1
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Kaiser F, Endeward B, Collauto A, Scheffer U, Prisner TF, Göbel MW. Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block. Chemistry 2022; 28:e202201822. [PMID: 35903916 PMCID: PMC9804336 DOI: 10.1002/chem.202201822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Indexed: 01/05/2023]
Abstract
The nitroxide TPA (2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene) is an excellent spin label for EPR studies of RNA. Previous synthetic methods, however, are complicated and require special equipment. Herein, we describe a uridine derived phosphoramidite with a photocaged TPA unit attached. The light sensitive 2-nitrobenzyloxymethyl group can be removed in high yield by short irradiation at 365 nm. Based on this approach, a doubly spin-labeled 27mer neomycin sensing riboswitch was synthesized and studied by PELDOR. The overall thermal stability of the fold is not much reduced by TPA. In-line probing nevertheless detected changes in local mobility.
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Affiliation(s)
- Frank Kaiser
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Burkhard Endeward
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Alberto Collauto
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Ute Scheffer
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Thomas F. Prisner
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Michael W. Göbel
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
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2
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Dong P, Stellmacher J, Bouchet LM, Nieke M, Kumar A, Osorio‐Blanco ER, Nagel G, Lohan SB, Teutloff C, Patzelt A, Schäfer‐Korting M, Calderón M, Meinke MC, Alexiev U. A Dual Fluorescence–Spin Label Probe for Visualization and Quantification of Target Molecules in Tissue by Multiplexed FLIM–EPR Spectroscopy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Pin Dong
- Department of Dermatology, Venereology and Allergology Charité Universitätsmedizin Berlin corporate member of Freie Universität Berlin Humboldt-Universität zu Berlin, and Berlin Institute of Health Berlin Germany
- Freie Universität Berlin Institute of Pharmacy Berlin Germany
| | - Johannes Stellmacher
- Freie Universität Berlin Institute of Experimental Physics Department of Physics Berlin Germany
| | - Lydia M. Bouchet
- Freie Universität Berlin Institute of Chemistry and Biochemistry Berlin Germany
| | - Marius Nieke
- Freie Universität Berlin Institute of Experimental Physics Department of Physics Berlin Germany
- Humboldt-Universität zu Berlin Institute of Biology Berlin Germany
| | - Amit Kumar
- Freie Universität Berlin Institute of Chemistry and Biochemistry Berlin Germany
| | | | - Gregor Nagel
- Freie Universität Berlin Institute of Chemistry and Biochemistry Berlin Germany
| | - Silke B. Lohan
- Department of Dermatology, Venereology and Allergology Charité Universitätsmedizin Berlin corporate member of Freie Universität Berlin Humboldt-Universität zu Berlin, and Berlin Institute of Health Berlin Germany
| | - Christian Teutloff
- Freie Universität Berlin Institute of Experimental Physics Department of Physics Berlin Germany
| | - Alexa Patzelt
- Department of Dermatology, Venereology and Allergology Charité Universitätsmedizin Berlin corporate member of Freie Universität Berlin Humboldt-Universität zu Berlin, and Berlin Institute of Health Berlin Germany
| | | | - Marcelo Calderón
- Freie Universität Berlin Institute of Chemistry and Biochemistry Berlin Germany
- POLYMAT Faculty of Chemistry University of the Basque Country UPV/EHU 20018 Donostia-San Sebastián Spain
- IKERBASQUE Basque Foundation for Science 48013 Bilbao Spain
| | - Martina C. Meinke
- Department of Dermatology, Venereology and Allergology Charité Universitätsmedizin Berlin corporate member of Freie Universität Berlin Humboldt-Universität zu Berlin, and Berlin Institute of Health Berlin Germany
| | - Ulrike Alexiev
- Freie Universität Berlin Institute of Experimental Physics Department of Physics Berlin Germany
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3
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Dong P, Stellmacher J, Bouchet LM, Nieke M, Kumar A, Osorio‐Blanco ER, Nagel G, Lohan SB, Teutloff C, Patzelt A, Schäfer‐Korting M, Calderón M, Meinke MC, Alexiev U. A Dual Fluorescence-Spin Label Probe for Visualization and Quantification of Target Molecules in Tissue by Multiplexed FLIM-EPR Spectroscopy. Angew Chem Int Ed Engl 2021; 60:14938-14944. [PMID: 33544452 PMCID: PMC8251738 DOI: 10.1002/anie.202012852] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/27/2021] [Indexed: 12/30/2022]
Abstract
Simultaneous visualization and concentration quantification of molecules in biological tissue is an important though challenging goal. The advantages of fluorescence lifetime imaging microscopy (FLIM) for visualization, and electron paramagnetic resonance (EPR) spectroscopy for quantification are complementary. Their combination in a multiplexed approach promises a successful but ambitious strategy because of spin label-mediated fluorescence quenching. Here, we solved this problem and present the molecular design of a dual label (DL) compound comprising a highly fluorescent dye together with an EPR spin probe, which also renders the fluorescence lifetime to be concentration sensitive. The DL can easily be coupled to the biomolecule of choice, enabling in vivo and in vitro applications. This novel approach paves the way for elegant studies ranging from fundamental biological investigations to preclinical drug research, as shown in proof-of-principle penetration experiments in human skin ex vivo.
