DEER trace. Depending on the dipolar evolution time, this can significantly increase the noise level towards the end of the form factor and limit the potential increase in the modulation-to-noise ratio (MNR). We found asymmetric hyperbolic secant (HS{ 1 , 6 } ) pulses to perform best for short DEER traces, leading to a MNR improvement of up to 86 % compared to rectangular pulses. For longer traces we found symmetric hyperbolic secant (HS{ 1 , 1 } ) pulses to perform best; however, the increase compared to rectangular pulses goes down to 43 %.
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Affiliation(s)
- Andreas Scherer
- Department of Chemistry and Konstanz Research School Chemical Biology,
University of Konstanz, Konstanz, Germany
| | - Sonja Tischlik
- Department of Chemistry and Konstanz Research School Chemical Biology,
University of Konstanz, Konstanz, Germany
| | - Sabrina Weickert
- Department of Chemistry and Konstanz Research School Chemical Biology,
University of Konstanz, Konstanz, Germany
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology,
University of Konstanz, Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology,
University of Konstanz, Konstanz, Germany
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9
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Juliusson HY, Sigurdsson ST. Reduction Resistant and Rigid Nitroxide Spin-Labels for DNA and RNA. J Org Chem 2020; 85:4036-4046. [PMID: 32103670 DOI: 10.1021/acs.joc.9b02988] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy, coupled with site-directed spin labeling (SDSL), is a useful method for studying conformational changes of biomolecules in cells. To employ in-cell EPR using nitroxide-based spin labels, the structure of the nitroxides must confer reduction resistance to withstand the reductive environment within cells. Here, we report the synthesis of two new spin labels, EÇ and EÇm, both of which possess the rigidity and the reduction resistance needed for extracting detailed structural information by EPR spectroscopy. EÇ and EÇm were incorporated into DNA and RNA, respectively, by oligonucleotide synthesis. Both labels were shown to be nonperturbing of the duplex structure. The partial reduction of EÇm during RNA synthesis was circumvented by the protection of the nitroxide as a benzoylated hydroxylamine.
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Affiliation(s)
- Haraldur Y Juliusson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
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10
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Hetzke T, Vogel M, Gophane DB, Weigand JE, Suess B, Sigurdsson ST, Prisner TF. Influence of Mg 2+ on the conformational flexibility of a tetracycline aptamer. RNA (NEW YORK, N.Y.) 2019; 25:158-167. [PMID: 30337459 PMCID: PMC6298572 DOI: 10.1261/rna.068684.118] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/16/2018] [Indexed: 05/06/2023]
Abstract
The tetracycline-binding RNA aptamer (TC-aptamer) is a synthetic riboswitch that binds the antibiotic tetracycline (TC) with exceptionally high affinity. Although a crystal structure exists of the TC-bound state, little is known about the conformational dynamics and changes upon ligand binding. In this study, pulsed electron paramagnetic resonance techniques for measuring distances (PELDOR) in combination with rigid nitroxide spin labels (Çm spin label) were used to investigate the conformational flexibility of the TC-aptamer in the presence and absence of TC at different Mg2+ concentrations. TC was found to be the essential factor for stabilizing the tertiary structure at intermediate Mg2+ concentrations. At higher Mg2+ concentrations, Mg2+ alone is sufficient to stabilize the tertiary structure. In addition, the orientation of the two spin-labeled RNA helices with respect to each other was analyzed with orientation-selective PELDOR and compared to the crystal structure. These results demonstrate for the first time the unique value of the Çm spin label in combination with PELDOR to provide information about conformational flexibilities and orientations of secondary structure elements of biologically relevant RNAs.
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Affiliation(s)
- Thilo Hetzke
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Marc Vogel
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Dnyaneshwar B Gophane
- Department of Chemistry, Science Institute, University of Iceland, 101 Reykjavik, Iceland
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, 101 Reykjavik, Iceland
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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11
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Weinrich T, Jaumann EA, Scheffer UM, Prisner TF, Göbel MW. Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA. Beilstein J Org Chem 2018; 14:1563-1569. [PMID: 30013683 PMCID: PMC6036967 DOI: 10.3762/bjoc.14.133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/14/2018] [Indexed: 12/23/2022] Open
Abstract
TEMPO spin labels protected with 2-nitrobenzyloxymethyl groups were attached to the amino residues of three different nucleosides: deoxycytidine, deoxyadenosine, and adenosine. The corresponding phosphoramidites could be incorporated by unmodified standard procedures into four different self-complementary DNA and two RNA oligonucleotides. After photochemical removal of the protective group, elimination of formic aldehyde and spontaneous air oxidation, the nitroxide radicals were regenerated in high yield. The resulting spin-labeled palindromic duplexes could be directly investigated by PELDOR spectroscopy without further purification steps. Spin–spin distances measured by PELDOR correspond well to the values obtained from molecular models.
