1
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Awad SI, Smadi OA, Tomeh MF, Alzghoul SM. A guideline for the distance measurement plans of site-directed spin labels for structural prediction of nucleic acids. J Mol Model 2023; 30:16. [PMID: 38157075 DOI: 10.1007/s00894-023-05808-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
CONTEXT AND RESULTS Site-directed spin labeling (SDSL) combined with electron paramagnetic resonance spectroscopy methods has been successfully used to predict the structures of nucleic acids. These methods measure the distances between spin labels yielding distance equations that are solved using numerical algorithms to provide one or several structural predictions. In this work, the minimum number of SDSL distance measurements and distance measurement types required to predict a unique nucleic acid structure were investigated. Our results indicate that at least six distance measurements should be obtained given that the distance measurements do not connect one SDSL on one arm with more than three SDSLs on the other arm. Moreover, there may be a preference for 1-to-1 SLs distance measurements rather than 1-to-many SLs as the latter was linked to undefined structures discussed in this study. METHODS Pairs of double-helical arms of nucleic acid were simulated using the finite element software Pro/ENGINEER (PTC Inc., Boston, MA). In each simulation, a specific SDSL distance measurement plan was adopted and the resulting structure was tested for movability. Immovable structures indicate that this plan will potentially result in a unique structural prediction of the nucleic acid. All the possible plans for SDSL distance measurements were investigated either by direct measurement or by extrapolation.
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Affiliation(s)
- Samer I Awad
- Department of Biomedical Engineering, Faculty of Engineering, The Hashemite University, P.O. Box 330127, Zarqa, 13133, Jordan.
| | - Othman A Smadi
- Department of Biomedical Engineering, Faculty of Engineering, The Hashemite University, P.O. Box 330127, Zarqa, 13133, Jordan
| | - Mohammed F Tomeh
- Department of Industrial Engineering, Faculty of Engineering, The Hashemite University, P.O. Box 330127, Zarqa, 13133, Jordan
| | - Salah M Alzghoul
- Department of Biomedical Engineering, Faculty of Engineering, The Hashemite University, P.O. Box 330127, Zarqa, 13133, Jordan
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2
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Singh J, Liu KG, Allen A, Jiang W, Qin PZ. A DNA Unwinding Equilibrium Serves as a Checkpoint for CRISPR-Cas12a Target Discrimination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541046. [PMID: 37292754 PMCID: PMC10245671 DOI: 10.1101/2023.05.16.541046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
CRISPR-associated proteins such as Cas9 and Cas12a are programable RNA-guided nucleases that have emerged as powerful tools for genome manipulation and molecular diagnostics. However, these enzymes are prone to cleaving off-target sequences that contain mismatches between the RNA guide and DNA protospacer. In comparison to Cas9, Cas12a has demonstrated distinct sensitivity to protospacer-adjacent-motif (PAM) distal mismatches, and the molecular basis of Cas12a's enhanced target discrimination is of great interest. In this study, we investigated the mechanism of Cas12a target recognition using a combination of site-directed spin labeling, fluorescent spectroscopy, and enzyme kinetics. With a fully matched RNA guide, the data revealed an inherent equilibrium between a DNA unwound state and a DNA-paired duplex-like state. Experiments with off-target RNA guides and pre-nicked DNA substrates identified the PAM-distal DNA unwinding equilibrium as a mismatch sensing checkpoint prior to the first step of DNA cleavage. The data sheds light on the distinct targeting mechanism of Cas12a and may better inform CRISPR based biotechnology developments.
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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: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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4
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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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5
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Torricella F, Pierro A, Mileo E, Belle V, Bonucci A. Nitroxide spin labels and EPR spectroscopy: A powerful association for protein dynamics studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140653. [PMID: 33757896 DOI: 10.1016/j.bbapap.2021.140653] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/01/2023]
Abstract
Site-Directed Spin Labelling (SDSL) technique is based on the attachment of a paramagnetic label onto a specific position of a protein (or other bio-molecules) and the subsequent study by Electron Paramagnetic Resonance (EPR) spectroscopy. In particular, continuous-wave EPR (cw-EPR) spectra can detect the local conformational dynamics for proteins under various conditions. Moreover, pulse-EPR experiments on doubly spin-labelled proteins allow measuring distances between spin centres in the 1.5-8 nm range, providing information about structures and functions. This review focuses on SDSL-EPR spectroscopy as a structural biology tool to investigate proteins using nitroxide labels. The versatility of this spectroscopic approach for protein structural characterization has been demonstrated through the choice of recent studies. The main aim is to provide a general overview of the technique, particularly for non-experts, to spread the applicability of this technique in various fields of structural biology.
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Affiliation(s)
- F Torricella
- CERM-Magnetic Resonance Center, Department of Chemistry, University of Florence, via L.Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - A Pierro
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - E Mileo
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - V Belle
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - A Bonucci
- CERM-Magnetic Resonance Center, Department of Chemistry, University of Florence, via L.Sacconi 6, 50019 Sesto Fiorentino, Italy; Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France.
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6
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Wang Y, Kathiresan V, Chen Y, Hu Y, Jiang W, Bai G, Liu G, Qin PZ, Fang X. Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions. Chem Sci 2020; 11:9655-9664. [PMID: 33224460 PMCID: PMC7667596 DOI: 10.1039/d0sc01717e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/19/2020] [Indexed: 12/25/2022] Open
Abstract
Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date.
Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date. We here demonstrate an efficient and generally applicable posttranscriptional SDSL method for large RNAs using an expanded genetic alphabet containing the NaM-TPT3 unnatural base pair (UBP). An alkyne-modified TPT3 ribonucleotide triphosphate (rTPT3COTP) is synthesized and site-specifically incorporated into large RNAs by in vitro transcription, which allows attachment of the azide-containing nitroxide through click chemistry. We validate this strategy by SDSL of a 419-nucleotide ribonuclease P (RNase P) RNA from Bacillus stearothermophilus under non-denaturing conditions. The effects of site-directed UBP incorporation and subsequent spin labeling on the global structure and function of RNase P are marginal as evaluated by Circular Dichroism spectroscopy, Small Angle X-ray Scattering, Sedimentation Velocity Analytical Ultracentrifugation and enzymatic assay. Continuous-Wave EPR analyses reveal that the labeling reaction is efficient and specific, and Pulsed Electron–Electron Double Resonance measurements yield an inter-spin distance distribution that agrees with the crystal structure. The labeling strategy as presented overcomes the size constraint of RNA labeling, opening new avenues of spin labeling and EPR spectroscopy for investigating the structure and dynamics of large RNAs.