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Affiliation(s)
- Pin Dong
- Department of Dermatology, Venereology and AllergologyCharité Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt-Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Freie Universität BerlinInstitute of PharmacyBerlinGermany
| | - Johannes Stellmacher
- Freie Universität BerlinInstitute of Experimental PhysicsDepartment of PhysicsBerlinGermany
| | - Lydia M. Bouchet
- Freie Universität BerlinInstitute of Chemistry and BiochemistryBerlinGermany
| | - Marius Nieke
- Freie Universität BerlinInstitute of Experimental PhysicsDepartment of PhysicsBerlinGermany
- Humboldt-Universität zu BerlinInstitute of BiologyBerlinGermany
| | - Amit Kumar
- Freie Universität BerlinInstitute of Chemistry and BiochemistryBerlinGermany
| | | | - Gregor Nagel
- Freie Universität BerlinInstitute of Chemistry and BiochemistryBerlinGermany
| | - Silke B. Lohan
- Department of Dermatology, Venereology and AllergologyCharité Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt-Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | - Christian Teutloff
- Freie Universität BerlinInstitute of Experimental PhysicsDepartment of PhysicsBerlinGermany
| | - Alexa Patzelt
- Department of Dermatology, Venereology and AllergologyCharité Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt-Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | | | - Marcelo Calderón
- Freie Universität BerlinInstitute of Chemistry and BiochemistryBerlinGermany
- POLYMATFaculty of ChemistryUniversity of the Basque CountryUPV/EHU20018Donostia-San SebastiánSpain
- IKERBASQUEBasque Foundation for Science48013BilbaoSpain
| | - Martina C. Meinke
- Department of Dermatology, Venereology and AllergologyCharité Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt-Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | - Ulrike Alexiev
- Freie Universität BerlinInstitute of Experimental PhysicsDepartment of PhysicsBerlinGermany
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4
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Heinz M, Erlenbach N, Stelzl LS, Thierolf G, Kamble NR, Sigurdsson ST, Prisner TF, Hummer G. High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label. Nucleic Acids Res 2020; 48:924-933. [PMID: 31777925 PMCID: PMC6954412 DOI: 10.1093/nar/gkz1096] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/01/2019] [Accepted: 11/20/2019] [Indexed: 12/25/2022] Open
Abstract
Pulsed electron paramagnetic resonance (EPR) experiments, among them most prominently pulsed electron-electron double resonance experiments (PELDOR/DEER), resolve the conformational dynamics of nucleic acids with high resolution. The wide application of these powerful experiments is limited by the synthetic complexity of some of the best-performing spin labels. The recently developed $\bf\acute{G}$ (G-spin) label, an isoindoline-nitroxide derivative of guanine, can be incorporated non-covalently into DNA and RNA duplexes via Watson-Crick base pairing in an abasic site. We used PELDOR and molecular dynamics (MD) simulations to characterize $\bf\acute{G}$, obtaining excellent agreement between experiments and time traces calculated from MD simulations of RNA and DNA double helices with explicitly modeled $\bf\acute{G}$ bound in two abasic sites. The MD simulations reveal stable hydrogen bonds between the spin labels and the paired cytosines. The abasic sites do not significantly perturb the helical structure. $\bf\acute{G}$ remains rigidly bound to helical RNA and DNA. The distance distributions between the two bound $\bf\acute{G}$ labels are not substantially broadened by spin-label motions in the abasic site and agree well between experiment and MD. $\bf\acute{G}$ and similar non-covalently attached spin labels promise high-quality distance and orientation information, also of complexes of nucleic acids and proteins.
