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Chai Z, Li C. In-Cell 19F NMR of Proteins: Recent Progress and Future Opportunities. Chemistry 2024; 30:e202303988. [PMID: 38269421 DOI: 10.1002/chem.202303988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 01/26/2024]
Abstract
In vitro, 19F NMR methodology is preferably selected as a complementary and straightforward method for unveiling the conformations, dynamics, and interactions of biological molecules. Its effectiveness in vivo has seen continuous improvement, addressing challenges faced by conventional heteronuclear NMR experiments on structured proteins, such as severe line broadening, low signal-to-noise ratio, and background signals. Herein, we summarize the distinctive advantages of 19F NMR, along with recent progress in sample preparation and applications within the realm of in-cell NMR. Additionally, we offer insights into the future directions and prospects of this methodology based on our understanding.
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Affiliation(s)
- Zhaofei Chai
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
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2
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Juen F, Glänzer D, Plangger R, Kugler V, Fleischmann J, Stefan E, Case DA, Kovacs H, Dayie TK, Kreutz C. Enhanced TROSY Effect in [2- 19 F, 2- 13 C] Adenosine and ATP Analogs Facilitates NMR Spectroscopy of Very Large Biological RNAs in Solution. Angew Chem Int Ed Engl 2024; 63:e202316273. [PMID: 38185473 PMCID: PMC10922520 DOI: 10.1002/anie.202316273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/28/2023] [Accepted: 12/27/2023] [Indexed: 01/09/2024]
Abstract
Large RNAs are central to cellular functions, but characterizing such RNAs remains challenging by solution NMR. We present two labeling technologies based on [2-19 F, 2-13 C]-adenosine, which allow the incorporation of aromatic 19 F-13 C spin pairs. The labels when coupled with the transverse relaxation optimized spectroscopy (TROSY) enable us to probe RNAs comprising up to 124 nucleotides. With our new [2-19 F, 2-13 C]-adenosine-phosphoramidite, all resonances of the human hepatitis B virus epsilon RNA could be readily assigned. With [2-19 F, 2-13 C]-adenosine triphosphate, the 124 nt pre-miR-17-NPSL1-RNA was produced via in vitro transcription and the TROSY spectrum of this 40 kDa [2-19 F, 2-13 C]-A-labeled RNA featured sharper resonances than the [2-1 H, 2-13 C]-A sample. The mutual cancelation of the chemical-shift-anisotropy and the dipole-dipole-components of TROSY-resonances leads to narrow linewidths over a wide range of molecular weights. With the synthesis of a non-hydrolysable [2-19 F, 2-13 C]-adenosine-triphosphate, we facilitate the probing of co-factor binding in kinase complexes and NMR-based inhibitor binding studies in such systems. Our labels allow a straightforward assignment for larger RNAs via a divide-and-conquer/mutational approach. The new [2-19 F, 2-13 C]-adenosine precursors are a valuable addition to the RNA NMR toolbox and will allow the study of large RNAs/RNA protein complexes in vitro and in cells.
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Affiliation(s)
- Fabian Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - David Glänzer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Valentina Kugler
- Institute of Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Jakob Fleischmann
- Institute of Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Eduard Stefan
- Institute of Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020 Innsbruck, Austria
| | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Theodore Kwaku Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20782, USA
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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3
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Wang C, Xu G, Liu X, Jiang L, Zhou X, Liu M, Li C. 19F Nuclear Magnetic Resonance Fingerprinting Technique for Identifying and Quantifying G-Quadruplex Topology in Human Telomeric Overhangs. J Am Chem Soc 2024; 146:4741-4751. [PMID: 38346932 DOI: 10.1021/jacs.3c12247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid secondary structures with diverse topological features and biological roles. Human telomeric (Htelo) overhangs consisting of TTAGGG repeats can fold into G4s that adopt different topologies under physiological conditions. These G4s are potential targets for anticancer drugs. Despite intensive research, the existence and topology of G4s at Htelo overhangs in vivo are still unclear because there is no method to distinguish and quantify the topology of Htelo overhangs with native lengths that can form more than three tandem G4s in living cells. Herein, we present a novel 19F chemical shift fingerprinting technique to identify and quantify the topology of the Htelo overhangs up to five G-quadruplexes (G4s) and 120 nucleotides long both in vitro and in living cells. Our results show that longer overhang sequences tend to form stable G4s at the 5'- and 3'-ends, while the interior G4s are dynamic and "sliding" along the sequence, with TTA or 1-3 TTAGGG repeats as a linker. Each G4 in the longer overhang is conformationally heterogeneous, but the predominant ones are hybrid-2, two- or three-tetrad antiparallel, and hybrid-1 at the 5'-terminal, interior, and 3'-terminal, respectively. Additionally, we observed a distinct behavior of different lengths of telomeric sequences in living cells, suggesting that the overhang length and protein accessibility are related to its function. This technique provides a powerful tool for quickly identifying the folding topology and relative population of long Htelo overhangs, which may provide valuable insights into telomere functionality and be beneficial for structure-based anticancer drug development targeting G4s.