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Affiliation(s)
- Yan Wang
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Venkatesan Kathiresan
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Yaoyi Chen
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Yanping Hu
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Wei Jiang
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Guangcan Bai
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Peter Z Qin
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
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7
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Kamble N, Wolfrum M, Halbritter T, Sigurdsson ST, Richert C. Noncovalent Spin-Labeling of DNA and RNA Triplexes. Chem Biodivers 2019; 17:e1900676. [PMID: 31872549 DOI: 10.1002/cbdv.201900676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/23/2019] [Indexed: 11/07/2022]
Abstract
Studying nucleic acids often requires labeling. Many labeling approaches require covalent bonds between the nucleic acid and the label, which complicates experimental procedures. Noncovalent labeling avoids the need for highly specific reagents and reaction conditions, and the effort of purifying bioconjugates. Among the least invasive techniques for studying biomacromolecules are NMR and EPR. Here, we report noncovalent labeling of DNA and RNA triplexes with spin labels that are nucleobase derivatives. Spectroscopic signals indicating strong binding were detected in EPR experiments in the cold, and filtration assays showed micromolar dissociation constants for complexes between a guanine-derived label and triplex motifs containing a single-nucleotide gap in the oligopurine strand. The advantages and challenges of noncovalent labeling via this approach that complements techniques relying on covalent links are discussed.
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Affiliation(s)
- Nilesh Kamble
- Science Institute, University of Iceland, Dunhaga 3, 107 R, eykjavik, Iceland
| | - Manpreet Wolfrum
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Thomas Halbritter
- Science Institute, University of Iceland, Dunhaga 3, 107 R, eykjavik, Iceland
| | - Snorri T Sigurdsson
- Science Institute, University of Iceland, Dunhaga 3, 107 R, eykjavik, Iceland
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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8
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Malygin AA, Graifer DM, Meschaninova MI, Venyaminova AG, Timofeev IO, Kuzhelev AA, Krumkacheva OA, Fedin MV, Karpova GG, Bagryanskaya EG. Structural rearrangements in mRNA upon its binding to human 80S ribosomes revealed by EPR spectroscopy. Nucleic Acids Res 2019; 46:897-904. [PMID: 29156000 PMCID: PMC5778603 DOI: 10.1093/nar/gkx1136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/30/2017] [Indexed: 12/21/2022] Open
Abstract
The model mRNA (MR), 11-mer RNA containing two nitroxide spin labels at the 5′- and 3′-terminal nucleotides and prone to form a stable homodimer (MR)2, was used for Electron Paramagnetic Resonance study of structural rearrangements in mRNA occurring upon its binding to human 80S ribosomes. The formation of two different types of ribosomal complexes with MR was observed. First, there were stable complexes where MR was fixed in the ribosomal mRNA-binding channel by the codon-anticodon interaction(s) with cognate tRNA(s). Second, we for the first time detected complexes assembled without tRNA due to the binding of MR most likely to an exposed peptide of ribosomal protein uS3 away from the mRNA channel. The analysis of interspin distances allowed the conclusion that 80S ribosomes facilitate dissociation of the duplex (MR)2: the equilibrium between the duplex and the single-stranded MR shifts to MR due to its efficient binding with ribosomes. Furthermore, we observed a significant influence of tRNA bound at the ribosomal exit (E) and/or aminoacyl (A) sites on the stability of ribosomal complexes. Our findings showed that a part of mRNA bound in the ribosome channel, which is not involved in codon-anticodon interactions, has more degrees of freedom than that interacting with tRNAs.
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Affiliation(s)
- Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Dmitri M Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Maria I Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia
| | - Ivan O Timofeev
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya str. 3a, Novosibirsk 630090, Russia.,N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, pr. Lavrentjeva 9, Novosibirsk 630090, Russia
| | - Andrey A Kuzhelev
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya str. 3a, Novosibirsk 630090, Russia.,N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, pr. Lavrentjeva 9, Novosibirsk 630090, Russia
| | - Olesya A Krumkacheva
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya str. 3a, Novosibirsk 630090, Russia.,N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, pr. Lavrentjeva 9, Novosibirsk 630090, Russia
| | - Matvey V Fedin
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya str. 3a, Novosibirsk 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, pr. Lavrentjeva 9, Novosibirsk 630090, Russia
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9
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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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10
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Gophane DB, Endeward B, Prisner TF, Sigurdsson ST. A semi-rigid isoindoline-derived nitroxide spin label for RNA. Org Biomol Chem 2019; 16:816-824. [PMID: 29326999 DOI: 10.1039/c7ob02870a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A new isoindoline-derived benzimidazole nitroxide spin label, ImUm, was synthesized and incorporated into RNA oligoribonucleotides. ImUm is the first example of a conformationally unambiguous spin label for RNA, in which the nitroxide N-O bond lies on the same axis as the single bond used to attach the rigid isoindoline-based spin label to a uridine base. This results in minimal displacement of the nitroxide upon rotation of this single bond, which is a useful property for a label to be used for distance measurements. Continuous-wave (CW) EPR measurements of RNA duplexes containing ImUm indicate a restricted rotation around this single bond, presumably due to an intramolecular hydrogen bond between the benzimidazole N-H and O4 of the uracil. Orientation-selective pulsed electron-electron double resonance (PELDOR, also called double electron-electron resonance, or DEER) distance measurements between two spin labels in two RNA duplexes showed in one case a strong orientation dependence, further confirming the restricted motion of the spin labels in RNA duplexes.
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Affiliation(s)
- Dnyaneshwar B Gophane
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland.
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11
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Saha S, Hetzke T, Prisner TF, Sigurdsson ST. Noncovalent spin-labeling of RNA: the aptamer approach. Chem Commun (Camb) 2018; 54:11749-11752. [PMID: 30276367 DOI: 10.1039/c8cc05597a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the first example of site-directed spin-labeling of unmodified RNA, a pyrrolidine-nitroxide derivative of tetramethylrosamine (TMR) was shown to bind with high affinity to the malachite green (MG) aptamer, as determined by continuous-wave (CW) electron paramagnetic resonance (EPR), pulsed electron-electron double resonance (PELDOR) and fluorescence spectroscopies.
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Affiliation(s)
- Subham Saha
- Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland.
