1
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Roy S, Majee P, Sudhakar S, Mishra S, Kalia J, Pradeepkumar PI, Srivatsan SG. Structural elucidation of HIV-1 G-quadruplexes in a cellular environment and their ligand binding using responsive 19F-labeled nucleoside probes. Chem Sci 2024; 15:7982-7991. [PMID: 38817587 PMCID: PMC11134374 DOI: 10.1039/d4sc01755b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Understanding the structure and recognition of highly conserved regulatory segments of the integrated viral DNA genome that forms unique topologies can greatly aid in devising novel therapeutic strategies to counter chronic infections. In this study, we configured a probe system using highly environment-sensitive nucleoside analogs, 5-fluoro-2'-deoxyuridine (FdU) and 5-fluorobenzofuran-2'-deoxyuridine (FBFdU), to investigate the structural polymorphism of HIV-1 long terminal repeat (LTR) G-quadruplexes (GQs) by fluorescence and 19F NMR. FdU and FBFdU, serving as hairpin and GQ sensors, produced distinct spectral signatures for different GQ topologies adopted by LTR G-rich oligonucleotides. Importantly, systematic 19F NMR analysis in Xenopus laevis oocytes gave unprecedented information on the structure adopted by the LTR G-rich region in the cellular environment. The results indicate that it forms a unique GQ-hairpin hybrid architecture, a potent hotspot for selective targeting. Furthermore, structural models generated using MD simulations provided insights on how the probe system senses different GQs. Using the responsiveness of the probes and Taq DNA polymerase stop assay, we monitored GQ- and hairpin-specific ligand interactions and their synergistic inhibitory effect on the replication process. Our findings suggest that targeting GQ and hairpin motifs simultaneously using bimodal ligands could be a new strategy to selectively block the viral replication.
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Affiliation(s)
- Sarupa Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr Homi Bhabha Road Pune 411008 India
| | - Priyasha Majee
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Satyajit Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
| | - Jeet Kalia
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 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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2
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Flemmich L, Bereiter R, Micura R. Chemical Synthesis of Modified RNA. Angew Chem Int Ed Engl 2024; 63:e202403063. [PMID: 38529723 DOI: 10.1002/anie.202403063] [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: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.
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Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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3
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Ceuninck A, Lequeux T, Pfund E. Expanding the Scope of Group Transfer Radical Reaction: Toward the Synthesis of Fluorinated Nucleoside Analogues Incorporating Difluorophosphonylated Allylic Ether Moieties. J Org Chem 2024. [PMID: 38758748 DOI: 10.1021/acs.joc.4c00763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
Scope and limitations of the group transfer radical reaction of diisopropyl iododifluoromethylphosphonate onto carbohydrates and nucleosides are described. This key step allowed us to explore the synthesis of new fluorinated nucleoside analogues containing a difluorophosphonylated allylic ether moiety onto the 2'-position, in purine and pyrimidine series (B = A, C, G, T, U). Indeed, two unprecedented chemical approaches involving a late introduction of either the nucleobase or the fluorinated moiety are discussed.
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Affiliation(s)
- Aurore Ceuninck
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique, LCMT UMR 6507 ENSICAEN, UNICAEN, CNRS, 6 Bd. du Maréchal Juin, 14050 Caen, France
| | - Thierry Lequeux
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique, LCMT UMR 6507 ENSICAEN, UNICAEN, CNRS, 6 Bd. du Maréchal Juin, 14050 Caen, France
| | - Emmanuel Pfund
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique, LCMT UMR 6507 ENSICAEN, UNICAEN, CNRS, 6 Bd. du Maréchal Juin, 14050 Caen, France
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4
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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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5
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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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6
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Eichler C, Himmelstoß M, Plangger R, Weber LI, Hartl M, Kreutz C, Micura R. Advances in RNA Labeling with Trifluoromethyl Groups. Chemistry 2023; 29:e202302220. [PMID: 37534701 PMCID: PMC10947337 DOI: 10.1002/chem.202302220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/04/2023]
Abstract
Fluorine labeling of ribonucleic acids (RNA) in conjunction with 19 F NMR spectroscopy has emerged as a powerful strategy for spectroscopic analysis of RNA structure and dynamics, and RNA-ligand interactions. This study presents the first syntheses of 2'-OCF3 guanosine and uridine phosphoramidites, their incorporation into oligoribonucleotides by solid-phase synthesis and a comprehensive study of their properties. NMR spectroscopic analysis showed that the 2'-OCF3 modification is associated with preferential C2'-endo conformation of the U and G ribose in single-stranded RNA. When paired to the complementary strand, slight destabilization of the duplex caused by the modification was revealed by UV melting curve analysis. Moreover, the power of the 2'-OCF3 label for NMR spectroscopy is demonstrated by dissecting RNA pseudoknot folding and its binding to a small molecule. Furthermore, the 2'-OCF3 modification has potential for applications in therapeutic oligonucleotides. To this end, three 2'-OCF3 modified siRNAs were tested in silencing of the BASP1 gene which indicated enhanced performance for one of them. Importantly, together with earlier work, the present study completes the set of 2'-OCF3 nucleoside phosphoramidites to all four standard nucleobases (A, U, C, G) and hence enables applications that utilize the favorable properties of the 2'-OCF3 group without any restrictions in placing the modification into the RNA target sequence.
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Affiliation(s)
- Clemens Eichler
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Maximilian Himmelstoß
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Plangger
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Leonie I. Weber
- Institute of BiochemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Markus Hartl
- Institute of BiochemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Christoph Kreutz
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
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7
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Reddy CR, Ajaykumar U, Kolgave DH, Ramesh R. CAN-Promoted Thiolative ipso-Annulation of Unactivated N-Benzyl Acrylamides: Access to SCN/SCF 3/SO 2Ar Containing Azaspirocycles. J Org Chem 2023. [PMID: 37192481 DOI: 10.1021/acs.joc.3c00374] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A variety of acrylamides holding an unactivated N-benzyl group underwent dearomative ipso-cyclization induced by sulfur-centered radicals (SCN/ SCF3/ SO2Ar) in the presence of ceric ammonium nitrate (CAN) as the oxidant to furnish azaspirocycles in good yields. This is the first report on ipso-dearomatization of N-benzyl acrylamides that proceeds without a substituent at the para-position of the aromatic ring. The developed conditions are also found to be suitable for substrates holding substituents such as F, NO2, OMe, OH, and OAc at the para-position. The reaction features water as the source of oxygen, is compatible with a variety of functional groups, and proceeds in a short time.