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Affiliation(s)
- Chen Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Xiaoli Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
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4
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Kara H, Axer A, Muskett FW, Bueno-Alejo CJ, Paschalis V, Taladriz-Sender A, Tubasum S, Vega MS, Zhao Z, Clark AW, Hudson AJ, Eperon IC, Burley GA, Dominguez C. 2'- 19F labelling of ribose in RNAs: a tool to analyse RNA/protein interactions by NMR in physiological conditions. Front Mol Biosci 2024; 11:1325041. [PMID: 38419689 PMCID: PMC10899400 DOI: 10.3389/fmolb.2024.1325041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Protein-RNA interactions are central to numerous cellular processes. In this work, we present an easy and straightforward NMR-based approach to determine the RNA binding site of RNA binding proteins and to evaluate the binding of pairs of proteins to a single-stranded RNA (ssRNA) under physiological conditions, in this case in nuclear extracts. By incorporation of a 19F atom on the ribose of different nucleotides along the ssRNA sequence, we show that, upon addition of an RNA binding protein, the intensity of the 19F NMR signal changes when the 19F atom is located near the protein binding site. Furthermore, we show that the addition of pairs of proteins to a ssRNA containing two 19F atoms at two different locations informs on their concurrent binding or competition. We demonstrate that such studies can be done in a nuclear extract that mimics the physiological environment in which these protein-ssRNA interactions occur. Finally, we demonstrate that a trifluoromethoxy group (-OCF3) incorporated in the 2'ribose position of ssRNA sequences increases the sensitivity of the NMR signal, leading to decreased measurement times, and reduces the issue of RNA degradation in cellular extracts.
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Affiliation(s)
- Hesna Kara
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Alexander Axer
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Frederick W Muskett
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Carlos J Bueno-Alejo
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- School of Chemistry, University of Leicester, Leicester, United Kingdom
| | - Vasileios Paschalis
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Andrea Taladriz-Sender
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Sumera Tubasum
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Marina Santana Vega
- Biomedical Engineering Research Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Zhengyun Zhao
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Alasdair W Clark
- Biomedical Engineering Research Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Andrew J Hudson
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- School of Chemistry, University of Leicester, Leicester, United Kingdom
| | - Ian C Eperon
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Glenn A Burley
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Cyril Dominguez
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
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5
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Singha Roy A, Majumder S, Saha P. Stable RNA G-Quadruplex in the 5'-UTR of Human cIAP1 mRNA Promotes Translation in an IRES-Independent Manner. Biochemistry 2024. [PMID: 38334276 DOI: 10.1021/acs.biochem.3c00521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
RNA G-quadruplex (rG4) structures can influence the fate and functions of mRNAs, especially the translation process. The presence of rG4 structures in 5'-untranslated regions (5'-UTRs) of mRNAs generally represses translation. However, rG4 structures can also promote internal ribosome entry site (IRES)-mediated translation as one of its determinants. Here, we report the identification of an evolutionary conserved rG4-forming sequence motif at the extreme 5'-end of the unusually long 5'-UTR (1.7 kb) in the transcript of human cIAP1 gene encoding the cellular inhibitor of apoptosis protein-1 that promotes cell survival by suppressing apoptosis and is overexpressed in various cancer cells. Expectedly, NMR study, CD spectroscopy, and UV melting assay confirm the formation of a potassium ion-dependent intramolecular and parallel rG4 structure at the sequence stretch. Moreover, the G4-RNA-specific precipitation using biotin-linked biomimetic BioCyTASQ validates the formation of the rG4 structure in the cIAP1 5'-UTR in cells. Interestingly, disruption of the rG4 structure in the cIAP1 5'-UTR results in a dramatic reduction in translation of the downstream luciferase reporter in cells, suggesting a translation-promoting effect of the rG4 structure, contrary to many earlier reports. Furthermore, enhancement of translation by the cIAP1 rG4 structure occurs in an IRES-independent manner.
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Affiliation(s)
- Aditya Singha Roy
- Crystallography and Molecular Biology Division, Biophysical Sciences Group, Saha Institute of Nuclear Physics, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
| | - Subhabrata Majumder
- Homi Bhabha National Institute, Mumbai 400094, India
- Biophysics and Structural Biology Division, Biophysical Sciences Group, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Partha Saha
- Crystallography and Molecular Biology Division, Biophysical Sciences Group, Saha Institute of Nuclear Physics, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
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6
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Wang S, Xu Y. RNA structure promotes liquid-to-solid phase transition of short RNAs in neuronal dysfunction. Commun Biol 2024; 7:137. [PMID: 38287096 PMCID: PMC10824717 DOI: 10.1038/s42003-024-05828-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
In nucleotide expansion disorders, RNA foci are reportedly associated with neurodegenerative disease pathogeneses. Characteristically, these RNAs exhibit long poly-RNA repeats, such as 47 × CAG, 47 × CUG, or 29 × GGGGCC, usually becoming abnormal pathological aggregations above a critical number of nucleotide repeats. However, it remains unclear whether short, predominantly cellular RNA molecules can cause phase transitions to induce RNA foci. Herein, we demonstrated that short RNAs even with only two repeats can aggregate into a solid-like state via special RNA G-quadruplex structures. In human cells, these solid RNA foci could not dissolve even when using agents that disrupt RNA gelation. The aggregation of shorter RNAs can be clearly observed in vivo. Furthermore, we found that RNA foci induce colocalization of the RNA-binding protein Sam68, a protein commonly found in patients with fragile X-associated tremor/ataxia syndrome, suppressing cell clonogenicity and eventually causing cell death. Our results suggest that short RNA gelation promoted by specific RNA structures contribute to the neurological diseases, which disturb functional cellular processes.
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Affiliation(s)
- Shiyu Wang
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.