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Affiliation(s)
- Marcel Heinz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Lukas S Stelzl
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Grace Thierolf
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Nilesh R Kamble
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavk, Iceland
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavk, Iceland
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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5
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Juliusson HY, Segler ALJ, Sigurdsson ST. Benzoyl-Protected Hydroxylamines for Improved Chemical Synthesis of Oligonucleotides Containing Nitroxide Spin Labels. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900553] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Haraldur Y. Juliusson
- Department of Chemistry; Science Institute; University of Iceland; Dunhaga 3 107 Reykjavik Iceland
| | - Anna-Lena J. Segler
- Department of Chemistry; Science Institute; University of Iceland; Dunhaga 3 107 Reykjavik Iceland
| | - Snorri Th. Sigurdsson
- Department of Chemistry; Science Institute; University of Iceland; Dunhaga 3 107 Reykjavik Iceland
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6
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Gränz M, Erlenbach N, Spindler P, Gophane DB, Stelzl LS, Sigurdsson ST, Prisner TF. Dynamics of Nucleic Acids at Room Temperature Revealed by Pulsed EPR Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Markus Gränz
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University Frankfurt Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany
| | - Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University Frankfurt Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany
| | - Philipp Spindler
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University Frankfurt Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany
| | - Dnyaneshwar B. Gophane
- Department of ChemistryScience InstituteUniversity of Iceland Dunhaga 3 107 Reykjavík Iceland
| | - Lukas S. Stelzl
- Department of Theoretical BiophysicsMax Planck Institute of Biophysics Max-von-Laue-Straße 3 60438 Frankfurt am Main Germany
| | - Snorri Th. Sigurdsson
- Department of ChemistryScience InstituteUniversity of Iceland Dunhaga 3 107 Reykjavík Iceland
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University Frankfurt Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany
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7
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Gränz M, Erlenbach N, Spindler P, Gophane DB, Stelzl LS, Sigurdsson ST, Prisner TF. Dynamics of Nucleic Acids at Room Temperature Revealed by Pulsed EPR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:10540-10543. [PMID: 29858557 DOI: 10.1002/anie.201803682] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/06/2018] [Indexed: 12/16/2022]
Abstract
The investigation of the structure and conformational dynamics of biomolecules under physiological conditions is challenging for structural biology. Although pulsed electron paramagnetic resonance (like PELDOR) techniques provide long-range distance and orientation information with high accuracy, such studies are usually performed at cryogenic temperatures. At room temperature (RT) PELDOR studies are seemingly impossible due to short electronic relaxation times and loss of dipolar interactions through rotational averaging. We incorporated the rigid nitroxide spin label Ç into a DNA duplex and immobilized the sample on a solid support to overcome this limitation. This enabled orientation-selective PELDOR measurements at RT. A comparison with data recorded at 50 K revealed averaging of internal dynamics, which occur on the ns time range at RT. Thus, our approach adds a new method to study structural and dynamical processes at physiological temperature in the <10 μs time range with atomistic resolution.
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Affiliation(s)
- Markus Gränz
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Philipp Spindler
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Dnyaneshwar B Gophane
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavík, Iceland
| | - Lukas S Stelzl
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavík, Iceland
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
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8
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Weinrich T, Jaumann EA, Scheffer U, Prisner TF, Göbel MW. A Cytidine Phosphoramidite with Protected Nitroxide Spin Label: Synthesis of a Full-Length TAR RNA and Investigation by In-Line Probing and EPR Spectroscopy. Chemistry 2018; 24:6202-6207. [PMID: 29485736 DOI: 10.1002/chem.201800167] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/23/2018] [Indexed: 01/20/2023]
Abstract
EPR studies on RNA are complicated by three major obstacles related to the chemical nature of nitroxide spin labels: Decomposition while oligonucleotides are chemically synthesized, further decay during enzymatic strand ligation, and undetected changes in conformational equilibria due to the steric demand of the label. Herein possible solutions for all three problems are presented: A 2-nitrobenzyloxymethyl protective group for nitroxides that is stable under all conditions of chemical RNA synthesis and can be removed photochemically. By careful selection of ligation sites and splint oligonucleotides, high yields were achieved in the assembly of a full-length HIV-1 TAR RNA labeled with two protected nitroxide groups. PELDOR measurements on spin-labeled TAR in the absence and presence of arginine amide indicated arrest of interhelical motions on ligand binding. Finally, even minor changes in conformation due to the presence of spin labels are detected with high sensitivity by in-line probing.