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12
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Kamble NR, Gränz M, Prisner TF, Sigurdsson ST. Noncovalent and site-directed spin labeling of duplex RNA. Chem Commun (Camb) 2018; 52:14442-14445. [PMID: 27901530 DOI: 10.1039/c6cc08387k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An isoindoline-nitroxide derivative of guanine (Ǵ, "G-spin") was shown to bind specifically and effectively to abasic sites in duplex RNAs. Distance measurements on a Ǵ-labeled duplex RNA with PELDOR (DEER) showed a strong orientation dependence. Thus, Ǵ is a readily synthesized, orientation-selective spin label for "mix and measure" PELDOR experiments.
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Affiliation(s)
- Nilesh R Kamble
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland.
| | - Markus Gränz
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Hessen, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Hessen, Germany
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland.
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13
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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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14
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Gustmann H, Lefrancois D, Reuss AJ, Gophane DB, Braun M, Dreuw A, Sigurdsson ST, Wachtveitl J. Spin the light off: rapid internal conversion into a dark doublet state quenches the fluorescence of an RNA spin label. Phys Chem Chem Phys 2018; 19:26255-26264. [PMID: 28933471 DOI: 10.1039/c7cp03975a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The spin label Çm and the fluorophore Çmf are close isosteric relatives: the secondary amine Çmf can be easily oxidized to a nitroxide group to form Çm. Thus, both compounds can serve as EPR and fluorescence labels, respectively, and their high structural similarity allows direct comparison of EPR and fluorescence data, e.g. in the context of investigations of RNA conformation and dynamics. Detailed UV/vis-spectroscopic studies demonstrate that the fluorescence lifetime and the quantum yield of Çmf are directly affected by intermolecular interactions, which makes it a sensitive probe of its microenvironment. On the other hand, Çm undergoes effective fluorescence quenching in the ps-time domain. The established quenching mechanisms that are usually operational for fluorophore-nitroxide compounds, do not explain the spectroscopic data for Çm. Quantum chemical calculations revealed that the lowest excited doublet state D1, which has no equivalent in Çmf, is a key state of the ultrafast quenching mechanism. This dark state is localized on the nitroxide group and is populated via rapid internal conversion.
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Affiliation(s)
- Henrik Gustmann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany.
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15
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Vazquez Reyes C, Tangprasertchai NS, Yogesha SD, Nguyen RH, Zhang X, Rajan R, Qin PZ. Nucleic Acid-Dependent Conformational Changes in CRISPR-Cas9 Revealed by Site-Directed Spin Labeling. Cell Biochem Biophys 2017; 75:203-210. [PMID: 27342128 PMCID: PMC5183522 DOI: 10.1007/s12013-016-0738-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/30/2016] [Indexed: 01/08/2023]
Abstract
In a type II clustered regularly interspaced short palindromic repeats (CRISPR) system, RNAs that are encoded at the CRISPR locus complex with the CRISPR-associated (Cas) protein Cas9 to form an RNA-guided nuclease that cleaves double-stranded DNAs at specific sites. In recent years, the CRISPR-Cas9 system has been successfully adapted for genome engineering in a wide range of organisms. Studies have indicated that a series of conformational changes in Cas9, coordinated by the RNA and the target DNA, direct the protein into its active conformation, yet details on these conformational changes, as well as their roles in the mechanism of function of Cas9, remain to be elucidated. Here, nucleic acid-dependent conformational changes in Streptococcus pyogenes Cas9 (SpyCas9) were investigated using the method of site-directed spin labeling (SDSL). Single nitroxide spin labels were attached, one at a time, at one of the two native cysteine residues (Cys80 and Cys574) of SpyCas9, and the spin-labeled proteins were shown to maintain their function. X-band continuous-wave electron paramagnetic resonance spectra of the nitroxide attached at Cys80 revealed conformational changes of SpyCas9 that are consistent with a large-scale domain re-arrangement upon binding to its RNA partner. The results demonstrate the use of SDSL to monitor conformational changes in CRISPR-Cas9, which will provide key information for understanding the mechanism of CRISPR function.
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Affiliation(s)
| | | | - S D Yogesha
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Richard H Nguyen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.
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16
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Babaylova ES, Malygin AA, Lomzov AA, Pyshnyi DV, Yulikov M, Jeschke G, Krumkacheva OA, Fedin MV, Karpova GG, Bagryanskaya EG. Complementary-addressed site-directed spin labeling of long natural RNAs. Nucleic Acids Res 2016; 44:7935-43. [PMID: 27269581 PMCID: PMC5027493 DOI: 10.1093/nar/gkw516] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/30/2016] [Indexed: 12/21/2022] Open
Abstract
Nanoscale distance measurements by pulse dipolar Electron paramagnetic resonance (EPR) spectroscopy allow new insights into the structure and dynamics of complex biopolymers. EPR detection requires site directed spin labeling (SDSL) of biomolecule(s), which remained challenging for long RNAs up-to-date. Here, we demonstrate that novel complementary-addressed SDSL approach allows efficient spin labeling and following structural EPR studies of long RNAs. We succeeded to spin-label Hepatitis C Virus RNA internal ribosome entry site consisting of ≈330 nucleotides and having a complicated spatial structure. Application of pulsed double electron–electron resonance provided spin–spin distance distribution, which agrees well with the results of molecular dynamics (MD) calculations. Thus, novel SDSL approach in conjunction with EPR and MD allows structural studies of long natural RNAs with nanometer resolution and can be applied to systems of biological and biomedical significance.
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Affiliation(s)
- Elena S Babaylova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Olesya A Krumkacheva
- Novosibirsk State University, Novosibirsk 630090, Russia International Tomography Center SB RAS, Novosibirsk 630090, Russia
| | - Matvey V Fedin
- Novosibirsk State University, Novosibirsk 630090, Russia International Tomography Center SB RAS, Novosibirsk 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- Novosibirsk State University, Novosibirsk 630090, Russia N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
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17
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Basso LGM, Mendes LFS, Costa-Filho AJ. The two sides of a lipid-protein story. Biophys Rev 2016; 8:179-191. [PMID: 28510056 DOI: 10.1007/s12551-016-0199-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 03/29/2016] [Indexed: 01/10/2023] Open
Abstract
Protein-membrane interactions play essential roles in a variety of cell functions such as signaling, membrane trafficking, and transport. Membrane-recruited cytosolic proteins that interact transiently and interfacially with lipid bilayers perform several of those functions. Experimental techniques capable of probing changes on the structural dynamics of this weak association are surprisingly limited. Among such techniques, electron spin resonance (ESR) has the enormous advantage of providing valuable local information from both membrane and protein perspectives by using intrinsic paramagnetic probes in metalloproteins or by attaching nitroxide spin labels to proteins and lipids. In this review, we discuss the power of ESR to unravel relevant structural and functional details of lipid-peripheral membrane protein interactions with special emphasis on local changes of specific regions of the protein and/or the lipids. First, we show how ESR can be used to investigate the direct interaction between a protein and a particular lipid, illustrating the case of lipid binding into a hydrophobic pocket of chlorocatechol 1,2-dioxygenase, a non-heme iron enzyme responsible for catabolism of aromatic compounds that are industrially released in the environment. In the second case, we show the effects of GPI-anchored tissue-nonspecific alkaline phosphatase, a protein that plays a crucial role in skeletal mineralization, and on the ordering and dynamics of lipid acyl chains. Then, switching to the protein perspective, we analyze the interaction with model membranes of the brain fatty acid binding protein, the major actor in the reversible binding and transport of hydrophobic ligands such as long-chain, saturated, or unsaturated fatty acids. Finally, we conclude by discussing how both lipid and protein views can be associated to address a common question regarding the molecular mechanism by which dihydroorotate dehydrogenase, an essential enzyme for the de novo synthesis of pyrimidine nucleotides, and how it fishes out membrane-embedded quinones to perform its function.