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7
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Xu Y, Komiyama M. G-Quadruplexes in Human Telomere: Structures, Properties, and Applications. Molecules 2023; 29:174. [PMID: 38202757 PMCID: PMC10780218 DOI: 10.3390/molecules29010174] [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: 11/27/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
G-quadruplexes, intricate four-stranded structures composed of G-tetrads formed by four guanine bases, are prevalent in both DNA and RNA. Notably, these structures play pivotal roles in human telomeres, contributing to essential cellular functions. Additionally, the existence of DNA:RNA hybrid G-quadruplexes adds a layer of complexity to their structural diversity. This review provides a comprehensive overview of recent advancements in unraveling the intricacies of DNA and RNA G-quadruplexes within human telomeres. Detailed insights into their structural features are presented, encompassing the latest developments in chemical approaches designed to probe these G-quadruplex structures. Furthermore, this review explores the applications of G-quadruplex structures in targeting human telomeres. Finally, the manuscript outlines the imminent challenges in this evolving field, setting the stage for future investigations.
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Affiliation(s)
- Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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8
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Wang S, Song Y, He Z, Saneyoshi H, Iwakiri R, Xu P, Zhao C, Qu X, Xu Y. Unusual topological RNA G-quadruplex formed by an RNA duplex: implications for the dimerization of SARS-CoV-2 RNA. Chem Commun (Camb) 2023; 59:12703-12706. [PMID: 37819218 DOI: 10.1039/d3cc03192f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The infectious disease coronavirus 2019 (SARS-CoV-2) is caused by a virus that has RNA as its genetic material. To understand the detailed structural features of SARS-COV-2 RNA, we probed the RNA structure by NMR. Two RNA sequences form a duplex and self-associate to form a dimeric G-quadruplex. The FrG nucleoside was employed as a 19F sensor to confirm the RNA structure in cells by 19F NMR. A FRET assay further demonstrated that the dimeric G-quadruplex resulted in RNA dimerization in cells. These results provide the basis for the elucidation of SARS-COV-2 RNA function, which provides new insights into developing novel antiviral drugs against SARS-COV-2.
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Affiliation(s)
- Shiyu Wang
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
| | - Yi Song
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
| | - Zhiyong He
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
| | - Hisao Saneyoshi
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
| | - Rie Iwakiri
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
| | - Pengyu Xu
- Shonan Laboratory, Corporate R&D Headquarters, Otsuka Chemical Co., Ltd., 2Chome26-1, Muraokahigashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
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9
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Bao HL, Xu Y. Oligonucleotide Containing 8-Trifluoromethyl-2'-Deoxyguanosine as a Z-DNA Probe. Methods Mol Biol 2023; 2651:115-130. [PMID: 36892763 DOI: 10.1007/978-1-0716-3084-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Z-DNA structure is a noncanonical left-handed alternative form of DNA, which has been suggested to be biologically important and is related to several genetic diseases and cancer. Therefore, investigation of Z-DNA structure associated with biological events is of great importance to understanding the functions of these molecules. Here, we described the development of a trifluoromethyl labeled deoxyguanosine derivative and employed it as a 19F NMR probe to study Z-form DNA structure in vitro and in living cells.
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Affiliation(s)
- Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Kiyotake, Miyazaki, Japan.,Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Kiyotake, Miyazaki, Japan.
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10
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Li Q, Trajkovski M, Fan C, Chen J, Zhou Y, Lu K, Li H, Su X, Xi Z, Plavec J, Zhou C. 4'-SCF 3 -Labeling Constitutes a Sensitive 19 F NMR Probe for Characterization of Interactions in the Minor Groove of DNA. Angew Chem Int Ed Engl 2022; 61:e202201848. [PMID: 36163470 PMCID: PMC9828712 DOI: 10.1002/anie.202201848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Indexed: 01/12/2023]
Abstract
Fluorinated nucleotides are invaluable for 19 F NMR studies of nucleic acid structure and function. Here, we synthesized 4'-SCF3 -thymidine (T 4 ' - SCF 3 ${{^{4{^\prime}\hbox{-}{\rm SCF}{_{3}}}}}$ ) and incorporated it into DNA by means of solid-phase DNA synthesis. NMR studies showed that the 4'-SCF3 group exhibited a flexible orientation in the minor groove of DNA duplexes and was well accommodated by various higher order DNA structures. The three magnetically equivalent fluorine atoms in 4'-SCF3 -DNA constitute an isolated spin system, offering high 19 F NMR sensitivity and excellent resolution of the positioning of T 4 ' - SCF 3 ${{^{4{^\prime}\hbox{-}{\rm SCF}{_{3}}}}}$ within various secondary and tertiary DNA structures. The high structural adaptability and high sensitivity of T 4 ' - SCF 3 ${{^{4{^\prime}\hbox{-}{\rm SCF}{_{3}}}}}$ make it a valuable 19 F NMR probe for quantitatively distinguishing diverse DNA structures with single-nucleotide resolution and for monitoring the dynamics of interactions in the minor groove of double-stranded DNA.