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Affiliation(s)
- Chada Raji Reddy
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Uprety Ajaykumar
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Dattahari H Kolgave
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Remya Ramesh
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
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8
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Porat-Dahlerbruch G, Struppe J, Quinn CM, Gronenborn AM, Polenova T. 19F fast MAS (60-111 kHz) dipolar and scalar based correlation spectroscopy of organic molecules and pharmaceutical formulations. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101831. [PMID: 36182713 DOI: 10.1016/j.ssnmr.2022.101831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
19F magic angle spinning (MAS) NMR spectroscopy is a powerful tool for characterization of fluorinated solids. The recent development of 19F MAS NMR probes, operating at spinning frequencies of 60-111 kHz, enabled analysis of systems spanning from organic molecules to pharmaceutical formulations to biological assemblies, with unprecedented resolution. Herein, we systematically evaluate the benefits of high MAS frequencies (60-111 kHz) for 1D and 2D 19F-detected experiments in two pharmaceuticals, the antimalarial drug mefloquine and a formulation of the cholesterol-lowering drug atorvastatin calcium. We demonstrate that 1H decoupling is essential and that scalar-based, heteronuclear single quantum coherence (HSQC) and heteronuclear multiple quantum coherence (HMQC) correlation experiments become feasible and efficient at the MAS frequency of 100 kHz. This study opens doors for the applications of high frequency 19F MAS NMR to a wide range of problems in chemistry and biology.
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Affiliation(s)
- Gal Porat-Dahlerbruch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, 01821, United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Angela M Gronenborn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States; Department of Structural Biology, University of Pittsburgh, School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA, 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States; Department of Structural Biology, University of Pittsburgh, School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA, 15261, United States.
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9
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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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10
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Shet H, Sahu R, Sanghvi YS, Kapdi AR. Strategies for the Synthesis of Fluorinated Nucleosides, Nucleotides and Oligonucleotides. CHEM REC 2022; 22:e202200066. [PMID: 35638251 DOI: 10.1002/tcr.202200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/11/2022] [Indexed: 11/09/2022]
Abstract
Fluorinated nucleosides and oligonucleotides are of specific interest as probes for studying nucleic acids interaction, structures, biological transformations, and its biomedical applications. Among various modifications of oligonucleotides, fluorination of preformed nucleoside and/or nucleotides have recently gained attention owing to the unique properties of fluorine atoms imparting medicinal properties with respect to the small size, electronegativity, lipophilicity, and ability for stereochemical control. This review deals with synthetic protocols for selective fluorination either at sugar or base moiety in a preformed nucleosides, nucleotides and nucleic acids using specific fluorinating reagents.
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Affiliation(s)
- Harshita Shet
- Department of Chemistry, Institute of Chemical Technology -, Indian Oil Odisha Campus, IIT Kharagpur Extension Centre, Mouza Samantpuri, Bhubaneswar, Odisha-751013, India.,Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh road, Matunga, Mumbai-400019, India
| | - Rajesh Sahu
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh road, Matunga, Mumbai-400019, India
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802, Crystal Ridge, Encinitas, CA92024-6615, California, USA
| | - Anant R Kapdi
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh road, Matunga, Mumbai-400019, India
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11
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Gimenez D, Phelan A, Murphy CD, Cobb SL. 19F NMR as a tool in chemical biology. Beilstein J Org Chem 2021; 17:293-318. [PMID: 33564338 PMCID: PMC7849273 DOI: 10.3762/bjoc.17.28] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
We previously reviewed the use of 19F NMR in the broad field of chemical biology [Cobb, S. L.; Murphy, C. D. J. Fluorine Chem. 2009, 130, 132-140] and present here a summary of the literature from the last decade that has the technique as the central method of analysis. The topics covered include the synthesis of new fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein-protein interactions, protein-ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate biosynthesis and biodegradation of fluorinated organic compounds is also described.
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Affiliation(s)
- Diana Gimenez
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
| | - Aoife Phelan
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cormac D Murphy
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Steven L Cobb
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
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12
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Broft P, Dzatko S, Krafcikova M, Wacker A, Hänsel‐Hertsch R, Dötsch V, Trantirek L, Schwalbe H. In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells. Angew Chem Int Ed Engl 2021; 60:865-872. [PMID: 32975353 PMCID: PMC7839747 DOI: 10.1002/anie.202007184] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/22/2020] [Indexed: 12/14/2022]
Abstract
We report here the in-cell NMR-spectroscopic observation of the binding of the cognate ligand 2'-deoxyguanosine to the aptamer domain of the bacterial 2'-deoxyguanosine-sensing riboswitch in eukaryotic cells, namely Xenopus laevis oocytes and in human HeLa cells. The riboswitch is sufficiently stable in both cell types to allow for detection of binding of the ligand to the riboswitch. Most importantly, we show that the binding mode established by in vitro characterization of this prokaryotic riboswitch is maintained in eukaryotic cellular environment. Our data also bring important methodological insights: Thus far, in-cell NMR studies on RNA in mammalian cells have been limited to investigations of short (<15 nt) RNA fragments that were extensively modified by protecting groups to limit their degradation in the intracellular space. Here, we show that the in-cell NMR setup can be adjusted for characterization of much larger (≈70 nt) functional and chemically non-modified RNA.