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Affiliation(s)
- Luis G Mansor Basso
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Luis F Santos Mendes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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18
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Xu CX, Zhang X, Zhou YW, Wang H, Cao Q, Shen Y, Ji LN, Mao ZW, Qin PZ. A Nitroxide-Tagged Platinum(II) Complex Enables the Identification of DNA G-Quadruplex Binding Mode. Chemistry 2016; 22:3405-3413. [PMID: 26845489 DOI: 10.1002/chem.201504960] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We reported a novel strategy for investigating small molecule binding to G-quadruplexes (GQs). A newly synthesized dinuclear platinum(II) complex (Pt2L) containing a nitroxide radical was shown to selectively bind a GQ-forming sequence derived from human telomere (hTel). Using the nitroxide moiety as a spin label, electron paramagnetic resonance (EPR) spectroscopy was carried out to investigate binding between Pt2L and hTel GQ. Measurements indicated that two molecules of Pt2L bind with one molecule of hTel GQ. The inter-spin distance measured between the two bound Pt2L, together with molecular docking analyses, revealed that Pt2L predominately binds to the neighboring narrow and wide grooves of the G-tetrads as hTel adopts the antiparallel conformation. The design and synthesis of nitroxide tagged GQ binders, and the use of spin-labeling/EPR to investigate their interactions with GQs, will aid the development of small molecules for manipulating GQs involved in crucial biological processes.
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Affiliation(s)
- Cui-Xia Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Xiaojun Zhang
- Department of Chemistry, University of Southern California Los Angeles, California, 90089 (USA)
| | - Yi-Wei Zhou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Hanqiang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Qian Cao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Yong Shen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Liang-Nian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Peter Z Qin
- Department of Chemistry, University of Southern California Los Angeles, California, 90089 (USA)
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19
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20
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Saha S, Jagtap AP, Sigurdsson ST. Site-Directed Spin Labeling of RNA by Postsynthetic Modification of 2'-Amino Groups. Methods Enzymol 2015; 563:397-414. [PMID: 26478493 DOI: 10.1016/bs.mie.2015.07.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To elucidate mechanisms that govern functions of nucleic acids, it is essential to understand their structure and dynamics. Electron paramagnetic resonance (EPR) spectroscopy is a valuable technique that is routinely used to study those aspects of nucleic acids. A prerequisite for most EPR studies of nucleic acids is incorporation of spin labels at specific sites, known as site-directed spin labeling (SDSL). There are two main strategies for SDSL through formation of covalent bonds, i.e., the phosphoramidite approach and postsynthetic spin-labeling. After describing briefly the advantages and disadvantages of these two strategies, postsynthetic labeling of 2'-amino groups in RNA is delineated. Postsynthetic labeling of 2'-amino groups in RNA using 4-isocyanato-TEMPO has long been established as a useful approach. However, this method has some drawbacks, both with regard to the spin-labeling protocol and the flexibility of the spin label itself. Recently reported isothiocyanate-substituted aromatic isoindoline-derived nitroxides can be used to quantitatively and selectively modify 2'-amino groups in RNA and do not have the drawbacks associated with 4-isocyanato-TEMPO. This chapter provides a detailed description of the postsynthetic spin-labeling methods of 2'-amino groups in RNA with a special focus on using the aromatic isothiocyanate spin labels.
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Affiliation(s)
- Subham Saha
- Department of Chemistry, Science Institute, University of Iceland, Reykjavik, Iceland
| | - Anil P Jagtap
- Department of Chemistry, Science Institute, University of Iceland, Reykjavik, Iceland
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Reykjavik, Iceland.
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21
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Shelke SA, Sandholt GB, Sigurdsson ST. Nitroxide-labeled pyrimidines for non-covalent spin-labeling of abasic sites in DNA and RNA duplexes. Org Biomol Chem 2015; 12:7366-74. [PMID: 25119508 DOI: 10.1039/c4ob01095g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Non-covalent and site-directed spin labeling gives easy access to spin-labeled nucleic acids for the study of their structure and dynamics by electron paramagnetic resonance (EPR) spectroscopy. In a search for improved spin labels for non-covalent binding to abasic sites in duplex DNA and RNA, ten pyrimidine-derived spin labels were prepared in good yields and their binding was evaluated by continuous wave (CW)-EPR spectroscopy. Most of the spin labels showed lower binding affinity than the previously reported label ç towards abasic sites in DNA and RNA. The most promising labels were triazole-linked spin labels and a pyrrolocytosine label. In particular, the N1-ethylamino derivative of a triazole-linked uracil spin label binds fully to both DNA and RNA containing an abasic site. This is the first example of a spin label that binds fully through non-covalent interactions with an abasic site in RNA.
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Affiliation(s)
- Sandip A Shelke
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland.