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Affiliation(s)
- Qiang Li
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China,Slovenian NMR CentreNational Institute of ChemistryHajdrihova 19SI-1000LjubljanaSlovenia
| | - Marko Trajkovski
- Slovenian NMR CentreNational Institute of ChemistryHajdrihova 19SI-1000LjubljanaSlovenia
| | - Chaochao Fan
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Jialiang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Kuan Lu
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Hongjun Li
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Janez Plavec
- Slovenian NMR CentreNational Institute of ChemistryHajdrihova 19SI-1000LjubljanaSlovenia
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
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11
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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12
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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13
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Manna S, Sontakke VA, Srivatsan SG. Incorporation and Utility of a Responsive Ribonucleoside Analogue in Probing the Conformation of a Viral RNA Motif by Fluorescence and 19 F NMR Spectroscopy. Chembiochem 2021; 23:e202100601. [PMID: 34821449 DOI: 10.1002/cbic.202100601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/24/2021] [Indexed: 11/09/2022]
Abstract
Development of versatile probes that can enable the study of different conformations and recognition properties of therapeutic nucleic acid motifs by complementing biophysical techniques can greatly aid nucleic acid analysis and therapy. Here, we report the design, synthesis and incorporation of an environment-sensitive ribonucleoside analogue, which serves as a two-channel biophysical platform to investigate RNA structure and recognition by fluorescence and 19 F NMR spectroscopy techniques. The nucleoside analogue is based on a 5-fluorobenzofuran-uracil core and its fluorescence and 19 F NMR chemical shifts are highly sensitive to changes in solvent polarity and viscosity. Notably, the modified ribonucleotide and phosphoramidite substrates can be efficiently incorporated into RNA oligonucleotides (ONs) by in vitro transcription and standard solid-phase ON synthesis protocol, respectively. Fluorescence and 19 F readouts of the nucleoside incorporated into model RNA ONs are sensitive to the neighbouring base environment. The responsiveness of the probe was aptly utilized in detecting and quantifying the metal ion-induced conformational change in an internal ribosome entry site RNA motif of hepatitis C virus, which is an important therapeutic target. Taken together, our probe is a good addition to the nucleic acid analysis toolbox with the advantage that it can be used to study nucleic acid conformation and recognition simultaneously by two biophysical techniques.
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Affiliation(s)
- Sudeshna Manna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
| | - Vyankat A Sontakke
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
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14
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Bao HL, Xu Y. Observation of Z-DNA Structure via the Synthesis of Oligonucleotide DNA Containing 8-Trifluoromethyl-2-Deoxyguanosine. Curr Protoc 2021; 1:e28. [PMID: 33484490 DOI: 10.1002/cpz1.28] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This article contains detailed synthetic protocols for the preparation of DNA oligonucleotides containing 8-trifluoromethyl-2'-deoxyguanosine (CF3 dG) and their application to observe Z-DNA structure in vitro and in living HeLa cells. First, using a catalytic system consisting of FeSO4 , H2 SO4 , and H2 O2 in DMSO, we achieved a one-step synthesis of CF3 dG through a radical reaction between deoxyguanosine (dG) and CF3 I, with a yield of 45%. We then obtained the 3'-phosphoramidite of CF3 dG through a routine three-step procedure. Next, we employed the CF3 dG phosphoramidite monomer in the synthesis of oligonucleotides on a solid-phase DNA synthesizer. Finally, we used the CF3 dG-modified DNA oligonucleotides to observe Z-DNA structure in vitro and in living HeLa cells through 19 F NMR spectroscopy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of CF3 dG phosphoramidites Basic Protocol 2: Preparation of CF3 dG-modified DNA oligonucleotides Basic Protocol 3: Evaluation of CF3 dG stabilization of Z-DNA structure by CD spectroscopy Basic Protocol 4: Investigation of Z-DNA structure in vitro and in HeLa cells with CF3 dG-modified DNA oligonucleotides and 19 F NMR spectroscopy.
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Affiliation(s)
- Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, Japan
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15
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Krafčík D, Ištvánková E, Džatko Š, Víšková P, Foldynová-Trantírková S, Trantírek L. Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy. Int J Mol Sci 2021; 22:6042. [PMID: 34205000 PMCID: PMC8199861 DOI: 10.3390/ijms22116042] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Recently, the 1H-detected in-cell NMR spectroscopy has emerged as a unique tool allowing the characterization of interactions between nucleic acid-based targets and drug-like molecules in living human cells. Here, we assess the application potential of 1H and 19F-detected in-cell NMR spectroscopy to profile drugs/ligands targeting DNA G-quadruplexes, arguably the most studied class of anti-cancer drugs targeting nucleic acids. We show that the extension of the original in-cell NMR approach is not straightforward. The severe signal broadening and overlap of 1H in-cell NMR spectra of polymorphic G-quadruplexes and their complexes complicate their quantitative interpretation. Nevertheless, the 1H in-cell NMR can be used to identify drugs that, despite strong interaction in vitro, lose their ability to bind G-quadruplexes in the native environment. The in-cell NMR approach is adjusted to a recently developed 3,5-bis(trifluoromethyl)phenyl probe to monitor the intracellular interaction with ligands using 19F-detected in-cell NMR. The probe allows dissecting polymorphic mixture in terms of number and relative populations of individual G-quadruplex species, including ligand-bound and unbound forms in vitro and in cellulo. Despite the probe's discussed limitations, the 19F-detected in-cell NMR appears to be a promising strategy to profile G-quadruplex-ligand interactions in the complex environment of living cells.
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Affiliation(s)
- Daniel Krafčík
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Eva Ištvánková
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Šimon Džatko
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavlína Víšková
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | | | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
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16
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Tomaszewska M, Szabat M, Zielińska K, Kierzek R. Identification and Structural Aspects of G-Quadruplex-Forming Sequences from the Influenza A Virus Genome. Int J Mol Sci 2021; 22:6031. [PMID: 34199658 PMCID: PMC8199785 DOI: 10.3390/ijms22116031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/19/2022] Open
Abstract
Influenza A virus (IAV) causes seasonal epidemics and sporadic pandemics, therefore is an important research subject for scientists around the world. Despite the high variability of its genome, the structure of viral RNA (vRNA) possesses features that remain constant between strains and are biologically important for virus replication. Therefore, conserved structural motifs of vRNA can represent a novel therapeutic target. Here, we focused on the presence of G-rich sequences within the influenza A/California/07/2009(H1N1) genome and their ability to form RNA G-quadruplex structures (G4s). We identified 12 potential quadruplex-forming sequences (PQS) and determined their conservation among the IAV strains using bioinformatics tools. Then we examined the propensity of PQS to fold into G4s by various biophysical methods. Our results revealed that six PQS oligomers could form RNA G-quadruplexes. However, three of them were confirmed to adopt G4 structures by all utilized methods. Moreover, we showed that these PQS motifs are present within segments encoding polymerase complex proteins indicating their possible role in the virus biology.