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Affiliation(s)
- Timo Weinrich
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Eva A Jaumann
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Ute Scheffer
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Michael W Göbel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
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9
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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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10
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Weinrich T, Gränz M, Grünewald C, Prisner TF, Göbel MW. Synthesis of a Cytidine Phosphoramidite with Protected Nitroxide Spin Label for EPR Experiments with RNA. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601174] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Timo Weinrich
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Markus Gränz
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Michael W. Göbel
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
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11
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Kurita M, Higuchi Y, Mirc JW, Matsumoto S, Usui K, Suemune H, Aso M. Synthesis and Electron Paramagnetic Resonance Studies of Oligodeoxynucleotides Containing 2-N-tert-Butylaminoxyl-2'-deoxyadenosines. Chembiochem 2016; 17:2346-2352. [PMID: 27809378 DOI: 10.1002/cbic.201600465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Indexed: 11/10/2022]
Abstract
Oligodeoxynucleotides (ODNs) containing 2-N-tert-butylaminoxyl-2'-deoxyadenosine (A*) residues were synthesized to allow accurate monitoring of adenine motion by EPR spectroscopy through the agency of direct linkage of the acyclic aminoxyl group to the nucleobase, and EPR studies of the ODNs in single- and double-stranded forms were performed. Upon duplex formation, peak broadening and decreases in peak height were observed in EPR spectra, and the synthesized ODNs were shown to be excellent monitors of hybridization. Comparison of peak height and the h1 /h0 signal ratio provided information on the relative mobility of A* in duplexes with different stability. A second set of ODNs each containing two A* residues at different intervals and four dA residues were also synthesized. For these ODNs, correlations were observed between the EPR spectral shapes of the duplexes and the number of dA residues between A* residues, thus demonstrating the potential of A* residues in monitoring of the structures of nucleic acids.
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Affiliation(s)
- Manami Kurita
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Yoshitaka Higuchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Japan
| | - J W Mirc
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Shintaro Matsumoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Kazuteru Usui
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Hiroshi Suemune
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Mariko Aso
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Japan
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12
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Kerzhner M, Abdullin D, Więcek J, Matsuoka H, Hagelueken G, Schiemann O, Famulok M. Post-synthetic Spin-Labeling of RNA through Click Chemistry for PELDOR Measurements. Chemistry 2016; 22:12113-21. [PMID: 27412453 DOI: 10.1002/chem.201601897] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Indexed: 01/24/2023]
Abstract
Site-directed spin labeling of RNA based on click chemistry is used in combination with pulsed electron-electron double resonance (PELDOR) to benchmark a nitroxide spin label, called here dŲ. We compare this approach with another established method that employs the rigid spin label Çm for RNA labeling. By using CD spectroscopy, thermal denaturation measurements, CW-EPR as well as PELDOR we analyzed and compared the influence of dŲ and Çm on a self-complementary RNA duplex. Our results demonstrate that the conformational diversity of dŲ is significantly reduced near the freezing temperature of a phosphate buffer, resulting in strongly orientation-selective PELDOR time traces of the dŲ-labeled RNA duplex.
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Affiliation(s)
- Mark Kerzhner
- Life & Medical Sciences Institute, Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Dinar Abdullin
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Jennifer Więcek
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Hideto Matsuoka
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Gregor Hagelueken
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Olav Schiemann
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany.
| | - Michael Famulok
- Life & Medical Sciences Institute, Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany. .,Max-Planck Fellow Group Chemical Biology, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.
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13
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Erlenbach N, Endeward B, Schöps P, Gophane DB, Sigurdsson ST, Prisner TF. Flexibilities of isoindoline-derived spin labels for nucleic acids by orientation selective PELDOR. Phys Chem Chem Phys 2016; 18:16196-201. [DOI: 10.1039/c6cp02475k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The conformational flexibility of new isoindoline-derived spin labels for nucleic acid have been analyzed by multi-frequency/multi-field PELDOR spectroscopy.