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22
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Duss O, Diarra Dit Konté N, Allain FHT. Cut and paste RNA for nuclear magnetic resonance, paramagnetic resonance enhancement, and electron paramagnetic resonance structural studies. Methods Enzymol 2015; 565:537-62. [PMID: 26577744 DOI: 10.1016/bs.mie.2015.05.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNA is a crucial regulator involved in most molecular processes of life. Understanding its function at the molecular level requires high-resolution structural information. However, the dynamic nature of RNA complicates structure determination because crystallization is often not possible or can result in crystal-packing artifacts resulting in nonnative structures. To study RNA and its complexes in solution, we described an approach in which large multi-domain RNA or protein-RNA complex structures can be determined at high resolution from isolated domains determined by nuclear magnetic resonance (NMR) spectroscopy, and then constructing the entire macromolecular structure using electron paramagnetic resonance (EPR) long-range distance constraints. Every step in this structure determination approach requires different types of isotope or spin-labeled RNAs. Here, we present a simple modular RNA cut and paste approach including protocols to generate (1) small isotopically labeled RNAs (<10 nucleotides) for NMR structural studies, which cannot be obtained by standard protocols, (2) large segmentally isotope and/or spin-labeled RNAs for diamagnetic NMR and paramagnetic relaxation enhancement NMR, and (3) large spin-labeled RNAs for pulse EPR spectroscopy.
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Affiliation(s)
- Olivier Duss
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
| | | | - Frédéric H-T Allain
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
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23
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Gophane DB, Sigurdsson ST. TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy. Beilstein J Org Chem 2015; 11:219-27. [PMID: 25815073 PMCID: PMC4362019 DOI: 10.3762/bjoc.11.24] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/15/2015] [Indexed: 02/04/2023] Open
Abstract
Three 2´-deoxynucleosides containing semi-flexible spin labels, namely (T)A, (U)A and (U)C, were prepared and incorporated into deoxyoligonucleotides using the phosphoramidite method. All three nucleosides contain 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) connected to the exocyclic amino group; (T)A directly and (U)A as well as (U)C through a urea linkage. (T)A and (U)C showed a minor destabilization of a DNA duplex, as registered by a small decrease in the melting temperature, while (U)A destabilized the duplex by more than 10 °C. Circular dichroism (CD) measurements indicated that all three labels were accommodated in B-DNA duplex. The mobility of the spin label (T)A varied with different base-pairing partners in duplex DNA, with the (T)A•T pair being the least mobile. Furthermore, (T)A showed decreased mobility under acidic conditions for the sequences (T)A•C and (T)A•G, to the extent that the EPR spectrum of the latter became nearly superimposable to that of (T)A•T. The reduced mobility of the (T)A•C and (T)A•G mismatches at pH 5 is consistent with the formation of (T)AH(+)•C and (T)AH(+)•G, in which protonation of N1 of A allows the formation of an additional hydrogen bond to N3 of C and N7 of G, respectively, with G in a syn-conformation. The urea-based spin labels (U)A and (U)C were more mobile than (T)A, but still showed a minor variation in their EPR spectra when paired with A, G, C or T in a DNA duplex. (U)A and (U)C had similar mobility order for the different base pairs, with the lowest mobility when paired with C and the highest when paired with T.
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Affiliation(s)
- Dnyaneshwar B Gophane
- 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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24
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25
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Tangprasertchai NS, Zhang X, Ding Y, Tham K, Rohs R, Haworth IS, Qin PZ. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids. Methods Enzymol 2015; 564:427-53. [PMID: 26477260 PMCID: PMC4641853 DOI: 10.1016/bs.mie.2015.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve "correct" all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements.
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Affiliation(s)
| | - Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Yuan Ding
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Kenneth Tham
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Remo Rohs
- Department of Chemistry, University of Southern California, Los Angeles, California, USA,Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Ian S. Haworth
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, California, USA,Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA,Corresponding author:
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26
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Combining NMR and EPR to Determine Structures of Large RNAs and Protein–RNA Complexes in Solution. Methods Enzymol 2015; 558:279-331. [DOI: 10.1016/bs.mie.2015.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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27
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Saha S, Jagtap AP, Sigurdsson ST. Site-directed spin labeling of 2′-amino groups in RNA with isoindoline nitroxides that are resistant to reduction. Chem Commun (Camb) 2015; 51:13142-5. [DOI: 10.1039/c5cc05014f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
2'-Amino groups in RNA were selectively spin labeled with reductively stable isoindoline nitroxides through a high-yielding reaction with aromatic isothiocyanates.
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Affiliation(s)
- Subham Saha
- University of Iceland
- Department of Chemistry
- Science Institute
- 107 Reykjavik
- Iceland
| | - Anil P. Jagtap
- University of Iceland
- Department of Chemistry
- Science Institute
- 107 Reykjavik
- Iceland
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28
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Jagtap AP, Krstic I, Kunjir NC, Hänsel R, Prisner TF, Sigurdsson ST. Sterically shielded spin labels for in-cell EPR spectroscopy: Analysis of stability in reducing environment. Free Radic Res 2014; 49:78-85. [DOI: 10.3109/10715762.2014.979409] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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29
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Chalmers BA, Saha S, Nguyen T, McMurtrie J, Sigurdsson ST, Bottle SE, Masters KS. TMIO-PyrImid Hybrids are Profluorescent, Site-Directed Spin Labels for Nucleic Acids. Org Lett 2014; 16:5528-31. [DOI: 10.1021/ol502003a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Benjamin A. Chalmers
- Faculty
of Science and Engineering, Queensland University of Technology, P.O. Box 2434, 2 George Street, Brisbane, QLD 4001, Australia
| | - Subham Saha
- University of Iceland, Department of Chemistry, Science
Institute, Dunhaga 3, 107 Reykjavík, Iceland
| | | | | | - Snorri Th. Sigurdsson
- University of Iceland, Department of Chemistry, Science
Institute, Dunhaga 3, 107 Reykjavík, Iceland
| | - Steven E. Bottle
- Faculty
of Science and Engineering, Queensland University of Technology, P.O. Box 2434, 2 George Street, Brisbane, QLD 4001, Australia
| | - Kye-Simeon Masters
- Faculty
of Science and Engineering, Queensland University of Technology, P.O. Box 2434, 2 George Street, Brisbane, QLD 4001, Australia
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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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31
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Ding Y, Zhang X, Tham KW, Qin PZ. Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe. Nucleic Acids Res 2014; 42:e140. [PMID: 25092920 PMCID: PMC4191381 DOI: 10.1093/nar/gku695] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as ‘DNA shape’, critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA duplexes that contain response elements of the p53 tumor suppressor. An R5a nitroxide spin label, which was covalently attached at a specific phosphate group, was scanned consecutively through the DNA duplex. X-band continuous-wave electron paramagnetic resonance spectroscopy was used to monitor rotational motions of R5a, which report on DNA structure and dynamics at the labeling site. An approach based on Pearson's coefficient analysis was developed to collectively examine the degree of similarity among the ensemble of R5a spectra. The resulting Pearson's coefficients were used to generate maps representing variation of R5a mobility along the DNA duplex. The R5a mobility maps were found to correlate with maps of certain DNA helical parameters, and were capable of revealing similarity and deviation in the shape of the two closely related DNA duplexes. Collectively, the R5a probe and the Pearson's coefficient-based lineshape analysis scheme yielded a generalizable method for examining sequence-dependent DNA shapes.