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Affiliation(s)
- Maria Tomaszewska
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
| | - Marta Szabat
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
| | - Karolina Zielińska
- Department of Biomolecular NMR, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
| | - Ryszard Kierzek
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
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17
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Zafferani M, Hargrove AE. Small molecule targeting of biologically relevant RNA tertiary and quaternary structures. Cell Chem Biol 2021; 28:594-609. [PMID: 33823146 DOI: 10.1016/j.chembiol.2021.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/03/2021] [Accepted: 03/10/2021] [Indexed: 02/06/2023]
Abstract
Initial successes in developing small molecule ligands for non-coding RNAs have underscored their potential as therapeutic targets. More recently, these successes have been aided by advances in biophysical and structural techniques for identification and characterization of more complex RNA structures; these higher-level folds present protein-like binding pockets that offer opportunities to design small molecules that could achieve a degree of selectivity often hard to obtain at the primary and secondary structure level. More specifically, identification and small molecule targeting of RNA tertiary and quaternary structures have allowed researchers to probe several human diseases and have resulted in promising clinical candidates. In this review we highlight a selection of diverse and exciting successes and the experimental approaches that led to their discovery. These studies include examples of recent developments in RNA-centric assays and ligands that provide insight into the features responsible for the affinity and biological outcome of RNA-targeted chemical probes. This report highlights the potential and emerging opportunities to selectively target RNA tertiary and quaternary structures as a route to better understand and, ultimately, treat many diseases.
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18
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Thole JF, Fadero TC, Bonin JP, Stadmiller SS, Giudice JA, Pielak GJ. Danio rerio Oocytes for Eukaryotic In-Cell NMR. Biochemistry 2021; 60:451-459. [PMID: 33534998 DOI: 10.1021/acs.biochem.0c00922] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Understanding how the crowded and complex cellular milieu affects protein stability and dynamics has only recently become possible by using techniques such as in-cell nuclear magnetic resonance. However, the combination of stabilizing and destabilizing interactions makes simple predictions difficult. Here we show the potential of Danio rerio oocytes as an in-cell nuclear magnetic resonance model that can be widely used to measure protein stability and dynamics. We demonstrate that in eukaryotic oocytes, which are 3-6-fold less crowded than other cell types, attractive chemical interactions still dominate effects on protein stability and slow tumbling times, compared to the effects of dilute buffer.
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Affiliation(s)
- Joseph F Thole
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Tanner C Fadero
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jeffrey P Bonin
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Samantha S Stadmiller
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jonathan A Giudice
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Gary J Pielak
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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19
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Bao HL, Ishizuka T, Yamashita A, Furukoji E, Asada Y, Xu Y. Improving Thermodynamic Stability and Anticoagulant Activity of a Thrombin Binding Aptamer by Incorporation of 8-trifluoromethyl-2'-deoxyguanosine. J Med Chem 2020; 64:711-718. [PMID: 33289557 DOI: 10.1021/acs.jmedchem.0c01711] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In this study, we incorporated 8-trifluoromethyl-2'-deoxyguanosine (FG) into a thrombin binding aptamer (TBA). Circular dichroism, nuclear magnetic resonance (NMR), electrophoresis, and prothrombin time (PT) assay were performed to investigate the structure, thermodynamic stability, biological stability, and anticoagulant activity of the FG-modified TBA sequences. We found that the replacement of FG into TBA sequences led to a remarkable improvement in the melting temperature up to 30 °C compared with the native sequence. The trifluoromethyl group allowed us to investigate the TBA G-quadruplex structure by 19F NMR spectroscopy. Furthermore, PT assays showed that the modified sequences can significantly improve the anticoagulant activity in comparison with the native TBA. Finally, we demonstrated that the trifluoromethyl-modified TBA sequence could function as an anticoagulant reagent in live rats. Our results strongly suggested that FG is a powerful nucleoside derivative to increase the thermodynamic stability and anticoagulant activity of TBA.
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Affiliation(s)
- Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Atsushi Yamashita
- Department of Pathology, Division of Pathophysiology, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Eiji Furukoji
- Department of Radiology, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yujiro Asada
- Department of Pathology, Division of Pathophysiology, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
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20
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Bao HL, Masuzawa T, Oyoshi T, Xu Y. Oligonucleotides DNA containing 8-trifluoromethyl-2'-deoxyguanosine for observing Z-DNA structure. Nucleic Acids Res 2020; 48:7041-7051. [PMID: 32678885 PMCID: PMC7367190 DOI: 10.1093/nar/gkaa505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/01/2020] [Accepted: 06/10/2020] [Indexed: 01/05/2023] Open
Abstract
Z-DNA is known to be a left-handed alternative form of DNA and has important biological roles as well as being related to cancer and other genetic diseases. It is therefore important to investigate Z-DNA structure and related biological events in living cells. However, the development of molecular probes for the observation of Z-DNA structures inside living cells has not yet been realized. Here, we have succeeded in developing site-specific trifluoromethyl oligonucleotide DNA by incorporation of 8-trifluoromethyl-2′-deoxyguanosine (FG). 2D NMR strongly suggested that FG adopted a syn conformation. Trifluoromethyl oligonucleotides dramatically stabilized Z-DNA, even under physiological salt concentrations. Furthermore, the trifluoromethyl DNA can be used to directly observe Z-form DNA structure and interaction of DNA with proteins in vitro, as well as in living human cells by19F NMR spectroscopy for the first time. These results provide valuable information to allow understanding of the structure and function of Z-DNA.