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Affiliation(s)
- N. Erlenbach
- Institute of Physical and Theoretical Chemistry
- Center of Biomolecular Magnetic Resonance
- Goethe University
- D-60438 Frankfurt am Main
- Germany
| | - B. Endeward
- Institute of Physical and Theoretical Chemistry
- Center of Biomolecular Magnetic Resonance
- Goethe University
- D-60438 Frankfurt am Main
- Germany
| | - P. Schöps
- Institute of Physical and Theoretical Chemistry
- Center of Biomolecular Magnetic Resonance
- Goethe University
- D-60438 Frankfurt am Main
- Germany
| | - D. B. Gophane
- Department of Chemistry
- Science Institute University of Iceland
- 107 Reykjavik
- Iceland
| | - S. Th. Sigurdsson
- Department of Chemistry
- Science Institute University of Iceland
- 107 Reykjavik
- Iceland
| | - T. F. Prisner
- Institute of Physical and Theoretical Chemistry
- Center of Biomolecular Magnetic Resonance
- Goethe University
- D-60438 Frankfurt am Main
- Germany
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14
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Gophane DB, Endeward B, Prisner TF, Sigurdsson ST. Conformationally restricted isoindoline-derived spin labels in duplex DNA: distances and rotational flexibility by pulsed electron-electron double resonance spectroscopy. Chemistry 2014; 20:15913-9. [PMID: 25296640 DOI: 10.1002/chem.201403726] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/10/2014] [Indexed: 12/25/2022]
Abstract
Three structurally related isoindoline-derived spin labels that have different mobilities were incorporated into duplex DNA to systematically study the effect of motion on orientation-dependent pulsed electron-electron double resonance (PELDOR) measurements. To that end, a new nitroxide spin label, (ExIm)U, was synthesized and incorporated into DNA oligonucleotides. (ExIm)U is the first example of a conformationally unambiguous spin label for nucleic acids, in which the nitroxide N-O bond lies on the same axis as the three single bonds used to attach the otherwise rigid isoindoline-based spin label to a uridine base. Continuous-wave (CW) EPR measurements of (ExIm)U confirm a very high rotational mobility of the spin label in duplex DNA relative to the structurally related spin label (Im)U, which has restricted mobility due to an intramolecular hydrogen bond. The X-band CW-EPR spectra of (ExIm)U can be used to identify mismatches in duplex DNA. PELDOR distance measurements between pairs of the spin labels (Im)U, (Ox)U, and (ExIm)U in duplex DNA showed a strong angular dependence for (Im)U, a medium dependence for (Ox)U, and no orientation effect for (ExIm)U. Thus, precise distances can be extracted from (ExIm)U without having to take orientational effects into account.
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Affiliation(s)
- Dnyaneshwar B Gophane
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik (Iceland), Fax: (+354)5528911
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Rodgers BJ, Elsharif NA, Vashisht N, Mingus MM, Mulvahill MA, Stengel G, Kuchta RD, Purse BW. Functionalized tricyclic cytosine analogues provide nucleoside fluorophores with improved photophysical properties and a range of solvent sensitivities. Chemistry 2013; 20:2010-5. [PMID: 24311229 DOI: 10.1002/chem.201303410] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Indexed: 12/11/2022]
Abstract
Tricyclic cytosines (tC and tC(O) frameworks) have emerged as a unique class of fluorescent nucleobase analogues that minimally perturb the structure of B-form DNA and that are not quenched in duplex nucleic acids. Systematic derivatization of these frameworks is a likely approach to improve on and diversify photophysical properties, but has not so far been examined. Synthetic methods were refined to improve on tolerance for electron-donating and electron-withdrawing groups, resulting in a series of eight new, fluorescent cytidine analogues. Photophysical studies show that substitution of the framework results in a pattern of effects largely consistent across tC and tC(O) and provides nucleoside fluorophores that are brighter than either parent. Moreover, a range of solvent sensitivities is observed, offering promise that this family of probes can be extended to new applications that require reporting on the local environment.
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Affiliation(s)
- Brittney J Rodgers
- Department of Chemistry and Biochemistry, University of Denver, 2199 S. University Blvd., Denver, CO 80208 (USA)
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16
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Nguyen P, Shi X, Sigurdsson ST, Herschlag D, Qin PZ. A single-stranded junction modulates nanosecond motional ordering of the substrate recognition duplex of a group I ribozyme. Chembiochem 2013; 14:1720-3. [PMID: 23900919 DOI: 10.1002/cbic.201300376] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Indexed: 12/26/2022]
Abstract
Rigid spinning: Site-directed spin-labeling studies using a rigid nitroxide spin label (Ç) reveal that both length and sequence of a single-stranded junction (J1/2) modulate nanosecond motional ordering of the substrate-recognition duplex (P1) of the 120 kD group I ribozyme. The studies demonstrate an approach for experimental measurements of nanosecond dynamics in high-molecular-weight RNA complexes.