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Affiliation(s)
- Yuan Ding
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Kenneth W Tham
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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Casey TM, Liu Z, Esquiaqui JM, Pirman NL, Milshteyn E, Fanucci GE. Continuous wave W- and D-band EPR spectroscopy offer "sweet-spots" for characterizing conformational changes and dynamics in intrinsically disordered proteins. Biochem Biophys Res Commun 2014; 450:723-8. [PMID: 24950408 DOI: 10.1016/j.bbrc.2014.06.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 06/10/2014] [Indexed: 11/28/2022]
Abstract
Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for characterizing conformational sampling and dynamics in biological macromolecules. Here we demonstrate that nitroxide spectra collected at frequencies higher than X-band (∼9.5 GHz) have sensitivity to the timescale of motion sampled by highly dynamic intrinsically disordered proteins (IDPs). The 68 amino acid protein IA3, was spin-labeled at two distinct sites and a comparison of X-band, Q-band (35 GHz) and W-band (95 GHz) spectra are shown for this protein as it undergoes the helical transition chemically induced by tri-fluoroethanol. Experimental spectra at W-band showed pronounced line shape dispersion corresponding to a change in correlation time from ∼0.3 ns (unstructured) to ∼0.6 ns (α-helical) as indicated by comparison with simulations. Experimental and simulated spectra at X- and Q-bands showed minimal dispersion over this range, illustrating the utility of SDSL EPR at higher frequencies for characterizing structural transitions and dynamics in IDPs.
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Affiliation(s)
- Thomas M Casey
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Zhanglong Liu
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Jackie M Esquiaqui
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Natasha L Pirman
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Eugene Milshteyn
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA.
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Esquiaqui JM, Sherman EM, Ye JD, Fanucci GE. Site-directed spin-labeling strategies and electron paramagnetic resonance spectroscopy for large riboswitches. Methods Enzymol 2014; 549:287-311. [PMID: 25432754 DOI: 10.1016/b978-0-12-801122-5.00013-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genetic regulation effected by RNA riboswitches is governed by ligand-induced structural reorganization with modulation of RNA conformation and dynamics. Characterization of the conformational states of riboswitches in the presence or absence of salts and ligands is important for understanding how interconversion of riboswitch RNA folding states influences function. The methodology of site-directed spin labeling (SDSL) coupled with electron paramagnetic resonance (EPR) spectroscopy is suitable for such studies, wherein site-specific incorporation of a nitroxide radical spin probe allows for local dynamics and conformational changes to be investigated. This chapter reviews a strategy for SDSL-EPR studies of large riboswitches and uses the full length 232 nucleotide (nt) kink-turn motif-containing Vibrio cholerae (VC) glycine riboswitch as an example. Spin-labeling strategies and the challenges of incorporating spin labels into large riboswitches are reviewed and the approach to overcome these challenges is described. Results are subsequently presented illustrating changes in dynamics within the labeled region of the VC glycine riboswitch as observed using SDSL-EPR.
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Affiliation(s)
- Jackie M Esquiaqui
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Eileen M Sherman
- Department of Chemistry, University of Central Florida, Orlando, Florida, USA
| | - Jing-Dong Ye
- Department of Chemistry, University of Central Florida, Orlando, Florida, USA.
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, Gainesville, Florida, USA.
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Zhang X, Dantas Machado AC, Ding Y, Chen Y, Lu Y, Duan Y, Tham KW, Chen L, Rohs R, Qin PZ. Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling. Nucleic Acids Res 2013; 42:2789-97. [PMID: 24293651 PMCID: PMC3936745 DOI: 10.1093/nar/gkt1219] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The tumor suppressor protein p53 regulates numerous signaling pathways by specifically recognizing diverse p53 response elements (REs). Understanding the mechanisms of p53-DNA interaction requires structural information on p53 REs. However, such information is limited as a 3D structure of any RE in the unbound form is not available yet. Here, site-directed spin labeling was used to probe the solution structures of REs involved in p53 regulation of the p21 and Bax genes. Multiple nanometer distances in the p21-RE and BAX-RE, measured using a nucleotide-independent nitroxide probe and double-electron-electron-resonance spectroscopy, were used to derive molecular models of unbound REs from pools of all-atom structures generated by Monte-Carlo simulations, thus enabling analyses to reveal sequence-dependent DNA shape features of unbound REs in solution. The data revealed distinct RE conformational changes on binding to the p53 core domain, and support the hypothesis that sequence-dependent properties encoded in REs are exploited by p53 to achieve the energetically most favorable mode of deformation, consequently enhancing binding specificity. This work reveals mechanisms of p53-DNA recognition, and establishes a new experimental/computational approach for studying DNA shape in solution that has far-reaching implications for studying protein-DNA interactions.
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Affiliation(s)
- Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA and Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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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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36
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Chen Y, Zhang X, Dantas Machado AC, Ding Y, Chen Z, Qin PZ, Rohs R, Chen L. Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion. Nucleic Acids Res 2013; 41:8368-76. [PMID: 23836939 PMCID: PMC3783167 DOI: 10.1093/nar/gkt584] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The p53 core domain binds to response elements (REs) that contain two continuous half-sites as a cooperative tetramer, but how p53 recognizes discontinuous REs is not well understood. Here we describe the crystal structure of the p53 core domain bound to a naturally occurring RE located at the promoter of the Bcl-2-associated X protein (BAX) gene, which contains a one base-pair insertion between the two half-sites. Surprisingly, p53 forms a tetramer on the BAX-RE that is nearly identical to what has been reported on other REs with a 0-bp spacer. Each p53 dimer of the tetramer binds in register to a half-site and maintains the same protein–DNA interactions as previously observed, and the two dimers retain all the protein–protein contacts without undergoing rotation or translation. To accommodate the additional base pair, the DNA is deformed and partially disordered around the spacer region, resulting in an apparent unwinding and compression, such that the interactions between the dimers are maintained. Furthermore, DNA deformation within the p53-bound BAX-RE is confirmed in solution by site-directed spin labeling measurements. Our results provide a structural insight into the mechanism by which p53 binds to discontinuous sites with one base-pair spacer.