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Affiliation(s)
- Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Tatsuki Masuzawa
- Faculty of Science, Department of Chemistry, Shizuoka University, 836 Ohya Suruga Shizuoka 422-8529, Japan
| | - Takanori Oyoshi
- Faculty of Science, Department of Chemistry, Shizuoka University, 836 Ohya Suruga Shizuoka 422-8529, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
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21
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Nußbaumer F, Plangger R, Roeck M, Kreutz C. Aromatic
19
F–
13
C TROSY—[
19
F,
13
C]‐Pyrimidine Labeling for NMR Spectroscopy of RNA. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Felix Nußbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Manuel Roeck
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck Innrain 80/82 6020 Innsbruck Austria
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22
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Nußbaumer F, Plangger R, Roeck M, Kreutz C. Aromatic 19 F- 13 C TROSY-[ 19 F, 13 C]-Pyrimidine Labeling for NMR Spectroscopy of RNA. Angew Chem Int Ed Engl 2020; 59:17062-17069. [PMID: 32558232 PMCID: PMC7540360 DOI: 10.1002/anie.202006577] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 12/22/2022]
Abstract
We present the access to [5-19 F, 5-13 C]-uridine and -cytidine phosphoramidites for the production of site-specifically modified RNAs up to 65 nucleotides (nts). The amidites were used to introduce [5-19 F, 5-13 C]-pyrimidine labels into five RNAs-the 30 nt human immunodeficiency virus trans activation response (HIV TAR) 2 RNA, the 61 nt human hepatitis B virus ϵ (hHBV ϵ) RNA, the 49 nt SAM VI riboswitch aptamer domain from B. angulatum, the 29 nt apical stem loop of the pre-microRNA (miRNA) 21 and the 59 nt full length pre-miRNA 21. The main stimulus to introduce the aromatic 19 F-13 C-spin topology into RNA comes from a work of Boeszoermenyi et al., in which the dipole-dipole interaction and the chemical shift anisotropy relaxation mechanisms cancel each other leading to advantageous TROSY properties shown for aromatic protein sidechains. This aromatic 13 C-19 F labeling scheme is now transferred to RNA. We provide a protocol for the resonance assignment by solid phase synthesis based on diluted [5-19 F, 5-13 C]/[5-19 F] pyrimidine labeling. For the 61 nt hHBV ϵ we find a beneficial 19 F-13 C TROSY enhancement, which should be even more pronounced in larger RNAs and will facilitate the NMR studies of larger RNAs. The [19 F, 13 C]-labeling of the SAM VI aptamer domain and the pre-miRNA 21 further opens the possibility to use the biorthogonal stable isotope reporter nuclei in in vivo NMR to observe ligand binding and microRNA processing in a biological relevant setting.
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Affiliation(s)
- Felix Nußbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Manuel Roeck
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
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23
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Yamaoki Y, Nagata T, Sakamoto T, Katahira M. Observation of nucleic acids inside living human cells by in-cell NMR spectroscopy. Biophys Physicobiol 2020; 17:36-41. [PMID: 33110737 PMCID: PMC7550250 DOI: 10.2142/biophysico.bsj-2020006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
The intracellular environment is highly crowded with biomacromolecules such as proteins and nucleic acids. Under such conditions, the structural and biophysical features of nucleic acids have been thought to be different from those in vitro. To obtain high-resolution structural information on nucleic acids in living cells, the in-cell NMR method is a unique tool. Following the first in-cell NMR measurement of nucleic acids in 2009, several interesting insights were obtained using Xenopus laevis oocytes. However, the in-cell NMR spectrum of nucleic acids in living human cells was not reported until two years ago due to the technical challenges of delivering exogenous nucleic acids. We reported the first in-cell NMR spectra of nucleic acids in living human cells in 2018, where we applied a pore-forming toxic protein, streptolysin O. The in-cell NMR measurements demonstrated that the hairpin structures of nucleic acids can be detected in living human cells. In this review article, we summarize our recent work and discuss the future prospects of the in-cell NMR technique for nucleic acids.
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Affiliation(s)
- Yudai Yamaoki
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.,Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomoki Sakamoto
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.,Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
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24
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Bao HL, Xu Y. Telomeric DNA-RNA-hybrid G-quadruplex exists in environmental conditions of HeLa cells. Chem Commun (Camb) 2020; 56:6547-6550. [PMID: 32396161 DOI: 10.1039/d0cc02053b] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the present study, we employed a 19F NMR approach to study the association of telomere RNA and DNA in vitro and in living human cells. We successfully characterized the DNA-RNA hybrid G-quadruplex (HQ) structure formed by telomeric DNA and RNA. We further demonstrated for the first time that an HQ conformation can exist in the environmental conditions of HeLa cells.