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Affiliation(s)
- P. Broft
- Center for Biomolecular Magnetic Resonance (BMRZ)Institute for Organic Chemistry and Chemical BiologyGoethe UniversityMax-von-Laue-Str. 760438Frankfurt/M.Germany
| | - S. Dzatko
- National Centre for Biomolecular ResearchMasaryk UniversityKamenice 5625 00BrnoCzech Republic
- Central European Institute of Technology (CEITEC)Masaryk UniversityKamenice 753/5625 00BrnoCzech Republic
| | - M. Krafcikova
- National Centre for Biomolecular ResearchMasaryk UniversityKamenice 5625 00BrnoCzech Republic
- Institute of BiophysicsCzech Academy of SciencesKralovopolska 135612 65BrnoCzech Republic
| | - A. Wacker
- Center for Biomolecular Magnetic Resonance (BMRZ)Institute for Organic Chemistry and Chemical BiologyGoethe UniversityMax-von-Laue-Str. 760438Frankfurt/M.Germany
| | - Robert Hänsel‐Hertsch
- Present address: Center for Molecular Medicine CologneRobert-Koch-Str. 2150931CologneGermany
| | - Volker Dötsch
- Center for Biomolecular Magnetic Resonance (BMRZ)Institute of Biophysical ChemistryGoethe UniversityMax-von-Laue-Str. 960438Frankfurt/M.Germany
| | - L. Trantirek
- Central European Institute of Technology (CEITEC)Masaryk UniversityKamenice 753/5625 00BrnoCzech Republic
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ)Institute for Organic Chemistry and Chemical BiologyGoethe UniversityMax-von-Laue-Str. 760438Frankfurt/M.Germany
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13
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Broft P, Dzatko S, Krafcikova M, Wacker A, Hänsel‐Hertsch R, Dötsch V, Trantirek L, Schwalbe H. In‐Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- P. Broft
- Center for Biomolecular Magnetic Resonance (BMRZ) Institute for Organic Chemistry and Chemical Biology Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M. Germany
| | - S. Dzatko
- National Centre for Biomolecular Research Masaryk University Kamenice 5 625 00 Brno Czech Republic
- Central European Institute of Technology (CEITEC) Masaryk University Kamenice 753/5 625 00 Brno Czech Republic
| | - M. Krafcikova
- National Centre for Biomolecular Research Masaryk University Kamenice 5 625 00 Brno Czech Republic
- Institute of Biophysics Czech Academy of Sciences Kralovopolska 135 612 65 Brno Czech Republic
| | - A. Wacker
- Center for Biomolecular Magnetic Resonance (BMRZ) Institute for Organic Chemistry and Chemical Biology Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M. Germany
| | - Robert Hänsel‐Hertsch
- Present address: Center for Molecular Medicine Cologne Robert-Koch-Str. 21 50931 Cologne Germany
| | - Volker Dötsch
- Center for Biomolecular Magnetic Resonance (BMRZ) Institute of Biophysical Chemistry Goethe University Max-von-Laue-Str. 9 60438 Frankfurt/M. Germany
| | - L. Trantirek
- Central European Institute of Technology (CEITEC) Masaryk University Kamenice 753/5 625 00 Brno Czech Republic
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ) Institute for Organic Chemistry and Chemical Biology Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M. Germany
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14
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Abstract
A chemo- and regioselective perfluoromethylation using thioamides/selenoamides (prepared one step from corresponding lactams) as starting materials has been discovered. The reaction demonstrated complementary chemoselectivity to the C-H trifluoromethylation of (hetero)arenes as well as remarkable functional group compatibility especially toward radical sensitive olefin-, alkyne-, and arylhalide-bearing substrates. The examples of perfluorothio-/selenolated drug molecules indicated application potential of this strategy in drug modification and drug-analogue preparation.
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Affiliation(s)
- Xianhong Xu
- Molecular Synthesis Center & Key Laboratory of Marine Drugs, Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jianyu Zhang
- Molecular Synthesis Center & Key Laboratory of Marine Drugs, Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Tao Xu
- Molecular Synthesis Center & Key Laboratory of Marine Drugs, Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts & Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, China
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15
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Rahimidashaghoul K, Klimánková I, Hubálek M, Matoušek V, Filgas J, Slavíček P, Slanina T, Beier P. Visible‐Light‐Driven Fluoroalkylation of Tryptophan Residues in Peptides. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Kheironnesae Rahimidashaghoul
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science Charles University Hlavova 2030/8 128 43 Prague Czech Republic
| | - Iveta Klimánková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Václav Matoušek
- CF Plus Chemicals s.r.o., Karásek 1767/1 621 00 Brno Czech Republic
| | - Josef Filgas
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
- University of Chemistry and Technology Technická 5 160 00 Prague 6 Czech Republic
| | - Petr Slavíček
- University of Chemistry and Technology Technická 5 160 00 Prague 6 Czech Republic
| | - Tomáš Slanina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Petr Beier
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
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16
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Himmelstoß M, Erharter K, Renard E, Ennifar E, Kreutz C, Micura R. 2'- O-Trifluoromethylated RNA - a powerful modification for RNA chemistry and NMR spectroscopy. Chem Sci 2020; 11:11322-11330. [PMID: 34094374 PMCID: PMC8162808 DOI: 10.1039/d0sc04520a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/18/2020] [Indexed: 11/21/2022] Open
Abstract
New RNA modifications are needed to advance our toolbox for targeted manipulation of RNA. In particular, the development of high-performance reporter groups facilitating spectroscopic analysis of RNA structure and dynamics, and of RNA-ligand interactions has attracted considerable interest. To this end, fluorine labeling in conjunction with 19F-NMR spectroscopy has emerged as a powerful strategy. Appropriate probes for RNA previously focused on single fluorine atoms attached to the 5-position of pyrimidine nucleobases or at the ribose 2'-position. To increase NMR sensitivity, trifluoromethyl labeling approaches have been developed, with the ribose 2'-SCF3 modification being the most prominent one. A major drawback of the 2'-SCF3 group, however, is its strong impact on RNA base pairing stability. Interestingly, RNA containing the structurally related 2'-OCF3 modification has not yet been reported. Therefore, we set out to overcome the synthetic challenges toward 2'-OCF3 labeled RNA and to investigate the impact of this modification. We present the syntheses of 2'-OCF3 adenosine and cytidine phosphoramidites and their incorporation into oligoribonucleotides by solid-phase synthesis. Importantly, it turns out that the 2'-OCF3 group has only a slight destabilizing effect when located in double helical regions which is consistent with the preferential C3'-endo conformation of the 2'-OCF3 ribose as reflected in the 3 J (H1'-H2') coupling constants. Furthermore, we demonstrate the exceptionally high sensitivity of the new label in 19F-NMR analysis of RNA structure equilibria and of RNA-small molecule interactions. The study is complemented by a crystal structure at 0.9 Å resolution of a 27 nt hairpin RNA containing a single 2'-OCF3 group that well integrates into the minor groove. The new label carries high potential to outcompete currently applied fluorine labels for nucleic acid NMR spectroscopy because of its significantly advanced performance.