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Affiliation(s)
- Yongheng Chen
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA, Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China, Department of Chemistry, Norris Comprehensive Cancer Center, Department of Physics and Astronomy and Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
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37
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Fedorova OS, Tsvetkov YD. Pulsed electron double resonance in structural studies of spin-labeled nucleic acids. Acta Naturae 2013; 5:9-32. [PMID: 23556128 PMCID: PMC3612823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
This review deals with the application of the pulsed electron double resonance (PELDOR) method to studies of spin-labeled DNA and RNA with complicated spatial structures, such as tetramers, aptamers, riboswitches, and three- and four-way junctions. The use of this method for studying DNA damage sites is also described.
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Affiliation(s)
- O. S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk, 630090
| | - Yu. D. Tsvetkov
- Institute of Chemical Kinetics and Combustion, Siberian Branch, Russian Academy of Sciences, Institutskaya Str. 3, Novosibirsk, 630090
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Höbartner C, Sicoli G, Wachowius F, Gophane DB, Sigurdsson ST. Synthesis and Characterization of RNA Containing a Rigid and Nonperturbing Cytidine-Derived Spin Label. J Org Chem 2012; 77:7749-54. [DOI: 10.1021/jo301227w] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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39
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Popova AM, Hatmal MM, Frushicheva M, Price EA, Qin PZ, Haworth IS. Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations. J Phys Chem B 2012; 116:6387-96. [PMID: 22574834 PMCID: PMC3382087 DOI: 10.1021/jp303303v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The behavior of the nitroxide spin labels 1-oxyl-4-bromo-2,2,5,5-tetramethylpyrroline (R5a) and 1-oxyl-2,2,5,5-tetramethylpyrroline (R5) attached at a phosphorothioate-substituted site in a DNA duplex is modulated by the DNA in a site- and stereospecific manner. A better understanding of the mechanisms of R5a/R5 sensing of the DNA microenvironment will enhance our capability to relate information from nitroxide spectra to sequence-dependent properties of DNA. Toward this goal, electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations were used to investigate R5 and R5a attached as R(p) and S(p) diastereomers at phosphorothioate (pS)C(7) of d(CTACTG(pS)C(7)Y(8)TTAG). d(CTAAAGCAGTAG) (Y = T or U). X-band continuous-wave EPR spectra revealed that the dT(8) to dU(8) change alters nanosecond rotational motions of R(p)-R5a but produces no detectable differences for S(p)-R5a, R(p)-R5, and S(p)-R5. MD simulations were able to qualitatively account for these spectral variations and provide a plausible physical basis for the R5/R5a behavior. The simulations also revealed a correlation between DNA backbone B(I)/B(II) conformations and R5/R5a rotational diffusion, thus suggesting a direct connection between DNA local backbone dynamics and EPR-detectable R5/R5a motion. These results advance our understanding of how a DNA microenvironment influences nitroxide motion and the observed EPR spectra. This may enable use of R5/R5a for a quantitative description of the sequence-dependent properties of large biologically relevant DNA molecules.
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Affiliation(s)
- Anna M. Popova
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
| | - Ma’mon M. Hatmal
- Department of Biochemistry, University of Southern California, Los Angeles, California 90033-1039
| | - Maria Frushicheva
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
| | - Eric A. Price
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0744
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
| | - Ian S. Haworth
- Department of Biochemistry, University of Southern California, Los Angeles, California 90033-1039
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121
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40
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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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41
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Zhang X, Tung CS, Sowa GZ, Hatmal MM, Haworth IS, Qin PZ. Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling. J Am Chem Soc 2012; 134:2644-52. [PMID: 22229766 DOI: 10.1021/ja2093647] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The condensation of bacteriophage phi29 genomic DNA into its preformed procapsid requires the DNA packaging motor, which is the strongest known biological motor. The packaging motor is an intricate ring-shaped protein/RNA complex, and its function requires an RNA component called packaging RNA (pRNA). Current structural information on pRNA is limited, which hinders studies of motor function. Here, we used site-directed spin labeling to map the conformation of a pRNA three-way junction that bridges binding sites for the motor ATPase and the procapsid. The studies were carried out on a pRNA dimer, which is the simplest ring-shaped pRNA complex and serves as a functional intermediate during motor assembly. Using a nucleotide-independent labeling scheme, stable nitroxide radicals were attached to eight specific pRNA sites without perturbing RNA folding and dimer formation, and a total of 17 internitroxide distances spanning the three-way junction were measured using Double Electron-Electron Resonance spectroscopy. The measured distances, together with steric chemical constraints, were used to select 3662 viable three-way junction models from a pool of 65 billion. The results reveal a similar conformation among the viable models, with two of the helices (H(T) and H(L)) adopting an acute bend. This is in contrast to a recently reported pRNA tetramer crystal structure, in which H(T) and H(L) stack onto each other linearly. The studies establish a new method for mapping global structures of complex RNA molecules, and provide information on pRNA conformation that aids investigations of phi29 packaging motor and developments of pRNA-based nanomedicine and nanomaterial.
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Affiliation(s)
- Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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42
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Shelke SA, Sigurdsson ST. Structural changes of an abasic site in duplex DNA affect noncovalent binding of the spin label ç. Nucleic Acids Res 2011; 40:3732-40. [PMID: 22210856 PMCID: PMC3333849 DOI: 10.1093/nar/gkr1210] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The influence of structural changes of an abasic site in duplex DNA on noncovalent and site-directed spin labeling (NC-SDSL) of the spin label ç were examined with electron paramagnetic resonance (EPR) spectroscopy. The binding affinities of ç to sixteen different DNA duplexes containing all possible sequences immediately flanking the abasic site were determined and the results showed that the binding of ç is highly flanking-sequence dependent. In general, a 5′-dG nucleotide favors the binding of the spin label. In particular, 5′-d(G__T) was the best binding sequence whereas 5′-d(C__T) showed the lowest affinity. Changing the structure of the abasic site linker from a tetrahydrofuran analog (F) to the anucleosidic C3-spacer (C3) does not appreciably affect the binding of ç to the abasic site. For efficient binding of ç, the abasic site needs to be located at least four base pairs away from the duplex end. Introducing a methyl substituent at N3 of ç did not change the binding affinity, but a decreased binding was observed for both N3-ethyl and -propyl groups. These results will guide the design of abasic site receptors and spin label ligands for NC-SDSL of nucleic acids.
