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Song Y, Meade TJ, Astashkin A, Klein E, Enemark J, Raitsimring A. Pulsed dipolar spectroscopy distance measurements in biomacromolecules labeled with Gd(III) markers. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 210:59-68. [PMID: 21388847 PMCID: PMC3081411 DOI: 10.1016/j.jmr.2011.02.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 02/03/2011] [Accepted: 02/08/2011] [Indexed: 05/11/2023]
Abstract
This work demonstrates the feasibility of using Gd(III) tags for long-range Double Electron Electron Resonance (DEER) distance measurements in biomacromolecules. Double-stranded 14- base pair Gd(III)-DNA conjugates were synthesized and investigated at K(a) band. For the longest Gd(III) tag the average distance and average deviation between Gd(III) ions determined from the DEER time domains was about 59±12Å. This result demonstrates that DEER measurements with Gd(III) tags can be routinely carried out for distances of at least 60Å, and analysis indicates that distance measurements up to 100Å are possible. Compared with commonly used nitroxide labels, Gd(III)-based labels will be most beneficial for the detection of distance variations in large biomacromolecules, with an emphasis on large scale changes in shape or distance. Tracking the folding/unfolding and domain interactions of proteins and the conformational changes in DNA are examples of such applications.
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Affiliation(s)
- Y. Song
- Departments of Chemistry; Molecular Biosciences; Neurobiology & Physiology; and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - T. J. Meade
- Departments of Chemistry; Molecular Biosciences; Neurobiology & Physiology; and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - A.V. Astashkin
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
| | - E.L. Klein
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
| | - J.H. Enemark
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
| | - A. Raitsimring
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
- Corresponding Author: Arnold Raitsimring, Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA.
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Potapov A, Song Y, Meade TJ, Goldfarb D, Astashkin A, Raitsimring A. Distance measurements in model bis-Gd(III) complexes with flexible "bridge". Emulation of biological molecules having flexible structure with Gd(III) labels attached. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 205:38-49. [PMID: 20418132 PMCID: PMC2885582 DOI: 10.1016/j.jmr.2010.03.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Revised: 03/30/2010] [Accepted: 03/30/2010] [Indexed: 05/18/2023]
Abstract
In this work, we continue to explore Gd(III) as a possible spin label for high-field Double Electron-Electron Resonance (DEER) based distance measurements in biological molecules with flexible geometry. For this purpose, a bis-Gd(III) complex with a flexible "bridge" was used as a model. The distances in the model were expected to be distributed in the range of 5-26 A, allowing us to probe the shortest limits of accessible distances which were found to be as small as 13 A. The upper distance limit for these labels was also evaluated and was found to be about 60 A. Various pulse duration setups can result in apparent differences in the distribution function derived from DEER kinetics due to short distance limit variations. The advantages, such as the ability to perform measurements at cryogenic temperatures and high repetition rates simultaneously, the use of very short pumping and observation pulses without mutual interference, the lack of orientational selectivity, as well as the shortcomings, such as the limited mw operational frequency range and intrinsically smaller amplitude of oscillation related to dipolar interaction as compared with nitroxide spin labels are discussed. Most probably the use of nitroxide and Gd-based labels for distance measurements will be complementary depending on the particulars of the problem and the availability of instrumentation.
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Affiliation(s)
- A. Potapov
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Y. Song
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - T. J. Meade
- Department of Chemistry; Department of Biochemistry, Cell Biology, and Molecular Biology; Neurobiology & Physiology; Department of Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - D. Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - A.V. Astashkin
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA
| | - A. Raitsimring
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA
- Corresponding author: Dr. A. Raitsimring, University of Arizona, Department of Chemistry, 1306 E. University Blvd, Tucson, AZ 85721. ; tel (520)621-9968; fax (520)621-8407
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Lovett JE, Hoffmann M, Cnossen A, Shutter ATJ, Hogben HJ, Kay CWM, Timmel CR, Anderson HL. Probing Flexibility in Porphyrin-Based Molecular Wires Using Double Electron Electron Resonance. J Am Chem Soc 2009; 131:13852-9. [DOI: 10.1021/ja905796z] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janet E. Lovett
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Markus Hoffmann
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Arjen Cnossen
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Alexander T. J. Shutter
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Hannah J. Hogben
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Christopher W. M. Kay
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Christiane R. Timmel
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Harry L. Anderson
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
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