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Affiliation(s)
- Maximilian Himmelstoß
- University of Innsbruck, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI) Innrain 80-82 6020 Innsbruck Austria
| | - Kevin Erharter
- University of Innsbruck, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI) Innrain 80-82 6020 Innsbruck Austria
| | - Eva Renard
- Université de Strasbourg, Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Eric Ennifar
- Université de Strasbourg, Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Christoph Kreutz
- University of Innsbruck, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI) Innrain 80-82 6020 Innsbruck Austria
| | - Ronald Micura
- University of Innsbruck, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI) Innrain 80-82 6020 Innsbruck Austria
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17
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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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18
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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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19
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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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20
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Baranowski MR, Warminski M, Jemielity J, Kowalska J. 5'-fluoro(di)phosphate-labeled oligonucleotides are versatile molecular probes for studying nucleic acid secondary structure and interactions by 19F NMR. Nucleic Acids Res 2020; 48:8209-8224. [PMID: 32514551 PMCID: PMC7470941 DOI: 10.1093/nar/gkaa470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 01/03/2023] Open
Abstract
The high sensitivity of 19F nucleus to changes in the chemical environment has promoted the use of fluorine-labeled molecular probes to study structure and interactions of nucleic acids by 19F NMR. So far, most efforts have focused on incorporating the fluorine atom into nucleobase and ribose moieties using either monomer building blocks for solid-phase synthesis, or nucleoside triphosphates for enzymatic synthesis. Here, we report a simple and efficient synthesis of 5'-fluoromonophosphorylated and 5'-fluorodiphosphorylated oligodeoxyribonucleotides, which combines solid-phase and in-solution synthesis methods and requires only commercially available nucleoside phosphoramidites, followed by their evaluation as 19F NMR probes. We confirmed that the fluorine atom at the oligonucleotide 5' end did not alter the secondary structure of DNA fragments. Moreover, at the same time, it enabled real-time 19F NMR monitoring of various DNA-related biophysical processes, such as oligonucleotide hybridization (including mismatch identification), G-quadruplex folding/unfolding and its interactions with thrombin, as well as formation of an i-motif structure and its interaction with small-molecule ligands.
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Affiliation(s)
- Marek R Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
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21
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Li Q, Chen J, Trajkovski M, Zhou Y, Fan C, Lu K, Tang P, Su X, Plavec J, Xi Z, Zhou C. 4′-Fluorinated RNA: Synthesis, Structure, and Applications as a Sensitive 19F NMR Probe of RNA Structure and Function. J Am Chem Soc 2020; 142:4739-4748. [DOI: 10.1021/jacs.9b13207] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Qiang Li
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jialiang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chaochao Fan
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Kuan Lu
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Pingping Tang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
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22
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Chrominski M, Baranowski MR, Chmielinski S, Kowalska J, Jemielity J. Synthesis of Trifluoromethylated Purine Ribonucleotides and Their Evaluation as 19F NMR Probes. J Org Chem 2020; 85:3440-3453. [PMID: 31994393 PMCID: PMC7497640 DOI: 10.1021/acs.joc.9b03198] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protected guanosine and adenosine ribonucleosides and guanine nucleotides are readily functionalized with CF3 substituents within the nucleobase. Protected guanosine is trifluoromethylated at the C8 position under radical-generating conditions in up to 95% yield and guanosine 5'-oligophosphates in up to 35% yield. In the case of adenosine, the selectivity of trifluoromethylation depends heavily on the functional group protection strategy and leads to a set of CF3-modified nucleosides with different substitution patterns (C8, C2, or both) in up to 37% yield. Further transformations based on phosphorimidazolide chemistry afford various CF3-substituted mono- and dinucleoside oligophosphates in good yields. The utility of the trifluoromethylated nucleotides as probes for 19F NMR-based real-time enzymatic reaction monitoring is demonstrated with three different human nucleotide hydrolases (Fhit, DcpS, and cNIIIB). Substrate and product(s) resonances were sufficiently separated to enable effective tracking of each enzymatic activity of interest.
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Affiliation(s)
- Mikolaj Chrominski
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Marek R Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Sebastian Chmielinski
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
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23
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Klimánková I, Hubálek M, Matoušek V, Beier P. Synthesis of water-soluble hypervalent iodine reagents for fluoroalkylation of biological thiols. Org Biomol Chem 2019; 17:10097-10102. [PMID: 31754683 DOI: 10.1039/c9ob02115a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New open-chain and water-soluble hypervalent iodine reagents were synthesized and used for the transfer of fluoroalkyl groups to sulfur atoms of cysteine and cysteine-containing peptides under biocompatible conditions. Some of the reagents displayed excellent reactivity despite their limited stability in aqueous media. In reactions with a short cysteine-containing peptide, in addition to the expected S-fluoroalkylated product, a range of side-products were obtained. The amount of side-products depended on the conditions used (type of reagent, concentration, and pH). With highly activated hypervalent iodine reagents, a new reactive mode was observed - reaction with disulfides to form fluoroalkyl thiols.
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Affiliation(s)
- Iveta Klimánková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic.