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Affiliation(s)
- Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
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Wang S, Liang L, Tang J, Cai Y, Zhao C, Fang S, Wang H, Weng T, Wang L, Wang D. Label-free single-molecule identification of telomere G-quadruplexes with a solid-state nanopore sensor. RSC Adv 2020; 10:27215-27224. [PMID: 35515777 PMCID: PMC9055465 DOI: 10.1039/d0ra05083k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
Telomere sequences can spontaneously form G-quadruplexes (G4) in the presence of some cations. In view of their relevance to genetic processes and potential as therapeutic-targets, hitherto, a wealth of conventional techniques have been reported for interrogation of G4 conformation diversity and corresponding folding kinetics, most of which are limited in precision and sensitivity. This work introduces a label-free solid-state nanopore (SSN) approach for the determination of inter-, intra- and tandem molecular G4 with distinct base permutation in various cation buffers with a tailored aperture and meanwhile captures the single-molecule G4 folding process. SSN translocation properties elucidated that both inter- and intramolecular G4 generated higher current blockage with longer duration than flexible homopolymer nucleotide, and intramolecular G4 are structurally more stable with higher event frequency and longer blockage time than intermolecular ones; base arrangement played weak role in translocation behaviors; the same sequences with one, two and three G4 skeletons displayed an increase in current blockage and a gradual extension in dwell time with the increase of molecule size recorded in the same nanopore. We observed the conformation change of single-molecule G4 which indicated the existence of folding/unfolding equilibration in nanopore, and real-time test suggested a gradual formation of G4 with time. Our results could provide a continued and improved understanding of the underlying relevance of structural stability and G4 folding process by utilizing SSN platform which exhibits strategic potential advances over the other methods with high spatial and temporal resolution. Nanopore detection of single-molecule G-quadruplexes.![]()
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Bao HL, Liu HS, Xu Y. Hybrid-type and two-tetrad antiparallel telomere DNA G-quadruplex structures in living human cells. Nucleic Acids Res 2019; 47:4940-4947. [PMID: 30976813 PMCID: PMC6547409 DOI: 10.1093/nar/gkz276] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 12/22/2022] Open
Abstract
Although the telomeric sequence has been reported to form various G-quadruplex topologies in vitro and in Xenopus laevis oocytes, in living human cells, the topology of telomeric DNA G-quadruplex remains a challenge. To investigate the human telomeric DNA G-quadruplex in a more realistic human cell environment, in the present study, we demonstrated that the telomeric DNA sequence can form two hybrid-type and two-tetrad antiparallel G-quadruplex structures by in-cell 19F NMR in living human cells (HELA CELLS). This result provides valuable information for understanding the structures of human telomeric DNA in living human cells and for the design of new drugs that target telomeric DNA.
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Affiliation(s)
- Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Hong-Shan Liu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
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Lightfoot HL, Hagen T, Tatum NJ, Hall J. The diverse structural landscape of quadruplexes. FEBS Lett 2019; 593:2083-2102. [PMID: 31325371 DOI: 10.1002/1873-3468.13547] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022]
Abstract
G-quadruplexes are secondary structures formed in G-rich sequences in DNA and RNA. Considerable research over the past three decades has led to in-depth insight into these unusual structures in DNA. Since the more recent exploration into RNA G-quadruplexes, such structures have demonstrated their in cellulo existence, function and roles in pathology. In comparison to Watson-Crick-based secondary structures, most G-quadruplexes display highly redundant structural characteristics. However, numerous reports of G-quadruplex motifs/structures with unique features (e.g. bulges, long loops, vacancy) have recently surfaced, expanding the repertoire of G-quadruplex scaffolds. This review addresses G-quadruplex formation and structure, including recent reports of non-canonical G-quadruplex structures. Improved methods of detection will likely further expand this collection of novel structures and ultimately change the face of quadruplex-RNA targeting as a therapeutic strategy.
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Affiliation(s)
- Helen L Lightfoot
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| | - Timo Hagen
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| | - Natalie J Tatum
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
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Kopec PM, Karlowski WM. Sequence Dynamics of Pre-mRNA G-Quadruplexes in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:812. [PMID: 31316532 PMCID: PMC6610454 DOI: 10.3389/fpls.2019.00812] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 06/05/2019] [Indexed: 06/01/2023]
Abstract
Intramolecular G-quadruplexes (G4s) are secondary structures that may form within G-rich stretches of nucleic acids. Although their presence has been associated with genomic instability and mutagenicity, recent reports suggest their involvement in regulation of diverse cellular events, including transcription and translation. The majority of data regarding G4s stems from mammalian and yeast studies, leaving the plant G4s almost unexplored. Using the publicly available Arabidopsis thaliana and Oryza sativa WGS data, we examined the single nucleotide variability of sequences predicted to form G4s (pG4s) structures. We focused our analysis on protein coding transcripts and compared the results to well-characterized Homo sapiens data. We demonstrate that the overall high variability of pG4s is not uniform and differs between gene structural elements. Specifically, plant AUG-containing pG4s, located within 5'UTR/CDS junctions, are abundant and appear not to be affected by a higher frequency of sequence change, indicating their functional relevance. Furthermore, we show that substitutions lowering the probability of G4s' formation are preferred over neutral or stabilizing modifications.
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Affiliation(s)
| | - Wojciech M. Karlowski
- Department of Computational Biology, Faculty of Biology, Mickiewicz University in Poznań, Poznań, Poland
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29
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Thompson RD, Baisden JT, Zhang Q. NMR characterization of RNA small molecule interactions. Methods 2019; 167:66-77. [PMID: 31128236 DOI: 10.1016/j.ymeth.2019.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 01/25/2023] Open
Abstract
Exciting discoveries of naturally occurring ligand-sensing and disease-linked noncoding RNAs have promoted significant interests in understanding RNA-small molecule interactions. NMR spectroscopy is a powerful tool for characterizing intermolecular interactions. In this review, we describe protocols and approaches for applying NMR spectroscopy to investigate interactions between RNA and small molecules. We review protocols for RNA sample preparation, methods for identifying RNA-binding small molecules, approaches for mapping RNA-small molecule interactions, determining complex structures, and characterizing binding kinetics. We hope this review will provide a guideline to streamline NMR applications in studying RNA-small molecule interactions, facilitating both basic mechanistic understandings of RNA functions and translational efforts in developing RNA-targeted therapeutics.