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Affiliation(s)
- Phuong Nguyen
- Department of Chemistry, University of Southern California, LJS-251, 840 Downey Way, Los Angeles, CA 90089-0744 (USA) http://pzqin.usc.edu/pzqhome
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17
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Marko A, Prisner TF. An algorithm to analyze PELDOR data of rigid spin label pairs. Phys Chem Chem Phys 2013. [DOI: 10.1039/c2cp42942j] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Shelke SA, Sigurdsson ST. Effect of N3 Modifications on the Affinity of Spin Label ç for Abasic Sites in Duplex DNA. Chembiochem 2012; 13:684-90. [DOI: 10.1002/cbic.201100728] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Indexed: 12/11/2022]
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19
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20
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Atsumi H, Maekawa K, Nakazawa S, Shiomi D, Sato K, Kitagawa M, Takui T, Nakatani K. Tandem Arrays of TEMPO and Nitronyl Nitroxide Radicals with Designed Arrangements on DNA. Chemistry 2011; 18:178-83. [DOI: 10.1002/chem.201102693] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Indexed: 12/24/2022]
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21
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Stoller S, Sicoli G, Baranova TY, Bennati M, Diederichsen U. TOPP: A Novel Nitroxide-Labeled Amino Acid for EPR Distance Measurements. Angew Chem Int Ed Engl 2011; 50:9743-6. [DOI: 10.1002/anie.201103315] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Indexed: 11/08/2022]
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22
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Sezer D, Sigurdsson ST. Simulating electron spin resonance spectra of macromolecules labeled with two dipolar-coupled nitroxide spin labels from trajectories. Phys Chem Chem Phys 2011; 13:12785-97. [PMID: 21691643 DOI: 10.1039/c1cp20430k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient method for simulating continuous-wave electron spin resonance spectra (ESR) of molecules labeled with two dipolar-coupled nitroxides from trajectories of the molecular motion is presented. Two approximate treatments of the dipolar spin evolution, resulting in significantly shorter simulation times, are examined in order to determine their range of applicability. The approach is illustrated in the context of a double-helical B-DNA. ESR spectra for DNA undergoing anisotropic global diffusion and internal stretching dynamics are calculated for three different labeling geometries with the spin labels bracketing, respectively, three, two and one base pairs. While multifrequency spectra of all three labeling schemes are very sensitive to DNA tumbling, the last one is found to be most informative about the local DNA dynamics.
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Affiliation(s)
- Deniz Sezer
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı-Tuzla, 34956 Istanbul, Turkey.
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23
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Gardarsson H, Kale AS, Sigurdsson ST. Structure-function relationships of phenoxazine nucleosides for identification of mismatches in duplex DNA by fluorescence spectroscopy. Chembiochem 2011; 12:567-75. [PMID: 21322103 DOI: 10.1002/cbic.201000478] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Indexed: 12/13/2022]
Abstract
The effects of the flanking sequence on the mismatch-detection capabilities of the fluorescent nucleoside phenoxazine (tC(O)) were examined in a systematic fashion, and compared to the previously reported fluorescent, phenoxazine-based nucleoside Ç(f) . We see some similarities for the two fluorescent nucleosides, for example, the emission intensity of the C-mismatched duplex is always the highest, and a three-peak pattern in the spectrum emerges when the fluorosides are base-paired with A. However, phenoxazine was only able to distinguish a mismatch from the fully base-paired duplex in 11 out of 16 flanking sequences, and was able to identify each of the mismatches in six of those sequences. Therefore, tC(O) shows poorer discrimination of mismatches than was previously reported for Ç(f) , which could be used to identify all base-pairing partners in all immediately flanking sequences, albeit in some cases by using mercuric ions to selectively quench the emission of the T-mismatched duplex. The mercuric titration might resolve the overlap of fluorescence curves of tC(O) in some flanking sequences, but not for 5'-d(CtC(O) G) and 5'-d(TtC(O) A) due to overlap of A-mismatch and G-match fluorescence curves. A pH titration was performed on Ç(f) , tC(O) and a N5-methylated derivative of tC(O) , which showed that the emergence of the three-peak pattern is associated with the de-protonation of N5 in the fluorosides. We also show that neither the α- nor β-anomer of the phenothiazine nucleoside (tC) was able to detect a mismatch in any of the flanking sequences examined.