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24
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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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25
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Meng H, Wen L, Xu Z, Li Y, Hao J, Zhao Y. Nonafluoro-tert-butoxylation of Diaryliodonium Salts. Org Lett 2019; 21:5206-5210. [DOI: 10.1021/acs.orglett.9b01813] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huan Meng
- Department of Chemistry, Innovative Drug Research Center, Shanghai University, Shanghai 200444, China
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Lixian Wen
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Zhenchuang Xu
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yipeng Li
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Jian Hao
- Department of Chemistry, Innovative Drug Research Center, Shanghai University, Shanghai 200444, China
| | - Yanchuan Zhao
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
- Key Laboratory of Energy Regulation Materials, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
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26
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Pfund E, Dupouy C, Rouanet S, Legay R, Lebargy C, Vasseur JJ, Lequeux T. Difluorophosphonylated Allylic Ether Moiety as a 2′-Modification of RNA-Type Molecules: Synthesis, Thermal, and Metabolic Studies. Org Lett 2019; 21:4803-4807. [DOI: 10.1021/acs.orglett.9b01689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emmanuel Pfund
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique, UMR 6507, ENSICAEN, UNICAEN, CNRS, 6 Bd du Maréchal Juin, 14050 Caen, France
| | - Christelle Dupouy
- Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier, CNRS, ENSCM, 34060 Montpellier, France
| | - Sonia Rouanet
- Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier, CNRS, ENSCM, 34060 Montpellier, France
| | - Rémi Legay
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique, UMR 6507, ENSICAEN, UNICAEN, CNRS, 6 Bd du Maréchal Juin, 14050 Caen, France
| | - Cyril Lebargy
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique, UMR 6507, ENSICAEN, UNICAEN, CNRS, 6 Bd du Maréchal Juin, 14050 Caen, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier, CNRS, ENSCM, 34060 Montpellier, France
| | - Thierry Lequeux
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique, UMR 6507, ENSICAEN, UNICAEN, CNRS, 6 Bd du Maréchal Juin, 14050 Caen, France
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27
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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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28
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Ishizuka T, Zhao PY, Bao HL, Xu Y. A multi-functional guanine derivative for studying the DNA G-quadruplex structure. Analyst 2018; 142:4083-4088. [PMID: 28932835 DOI: 10.1039/c7an00941k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the present study, we developed a multi-functional guanine derivative, 8FG, as a G-quadruplex stabilizer, a fluorescent probe for the detection of G-quadruplex formation, and a 19F sensor for the observation of the G-quadruplex. We demonstrate that the functional nucleoside bearing a 3,5-bis(trifluoromethyl)benzene group at the 8-position of guanine stabilizes the DNA G-quadruplex structure and fluoresces following the G-quadruplex formation. Furthermore, we show that the functional sensor can be used to directly observe DNA G-quadruplexes by 19F-NMR in living cells. To our knowledge, this is the first study showing that the nucleoside derivative simultaneously allows for three kinds of functions at a single G-quadruplex DNA. Our results suggest that the multi-functional nucleoside derivative can be broadly used for studying the G-quadruplex structure and serves as a powerful tool for examining the molecular basis of G-quadruplex formation 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, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
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29
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Affiliation(s)
- Zhenchuang Xu
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Chao Liu
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Shujuan Zhao
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Si Chen
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yanchuan Zhao
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
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30
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Investigation of higher-order RNA G-quadruplex structures in vitro and in living cells by 19F NMR spectroscopy. Nat Protoc 2018. [PMID: 29517770 DOI: 10.1038/nprot.2017.156] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Growing evidence indicates that RNA G-quadruplexes have important roles in various processes such as transcription, translation, regulation of telomere length, and formation of telomeric heterochromatin. Investigation of RNA G-quadruplex structures associated with biological events is therefore essential to understanding the functions of these RNA molecules. We recently demonstrated that the sensitivity and simplicity of 19F NMR can be used to directly observe higher-order telomeric G-quadruplexes of labeled RNA molecules in vitro and in living cells, as well as their interactions with ligands and proteins. This protocol describes detailed procedures for preparing 19F-labeled RNA, the evaluation of 19F-labeled RNA G-quadruplexes in vitro and in living Xenopus laevis oocytes by 19F NMR spectroscopy, the quantitative characterization of thermodynamic properties of the G-quadruplexes, and monitoring of RNA G-quadruplex interactions with ligand molecules and proteins. This approach has several advantages over existing techniques. First, it is relatively easy to prepare 19F-labeled RNA molecules by introducing a 3,5-bis(trifluoromethyl) benzene moiety into its 5' terminus. Second, the absence of any natural fluorine background signal in RNA and cells results in a simple and clear 19F NMR spectrum and does not suffer from high background signals as does 1H NMR. Finally, the simplicity and sensitivity of 19F NMR can be used to easily distinguish different RNA G-quadruplex conformations under various conditions, even in living cells, and to obtain the precise thermodynamic parameters of higher-order G-quadruplexes. This protocol can be completed in 2 weeks.
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31
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Guo F, Li Q, Zhou C. Synthesis and biological applications of fluoro-modified nucleic acids. Org Biomol Chem 2018; 15:9552-9565. [PMID: 29086791 DOI: 10.1039/c7ob02094e] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Owing to the unique physical properties of a fluorine atom, incorporating fluoro-modifications into nucleic acids offers striking biophysical and biochemical features, and thus significantly extends the breadth and depth of biological applications of nucleic acids. In this review, fluoro-modified nucleic acids that have been synthesized through either solid phase synthesis or the enzymatic approach are briefly summarised, followed by a section describing their biomedical applications in nucleic acid-based therapeutics, 18F PET imaging and mechanistic studies of DNA modifying enzymes. In the last part, the utility of 19F NMR and MRI for probing the structure, dynamics and molecular interactions of fluorinated nucleic acids is reviewed.
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Affiliation(s)
- Fengmin Guo
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China.
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32
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Ishizuka T, Yamashita A, Asada Y, Xu Y. Studying DNA G-Quadruplex Aptamer by 19F NMR. ACS OMEGA 2017; 2:8843-8848. [PMID: 30023592 PMCID: PMC6045382 DOI: 10.1021/acsomega.7b01405] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/22/2017] [Indexed: 06/08/2023]
Abstract
In this study, we demonstrated that 19F NMR can be used to study the thrombin-binding aptamer (TBA) DNA G-quadruplex, widely used as a model structure for studying G-quadruplex aptamers. We systematically examined the structural feature of the TBA G-quadruplex aptamer with fluorine-19 (19F) labels at all of the thymidine positions. We successfully observed the structural change between the G-quadruplex and the unstructured single strand by 19F NMR spectroscopy. The thermodynamic parameters of these DNA G-quadruplex aptamers were also determined from the 19F NMR signals. We further showed that the 19F NMR method can be used to observe the complex formed by TBA G-quadruplex and thrombin. Our results suggest that 19F NMR spectroscopy is a useful approach to study the aptamer G-quadruplex structure.