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Affiliation(s)
- Rhese D Thompson
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jared T Baisden
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Ishizuka T, Bao HL, Xu Y. 19F NMR Spectroscopy for the Analysis of DNA G-Quadruplex Structures Using 19F-Labeled Nucleobase. Methods Mol Biol 2019; 2035:407-433. [PMID: 31444766 DOI: 10.1007/978-1-4939-9666-7_26] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplex structures have been suggested to be biologically important in processes such as transcription and translation, gene expression and regulation in human cancer cells, and regulation of telomere length. Investigation of G-quadruplex structures associated with biological events is therefore essential to understanding the functions of these molecules. We developed the 19F-labeled nucleobases and introduced them into DNA sequences for the 19F NMR spectroscopy analysis. We present the 19F NMR methodology used in our research group for the study of G-quadruplex structures in vitro and in living cells.
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Affiliation(s)
- Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
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31
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Prado Martins R, Findakly S, Daskalogianni C, Teulade-Fichou MP, Blondel M, Fåhraeus R. In Cellulo Protein-mRNA Interaction Assay to Determine the Action of G-Quadruplex-Binding Molecules. Molecules 2018; 23:E3124. [PMID: 30501034 PMCID: PMC6321085 DOI: 10.3390/molecules23123124] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/25/2018] [Accepted: 11/26/2018] [Indexed: 11/16/2022] Open
Abstract
Protein-RNA interactions (PRIs) control pivotal steps in RNA biogenesis, regulate multiple physiological and pathological cellular networks, and are emerging as important drug targets. However, targeting of specific protein-RNA interactions for therapeutic developments is still poorly advanced. Studies and manipulation of these interactions are technically challenging and in vitro drug screening assays are often hampered due to the complexity of RNA structures. The binding of nucleolin (NCL) to a G-quadruplex (G4) structure in the messenger RNA (mRNA) of the Epstein-Barr virus (EBV)-encoded EBNA1 has emerged as an interesting therapeutic target to interfere with immune evasion of EBV-associated cancers. Using the NCL-EBNA1 mRNA interaction as a model, we describe a quantitative proximity ligation assay (PLA)-based in cellulo approach to determine the structure activity relationship of small chemical G4 ligands. Our results show how different G4 ligands have different effects on NCL binding to G4 of the EBNA1 mRNA and highlight the importance of in-cellulo screening assays for targeting RNA structure-dependent interactions.
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Affiliation(s)
| | - Sarah Findakly
- Université Paris 7, Inserm, UMR 1162, 75013 Paris, France.
| | - Chrysoula Daskalogianni
- Université Paris 7, Inserm, UMR 1162, 75013 Paris, France.
- ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Marie-Paule Teulade-Fichou
- Chemistry, Modelling and Imaging for Biology, CNRS UMR9187-Inserm U1196, Institut Curie, Université Paris-Sud, F-91405, Orsay, France.
| | - Marc Blondel
- GGB, Université de Brest, Inserm, CHRU Brest, EFS, UMR 1078, F-29200 Brest, France.
| | - Robin Fåhraeus
- Université Paris 7, Inserm, UMR 1162, 75013 Paris, France.
- ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
- Department of Medical Biosciences, Umeå University, 90187 Umeå, Sweden.
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653 Brno, Czech Republic.
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32
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Xu Y. Recent progress in human telomere RNA structure and function. Bioorg Med Chem Lett 2018; 28:2577-2584. [DOI: 10.1016/j.bmcl.2018.06.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/15/2018] [Accepted: 06/12/2018] [Indexed: 11/16/2022]
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Rosenau CP, Jelier BJ, Gossert AD, Togni A. Fluor-NMR-Spektroskopie rekalibriert. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802620] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Carl Philipp Rosenau
- Department Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Schweiz
| | - Benson J. Jelier
- Department Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Schweiz
| | - Alvar D. Gossert
- Biomolecular NMR Spectroscopy Platform, Department Biologie; Eidgenössische Technische Hochschule Zürich; Hönggerbergring 64 8093 Zürich Schweiz
| | - Antonio Togni
- Department Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Schweiz
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Rosenau CP, Jelier BJ, Gossert AD, Togni A. Exposing the Origins of Irreproducibility in Fluorine NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:9528-9533. [PMID: 29663671 DOI: 10.1002/anie.201802620] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Indexed: 01/07/2023]
Abstract
Fluorine chemistry has taken a pivotal role in chemical reaction discovery, drug development, and chemical biology. NMR spectroscopy, arguably the most important technique for the characterization of fluorinated compounds, is rife with highly inconsistent referencing of fluorine NMR chemical shifts, producing deviations larger than 1 ppm. Herein, we provide unprecedented evidence that both spectrometer design and the current unified scale system underpinning the calibration of heteronuclear NMR spectra have unintentionally led to widespread variation in the standardization of 19 F NMR spectral data. We demonstrate that internal referencing provides the most robust, practical, and reproducible method whereby chemical shifts can be consistently measured and confirmed between institutions to less than 30 ppb deviation. Finally, we provide a comprehensive table of appropriately calibrated chemical shifts of reference compounds that will serve to calibrate 19 F spectra correctly.
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Affiliation(s)
- Carl Philipp Rosenau
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Benson J Jelier
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Alvar D Gossert
- Biomolecular NMR Spectroscopy Platform, Department of Biology, Swiss Federal Institute of Technology, Hönggerbergring 64, 8093, Zürich, Switzerland
| | - Antonio Togni
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
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