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Sicoli G, Wachowius F, Bennati M, Höbartner C. Probing secondary structures of spin-labeled RNA by pulsed EPR spectroscopy. Angew Chem Int Ed Engl 2010; 49:6443-7. [PMID: 20665607 DOI: 10.1002/anie.201000713] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Giuseppe Sicoli
- Research group Electron Paramagnetic Resonance, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Jakobsen U, Shelke SA, Vogel S, Sigurdsson ST. Site-directed spin-labeling of nucleic acids by click chemistry: detection of abasic sites in duplex DNA by EPR spectroscopy. J Am Chem Soc 2010; 132:10424-8. [PMID: 20617829 DOI: 10.1021/ja102797k] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This paper describes a spin label that can detect and identify local structural deformations in duplex DNA, in particular abasic sites. The spin label was incorporated into DNA by a new postsynthetic approach using click-chemistry on a solid support, which simplified both the synthesis and purification of the spin-labeled oligonucleotides. A nitroxide-functionalized azide, prepared by a short synthetic route, was reacted with an oligomer containing 5-ethynyl-2'-dU. The conjugation proceeded in quantitative yield and resulted in a fairly rigid linker between the modified nucleotide and the nitroxide spin label. The spin label was used to detect, for the first time, abasic sites in duplex DNA by X-band CW-EPR spectroscopy and give information about other structural deformations as well as local conformational changes in DNA. For example, reduced mobility of the spin label in a mismatched pair with T was consistent with the spin label displacing the T from the duplex. Addition of mercury(II) to this mispair resulted in a substantial increase in the motion of the spin label, consistent with formation of a metallopair between the T and the spin-labeled base that results in movement of the spin label out of the duplex and toward the solution. Thus, reposition of the spin label, when acting as a mercury(II)-controlled mechanical lever, can be readily detected by EPR spectroscopy. The ease of incorporation and properties of the new spin label make it attractive for EPR studies of nucleic acids and other macromolecules.
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Affiliation(s)
- Ulla Jakobsen
- Department of Physics and Chemistry, University of Southern Denmark, Nucleic Acid Center Campusvej 55, 5230 Odense, Denmark
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Shelke SA, Sigurdsson ST. Noncovalent and Site-Directed Spin Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002637] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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27
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Shelke SA, Sigurdsson ST. Noncovalent and Site-Directed Spin Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2010; 49:7984-6. [DOI: 10.1002/anie.201002637] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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28
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Sicoli G, Wachowius F, Bennati M, Höbartner C. Sekundärstrukturanalyse von spinmarkierter RNA mit Puls-EPR-Spektroskopie. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000713] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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29
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Wachowius F, Höbartner C. Chemical RNA modifications for studies of RNA structure and dynamics. Chembiochem 2010; 11:469-80. [PMID: 20135663 DOI: 10.1002/cbic.200900697] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Falk Wachowius
- Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Schiemann O, Cekan P, Margraf D, Prisner T, Sigurdsson S. Relative Orientation of Rigid Nitroxides by PELDOR: Beyond Distance Measurements in Nucleic Acids. Angew Chem Int Ed Engl 2009; 48:3292-5. [DOI: 10.1002/anie.200805152] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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31
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Schiemann O, Cekan P, Margraf D, Prisner T, Sigurdsson S. Relative Orientation of Rigid Nitroxides by PELDOR: Beyond Distance Measurements in Nucleic Acids. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805152] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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32
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Margraf D, Cekan P, Prisner TF, Sigurdsson ST, Schiemann O. Ferro- and antiferromagnetic exchange coupling constants in PELDOR spectra. Phys Chem Chem Phys 2009; 11:6708-14. [DOI: 10.1039/b905524j] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Obeid S, Yulikov M, Jeschke G, Marx A. Enzymatic synthesis of multiple spin-labeled DNA. Angew Chem Int Ed Engl 2008; 47:6782-5. [PMID: 18671226 DOI: 10.1002/anie.200802314] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Samra Obeid
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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Obeid S, Yulikov M, Jeschke G, Marx A. Enzymatische Synthese mehrfach spinmarkierter DNA. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802314] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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