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Affiliation(s)
- Takumi Ishizuka
- Division
of Chemistry, Department of Medical Sciences, Faculty of
Medicine and Department of Pathology, Division of Pathophysiology, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Atsushi Yamashita
- Division
of Chemistry, Department of Medical Sciences, Faculty of
Medicine and Department of Pathology, Division of Pathophysiology, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yujiro Asada
- Division
of Chemistry, Department of Medical Sciences, Faculty of
Medicine and 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 and Department of Pathology, Division of Pathophysiology, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
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33
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Bao HL, Ishizuka T, Sakamoto T, Fujimoto K, Uechi T, Kenmochi N, Xu Y. Characterization of human telomere RNA G-quadruplex structures in vitro and in living cells using 19F NMR spectroscopy. Nucleic Acids Res 2017; 45:5501-5511. [PMID: 28180296 PMCID: PMC5435947 DOI: 10.1093/nar/gkx109] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/06/2017] [Indexed: 11/12/2022] Open
Abstract
Human telomeric RNA has been identified as a key component of the telomere machinery. Recently, the growing evidence suggests that the telomeric RNA forms G-quadruplex structures to play an important role in telomere protection and regulation. In the present studies, we developed a 19F NMR spectroscopy method to investigate the telomeric RNA G-quadruplex structures in vitro and in living cells. We demonstrated that the simplicity and sensitivity of 19F NMR approach can be used to directly observe the dimeric and two-subunits stacked G-quadruplexes in vitro and in living cells and quantitatively characterize the thermodynamic properties of the G-quadruplexes. By employing the 19F NMR in living cell experiment, we confirmed for the first time that the higher-order G-quadruplex exists in cells. We further demonstrated that telomere RNA G-quadruplexes are converted to the higher-order G-quadruplex under molecular crowding condition, a cell-like environment. We also show that the higher-order G-quadruplex has high thermal stability in crowded solutions. The finding provides new insight into the structural behavior of telomere RNA G-quadruplex in living cells. These results open new avenues for the investigation of G-quadruplex structures 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, 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
| | - Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Tamayo Uechi
- Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Naoya Kenmochi
- Frontier Science Research Center, 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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34
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Bao H, Ishizuka T, Iwanami A, Oyoshi T, Xu Y. A Simple and Sensitive
19
F NMR Approach for Studying the Interaction of RNA G‐Quadruplex with Ligand Molecule and Protein. ChemistrySelect 2017. [DOI: 10.1002/slct.201700711] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Hong‐Liang Bao
- Division of Chemistry, Department of Medical Sciences Department, Faculty of MedicineUniversity of Miyazaki 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences Department, Faculty of MedicineUniversity of Miyazaki 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Ayaka Iwanami
- Faculty of Science, Department of ChemistryShizuoka University 836 Ohya Suruga Shizuoka 422-8529 Japan
| | - Takanori Oyoshi
- Faculty of Science, Department of ChemistryShizuoka University 836 Ohya Suruga Shizuoka 422-8529 Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences Department, Faculty of MedicineUniversity of Miyazaki 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
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35
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Granqvist L, Virta P. Characterization of G-Quadruplex/Hairpin Transitions of RNAs by 19 F NMR Spectroscopy. Chemistry 2016; 22:15360-15372. [PMID: 27603896 DOI: 10.1002/chem.201602898] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Indexed: 12/21/2022]
Abstract
2'-O-[(4-Trifluoromethyl-triazol-1-yl)methyl] reporter groups have been incorporated into guanosine-rich RNA models (including a known bistable Qd/Hp RNA and two G-rich regions of mRNA of human prion protein, PrP) and applied for the 19 F NMR spectroscopic characterization of plausible G-quadruplex/hairpin (Qd/Hp) transitions in these RNA structures. For the synthesis of the CF3 -labeled RNAs, phosphoramidite building blocks of 2'-O-[(4-CF3 -triazol-1-yl)methyl] nucleosides (cytidine, adenosine, and guanosine) were prepared and used as an integral part of the standard solid-phase RNA synthesis. The obtained 19 F NMR spectra supported the usual characterization data (obtained by UV- and CD-melting profiles and by 1 H NMR spectra of the imino regions) and additionally gave more detailed information on the Qd/Hp transitions. The molar fractions of the secondary structural species (Qd, Hp) upon thermal denaturation and under varying ionic conditions could be determined from the intensities and shifts of the 19 F NMR signals. For a well-behaved Qd/Hp transition, thermodynamic parameters could be extracted.
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Affiliation(s)
- Lotta Granqvist
- Department of Chemistry, University of Turku, Turku, 20014, Finland.
| | - Pasi Virta
- Department of Chemistry, University of Turku, Turku, 20014, Finland.
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36
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Brantley J, Samant AV, Toste FD. Isolation and Reactivity of Trifluoromethyl Iodonium Salts. ACS CENTRAL SCIENCE 2016; 2:341-350. [PMID: 27280169 PMCID: PMC4882740 DOI: 10.1021/acscentsci.6b00119] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Indexed: 06/06/2023]
Abstract
The strategic incorporation of the trifluoromethyl (CF3) functionality within therapeutic or agrochemical agents is a proven strategy for altering their associated physicochemical properties (e.g., metabolic stability, lipophilicity, and bioavailability). Electrophilic trifluoromethylation has emerged as an important methodology for installing the CF3 moiety onto an array of molecular architectures, and, in particular, CF3 λ(3)-iodanes have garnered significant interest because of their unique reactivity and ease of handling. Trifluoromethylations mediated by these hypervalent iodine reagents often require activation through an exogenous Lewis or Brønsted acid; thus, putative intermediates invoked in these transformations are cationic CF3 iodoniums. These iodoniums have, thus far, eluded isolation and investigation of their innate reactivity (which has encouraged speculation that such species cannot be accessed). A more complete understanding of the mechanistic relevance of CF3 iodoniums is paramount for the development of new trifluoromethylative strategies involving λ(3)-iodanes. Here, we demonstrate that CF3 iodonium salts are readily prepared from common λ(3)-iodane precursors and exhibit remarkable persistence under ambient conditions. These reagents are competent electrophiles for a variety of trifluoromethylation reactions, and their reactivity is reminiscent of that observed when CF3 iodanes are activated using Lewis acids. As such, our results suggest the mechanistic relevance of CF3 iodonium intermediates in trifluoromethylative processes mediated by λ(3)-iodanes. The isolation of CF3 iodonium salts also presents the unique opportunity to employ them more generally as mechanistic probes.