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Affiliation(s)
- Sandip A Shelke
- Department of Chemistry, University of Iceland, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland
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44
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Nguyen P, Qin PZ. RNA dynamics: perspectives from spin labels. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:62-72. [PMID: 21882345 DOI: 10.1002/wrna.104] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dynamics are important and indispensible physical attributes that play essential roles in RNA function. RNA dynamics are complex, spanning vast timescales, and encompassing a large number of physical modes. The technique of site-directed spin labeling (SDSL), which derives information on local structural and dynamic features of a macromolecule by monitoring a chemically stable nitroxide radical using electron paramagnetic resonance spectroscopy, has been applied to monitor intrinsic dynamics at defined structural states as well as to probe conformational transition dynamics of RNAs. The current state of SDSL studies of RNA dynamics is summarized here. Further development and application of SDSL promise to open up many more opportunities for probing RNA dynamics and connecting dynamics to structure and function.
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Affiliation(s)
- Phuong Nguyen
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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45
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Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FHT. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:1-61. [PMID: 21241883 DOI: 10.1016/j.pnmrs.2010.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/24/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Cyril Dominguez
- Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
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46
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A nucleotide-independent nitroxide probe reports on site-specific stereomeric environment in DNA. Biophys J 2011; 99:2180-9. [PMID: 20923652 DOI: 10.1016/j.bpj.2010.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 08/04/2010] [Accepted: 08/05/2010] [Indexed: 11/22/2022] Open
Abstract
In this report, stereospecific structural and dynamic features in DNA are studied using the site-directed spin labeling technique. A stable nitroxide radical, 1-oxyl-4-bromo-2,2,5,5-tetramethylpyrroline (R5a), was attached postsynthetically to phosphorothioates that were chemically introduced, one at a time, at five sites of a DNA duplex. The two phosphorothioate diastereomers (R(p) or S(p)) were separated, and nitroxide rotational motions were monitored using electron paramagnetic resonance spectroscopy. The resulting spectra vary according to diastereomer identity and location of the labeling site, with R(p)-R5a spectra effectively reporting on local DNA structural features and S(p)-R5a spectra sensing variations in local DNA motions. This establishes R(p)- and S(p)-R5a as unique probes for investigating nucleic acids in a site- and stereospecific manner, which may aid studies of stereospecific DNA/protein interactions. In addition, weighted averages of individual R(p) and S(p) spectra match those of R5a attached to mixed diastereomers. This suggests that R5a linked to mixed diastereomers reports on the composite behaviors of R(p)- and S(p)-R5a and is useful in initial probing of the DNA local environment. This work advances understanding of R5a/DNA coupling, and is a key step forward in developing a nucleotide-independent spectroscopic probe for studying nucleic acids.
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Edwards TE, Cekan P, Reginsson GW, Shelke SA, Ferré-D'Amaré AR, Schiemann O, Sigurdsson ST. Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C. Nucleic Acids Res 2011; 39:4419-26. [PMID: 21252294 PMCID: PMC3105401 DOI: 10.1093/nar/gkr015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Previously, we developed the deoxycytosine analog Ç (C-spin) as a bi-functional spectroscopic probe for the study of nucleic acid structure and dynamics using electron paramagnetic resonance (EPR) and fluorescence spectroscopy. To understand the effect of Ç on nucleic acid structure, we undertook a detailed crystallographic analysis. A 1.7 Å resolution crystal structure of Ç within a decamer duplex A-form DNA confirmed that Ç forms a non-perturbing base pair with deoxyguanosine, as designed. In the context of double-stranded DNA Ç adopted a planar conformation. In contrast, a crystal structure of the free spin-labeled base ç displayed a ∼ 20° bend at the oxazine linkage. Density function theory calculations revealed that the bent and planar conformations are close in energy and exhibit the same frequency for bending. These results indicate a small degree of flexibility around the oxazine linkage, which may be a consequence of the antiaromaticity of a 16-π electron ring system. Within DNA, the amplitude of the bending motion is restricted, presumably due to base-stacking interactions. This structural analysis shows that the Ç forms a planar, structurally non-perturbing base pair with G indicating it can be used with high confidence in EPR- or fluorescence-based structural and dynamics studies.
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48
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Krstić I, Endeward B, Margraf D, Marko A, Prisner TF. Structure and dynamics of nucleic acids. Top Curr Chem (Cham) 2011; 321:159-98. [PMID: 22160388 DOI: 10.1007/128_2011_300] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this chapter we describe the application of CW and pulsed EPR methods for the investigation of structural and dynamical properties of RNA and DNA molecules and their interaction with small molecules and proteins. Special emphasis will be given to recent applications of dipolar spectroscopy on nucleic acids.
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Affiliation(s)
- Ivan Krstić
- Goethe University Frankfurt, Frankfurt am Main, Germany
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49
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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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50
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Zhang X, Lee SW, Zhao L, Xia T, Qin PZ. Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling. RNA (NEW YORK, N.Y.) 2010; 16:2474-2483. [PMID: 20980674 PMCID: PMC2995408 DOI: 10.1261/rna.2360610] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 09/11/2010] [Indexed: 05/30/2023]
Abstract
In bacteriophage λ, interactions between a 22-amino acid peptide (called the N-peptide) and a stem-loop RNA element (called boxB) play a critical role in transcription anti-termination. The N-peptide/boxB complex has been extensively studied, and serves as a paradigm for understanding mechanisms of protein/RNA recognition. Particularly, ultrafast spectroscopy techniques have been applied to monitor picosecond fluorescence decay behaviors of 2-aminopurines embedded at various positions of the boxB RNA. The studies have led to a model in which the bound N-peptide exists in dynamic equilibrium between two states, with peptide C-terminal fragment either stacking on (i.e., the stacked state) or peeling away from (i.e., the unstacked state) the RNA loop. The function of the N-peptide/boxB complex seems to correlate with the fraction of the stacked state. Here, the N-peptide/boxB system is studied using the site-directed spin labeling technique, in which X-band electron paramagnetic resonance spectroscopy is applied to monitor nanosecond rotational behaviors of stable nitroxide radicals covalently attached to different positions of the N-peptide. The data reveal that in the nanosecond regime the C-terminal fragment of bound N-peptide adopts multiple discrete conformations within the complex. The characteristics of these conformations are consistent with the proposed stacked and unstacked states, and their distributions vary upon mutations within the N-peptide. These results suggest that the dynamic two-state model remains valid in the nanosecond regime, and represents a unique mode of function in the N-peptide/boxB RNA complex. It also demonstrates a connection between picosecond and nanosecond dynamics in a biological complex.
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Affiliation(s)
- Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, USA
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