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Affiliation(s)
- Timo Weinrich
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Eva A Jaumann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Ute M Scheffer
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Michael W Göbel
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
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12
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Nichols PJ, Born A, Henen MA, Strotz D, Celestine CN, Güntert P, Vögeli B. Extending the Applicability of Exact Nuclear Overhauser Enhancements to Large Proteins and RNA. Chembiochem 2018; 19:1695-1701. [PMID: 29883016 DOI: 10.1002/cbic.201800237] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Indexed: 01/24/2023]
Abstract
Distance-dependent nuclear Overhauser enhancements (NOEs) are one of the most popular and important experimental restraints for calculating NMR structures. Despite this, they are mostly employed as semiquantitative upper distance bounds, and this discards the wealth of information that is encoded in the cross-relaxation rate constant. Information that is lost includes exact distances between protons and dynamics that occur on the sub-millisecond timescale. Our recently introduced exact measurement of the NOE (eNOE) requires little additional experimental effort relative to other NMR observables. So far, we have used eNOEs to calculate multistate ensembles of proteins up to approximately 150 residues. Here, we briefly revisit eNOE methodology and present two new directions for the use of eNOEs: applications to large proteins and RNA.
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Affiliation(s)
- Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Chi N Celestine
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123, Uppsala, Sweden
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
- Institute of Biophysical Chemistry, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438, Frankfurt am Main, Germany
- Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
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13
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Nichols PJ, Henen MA, Born A, Strotz D, Güntert P, Vögeli B. High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints. Commun Biol 2018; 1:61. [PMID: 30271943 PMCID: PMC6123705 DOI: 10.1038/s42003-018-0067-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/09/2018] [Indexed: 11/29/2022] Open
Abstract
RNA not only translates the genetic code into proteins, but also carries out important cellular functions. Understanding such functions requires knowledge of the structure and dynamics at atomic resolution. Almost half of the published RNA structures have been solved by nuclear magnetic resonance (NMR). However, as a result of severe resonance overlap and low proton density, high-resolution RNA structures are rarely obtained from nuclear Overhauser enhancement (NOE) data alone. Instead, additional semi-empirical restraints and labor-intensive techniques are required for structural averages, while there are only a few experimentally derived ensembles representing dynamics. Here we show that our exact NOE (eNOE) based structure determination protocol is able to define a 14-mer UUCG tetraloop structure at high resolution without other restraints. Additionally, we use eNOEs to calculate a two-state structure, which samples its conformational space. The protocol may open an avenue to obtain high-resolution structures of small RNA of unprecedented accuracy with moderate experimental efforts.
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Affiliation(s)
- Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora,, CO, 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora,, CO, 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora,, CO, 80045, USA
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zürich, ETH-Hönggerberg, Zürich, 8093, Switzerland
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, ETH-Hönggerberg, Zürich, 8093, Switzerland
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, 60438, Germany
- Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, 192-0397, Japan
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora,, CO, 80045, USA.
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14
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New limits of sensitivity of site-directed spin labeling electron paramagnetic resonance for membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:841-853. [DOI: 10.1016/j.bbamem.2017.12.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/27/2017] [Accepted: 12/09/2017] [Indexed: 01/27/2023]
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15
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Kamble NR, Sigurdsson ST. Purine-Derived Nitroxides for Noncovalent Spin-Labeling of Abasic Sites in Duplex Nucleic Acids. Chemistry 2018; 24:4157-4164. [DOI: 10.1002/chem.201705410] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Nilesh R. Kamble
- University of Iceland; Department of Chemistry; Science Institute; Dunhaga 3 107 Reykjavik Iceland
| | - Snorri Th. Sigurdsson
- University of Iceland; Department of Chemistry; Science Institute; Dunhaga 3 107 Reykjavik Iceland
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16
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Matveeva AG, Nekrasov VM, Maryasov AG. Analytical solution of the PELDOR inverse problem using the integral Mellin transform. Phys Chem Chem Phys 2018; 19:32381-32388. [PMID: 29185558 DOI: 10.1039/c7cp04059h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We describe a new model-free approach to solve the inverse problem in pulsed double electron-electron resonance (PELDOR, also known as DEER) spectroscopy and obtain the distance distribution function between two radicals from time-domain PELDOR data. The approach is based on analytical solutions of the Fredholm integral equations of the first kind using integral Mellin transforms to provide the distance distribution function directly. The approach appears to confine the noise in the computed distance distribution to short distances and does not introduce systematic distortions. Thus, the proposed analysis method can be a useful supplement to current methods to determine complicated distance distributions.
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Affiliation(s)
- Anna G Matveeva
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia.
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