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37
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Sochor F, Silvers R, Müller D, Richter C, Fürtig B, Schwalbe H. (19)F-labeling of the adenine H2-site to study large RNAs by NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2016; 64:63-74. [PMID: 26704707 DOI: 10.1007/s10858-015-0006-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/20/2015] [Indexed: 05/24/2023]
Abstract
In comparison to proteins and protein complexes, the size of RNA amenable to NMR studies is limited despite the development of new isotopic labeling strategies including deuteration and ligation of differentially labeled RNAs. Due to the restricted chemical shift dispersion in only four different nucleotides spectral resolution remains limited in larger RNAs. Labeling RNAs with the NMR-active nucleus (19)F has previously been introduced for small RNAs up to 40 nucleotides (nt). In the presented work, we study the natural occurring RNA aptamer domain of the guanine-sensing riboswitch comprising 73 nucleotides from Bacillus subtilis. The work includes protocols for improved in vitro transcription of 2-fluoroadenosine-5'-triphosphat (2F-ATP) using the mutant P266L of the T7 RNA polymerase. Our NMR analysis shows that the secondary and tertiary structure of the riboswitch is fully maintained and that the specific binding of the cognate ligand hypoxanthine is not impaired by the introduction of the (19)F isotope. The thermal stability of the (19)F-labeled riboswitch is not altered compared to the unmodified sequence, but local base pair stabilities, as measured by hydrogen exchange experiments, are modulated. The characteristic change in the chemical shift of the imino resonances detected in a (1)H,(15)N-HSQC allow the identification of Watson-Crick base paired uridine signals and the (19)F resonances can be used as reporters for tertiary and secondary structure transitions, confirming the potential of (19)F-labeling even for sizeable RNAs in the range of 70 nucleotides.
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Affiliation(s)
- F Sochor
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - R Silvers
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - D Müller
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - C Richter
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - B Fürtig
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany.
| | - H Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany.
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38
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Reddy L CS, Sharma VK, Kumar R, Singh A, Parmar VS, Sanghvi YS, Prasad AK. Facile Access to 5'-S-(4,4'-Dimethoxytrityl)-2',5'-Dideoxyribonucleosides via Stable Disulfide Intermediates. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2015; 62:1.34.1-1.34.9. [PMID: 26380902 DOI: 10.1002/0471142700.nc0134s62] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Thionucleosides represent an important class of modified nucleos(t)ides that have found distinct applications in the chemical biology of synthetic oligonucleotides, but the use of these compounds is substantially lessened by the instability or high reactivity of the sulfhydryl group. This unit describes a protocol for the synthesis of 2',5'-dideoxy-5'-thioribonucleoside disulfides by utilizing Mitsunobu reaction conditions on 3'-O-levulinyl-2'-deoxyribonucleosides in the presence of thiobenzoic acid followed by facile hydrolysis and in situ oxidation of the resulting 5'-thiolated nucleosides using methanolic ammonia. The utility of these disulfides has been demonstrated as stable precursors for the synthesis of 5'-thio-modified 2'-deoxynucleosides. To validate the potential of the methodology, 5'-S-(4,4'-dimethoxytrityl)-2',5'-dideoxythymidine phosphoramidite has been synthesized by in situ cleavage of the disulfide linkage of 2',5'-dideoxy-5'-thiothymidine disulfide followed by protection with a dimethoxytriphenyl (DMT) group and 3'-phosphitylation using 2-cyanoethyl N,N-diisopropylchlorophosphoramidite.
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Affiliation(s)
| | - Vivek K Sharma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Rajesh Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Ankita Singh
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Virinder S Parmar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | | | - Ashok K Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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39
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Granqvist L, Virta P. 2'-O-[(4-CF3-triazol-1-yl)methyl] Uridine - A Sensitive (19)F NMR Sensor for the Detection of RNA Secondary Structures. J Org Chem 2015. [PMID: 26214588 DOI: 10.1021/acs.joc.5b00973] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A sensitive uridine-derived sensor (viz., 2'-O-[(4-CF3-triazol-1-yl)methyl]uridine, 1) for (19)F NMR spectroscopic monitoring of RNA secondary structures is described. The applicability of 1 is demonstrated by monitoring the thermal denaturation of the following double and triple helical RNA models: (1) a miR 215 hairpin, (2) a poly U-A*U triple helix RNA (bearing two C-G*C(H+) interrupts), and (3) a polyadenylated nuclear-nuclear retention element complex. In these RNA models, the (19)F NMR shift of the 2'-O-(CF3-triazolylmethyl) group shows high sensitivity to secondary structural arrangements. Moreover, 1 favors the desired N-conformation, and its effect on both RNA duplex and triplex stabilities is marginal.
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Affiliation(s)
- Lotta Granqvist
- Department of Chemistry, University of Turku, Turku 20014, Finland
| | - Pasi Virta
- Department of Chemistry, University of Turku, Turku 20014, Finland
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40
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Scott LG, Hennig M. ¹⁹F-Site-Specific-Labeled Nucleotides for Nucleic Acid Structural Analysis by NMR. Methods Enzymol 2015; 566:59-87. [PMID: 26791976 DOI: 10.1016/bs.mie.2015.05.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Naturally occurring RNA lacks fluorine-19 ((19)F), thus, their specifically fluorinated counterparts are particularly well suited to noninvasively monitoring the dynamic conformational properties and ligand-binding interactions of the RNA. For nuclear magnetic resonance (NMR) spectroscopy, (19)F-NMR of fluorine-substituted RNA provides an attractive, site-specific probe for structure determination in solution. Advantages of (19)F include high NMR sensitivity (83% of (1)H), high natural abundance (100%), and the extreme sensitivity of (19)F to the chemical environment leading to a large range of chemical shifts. The preparation of base-substituted 2-fluoropurine and 5-fluoropyrimidine 5'-triphosphates (2F-ATP/5F-CTP/5F-UTP) can be carried out using efficient enzymatic synthesis methods. Both pyrimidine analogs, 5-fluorouridine and 5-fluorocytidine, as well as, 2-fluoroadenosine are readily incorporated into RNA transcribed in vitro using T7 RNA polymerase.
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Affiliation(s)
| | - Mirko Hennig
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina, USA.
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41
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Jud L, Košutić M, Schwarz V, Hartl M, Kreutz C, Bister K, Micura R. Expanding the Scope of 2'-SCF3 Modified RNA. Chemistry 2015; 21:10400-7. [PMID: 26074479 PMCID: PMC4515092 DOI: 10.1002/chem.201500415] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Indexed: 11/14/2022]
Abstract
The 2′-trifluoromethylthio (2′-SCF3) modification endows ribonucleic acids with exceptional properties and has attracted considerable interest as a reporter group for NMR spectroscopic applications. However, only modified pyrimidine nucleosides have been generated so far. Here, the syntheses of 2′-SCF3 adenosine and guanosine phosphoramidites of which the latter was obtained in highly efficient manner by an unconventional Boc-protecting group strategy, are reported. RNA solid-phase synthesis provided site-specifically 2′-SCF3-modified oligoribonucleotides that were investigated intensively. Their excellent behavior in 19F NMR spectroscopic probing of RNA ligand binding was exemplified for a noncovalent small molecule–RNA interaction. Moreover, comparably to the 2′-SCF3 pyrimidine nucleosides, the purine counterparts were also found to cause a significant thermodynamic destabilization when located in double helical regions. This property was considered beneficial for siRNA design under the aspect to minimize off-target effects and their performance in silencing of the BASP1 gene was demonstrated.
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Affiliation(s)
- Lukas Jud
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Marija Košutić
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Veronika Schwarz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Markus Hartl
- Institute of Biochemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Klaus Bister
- Institute of Biochemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria).
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42
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Baranowski MR, Nowicka A, Rydzik AM, Warminski M, Kasprzyk R, Wojtczak BA, Wojcik J, Claridge TDW, Kowalska J, Jemielity J. Synthesis of fluorophosphate nucleotide analogues and their characterization as tools for ¹⁹F NMR studies. J Org Chem 2015; 80:3982-97. [PMID: 25816092 DOI: 10.1021/acs.joc.5b00337] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To broaden the scope of existing methods based on (19)F nucleotide labeling, we developed a new method for the synthesis of fluorophosphate (oligo)nucleotide analogues containing an O to F substitution at the terminal position of the (oligo)phosphate moiety and evaluated them as tools for (19)F NMR studies. Using three efficient and comprehensive synthetic approaches based on phosphorimidazolide chemistry and tetra-n-butylammonium fluoride, fluoromonophosphate, or fluorophosphate imidazolide as fluorine sources, we prepared over 30 fluorophosphate-containing nucleotides, varying in nucleobase type (A, G, C, U, m(7)G), phosphate chain length (from mono to tetra), and presence of additional phosphate modifications (thio, borano, imido, methylene). Using fluorophosphate imidazolide as fluorophosphorylating reagent for 5'-phosphorylated oligos we also synthesized oligonucleotide 5'-(2-fluorodiphosphates), which are potentially useful as (19)F NMR hybridization probes. The compounds were characterized by (19)F NMR and evaluated as (19)F NMR molecular probes. We found that fluorophosphate nucleotide analogues can be used to monitor activity of enzymes with various specificities and metal ion requirements, including human DcpS enzyme, a therapeutic target for spinal muscular atrophy. The compounds can also serve as reporter ligands for protein binding studies, as exemplified by studying interaction of fluorophosphate mRNA cap analogues with eukaryotic translation initiation factor (eIF4E).
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Affiliation(s)
- Marek R Baranowski
- †Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Anna Nowicka
- †Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.,§Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Anna M Rydzik
- ‡Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Marcin Warminski
- †Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Renata Kasprzyk
- †Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Blazej A Wojtczak
- §Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Jacek Wojcik
- ∥Laboratory of Biological NMR, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Timothy D W Claridge
- ‡Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Joanna Kowalska
- †Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Jacek Jemielity
- §Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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43
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Jereb M, Dolenc D. Electrophilic trifluoromethylthiolation of thiols with trifluoromethanesulfenamide. RSC Adv 2015. [DOI: 10.1039/c5ra07316b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Efficient and highly selective, metal-free, acid promoted synthesis of trifluoromethyl disulfides from thiols and PhNHSCF3 is described.
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Affiliation(s)
- Marjan Jereb
- Department of Organic Chemistry
- Faculty of Chemistry and Chemical Technology
- 1001 Ljubljana
- Slovenia
| | - Darko Dolenc
- Department of Organic Chemistry
- Faculty of Chemistry and Chemical Technology
- 1001 Ljubljana
- Slovenia
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44
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Iannazzo L, Benedetti E, Catala M, Etheve-Quelquejeu M, Tisné C, Micouin L. Monitoring of reversible boronic acid–diol interactions by fluorine NMR spectroscopy in aqueous media. Org Biomol Chem 2015. [DOI: 10.1039/c5ob01362c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A new convenient method for monitoring boronic acid–diol interactions in aqueous media based on 19F NMR spectroscopy with fluorinated boronic acid probes is described.
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Affiliation(s)
- L. Iannazzo
- UMR 8601 CNRS
- Université Paris Descartes
- Sorbonne Paris Cité
- UFR Biomédicale
- 75006 Paris
| | - E. Benedetti
- UMR 8601 CNRS
- Université Paris Descartes
- Sorbonne Paris Cité
- UFR Biomédicale
- 75006 Paris
| | - M. Catala
- UMR 8015 CNRS
- Université Paris Descartes
- Sorbonne Paris Cité
- Faculté des Sciences Pharmaceutiques et Biologiques
- 75006 Paris
| | - M. Etheve-Quelquejeu
- UMR 8601 CNRS
- Université Paris Descartes
- Sorbonne Paris Cité
- UFR Biomédicale
- 75006 Paris
| | - C. Tisné
- UMR 8015 CNRS
- Université Paris Descartes
- Sorbonne Paris Cité
- Faculté des Sciences Pharmaceutiques et Biologiques
- 75006 Paris
| | - L. Micouin
- UMR 8601 CNRS
- Université Paris Descartes
- Sorbonne Paris Cité
- UFR Biomédicale
- 75006 Paris
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45
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Jereb M, Gosak K. Acid-promoted direct electrophilic trifluoromethylthiolation of phenols. Org Biomol Chem 2015; 13:3103-15. [DOI: 10.1039/c4ob02633k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A highly selective and effective, acid-promoted, electrophilic trifluoromethylthiolation of phenols is described.
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Affiliation(s)
- Marjan Jereb
- Department of Organic Chemistry
- Faculty of Chemistry and Chemical Technology
- 1000 Ljubljana
- Slovenia
| | - Kaja Gosak
- Department of Organic Chemistry
- Faculty of Chemistry and Chemical Technology
- 1000 Ljubljana
- Slovenia
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46
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Fürtig B, Reining A, Sochor F, Oberhauser EM, Heckel A, Schwalbe H. Characterization of conformational dynamics of bistable RNA by equilibrium and non-equilibrium NMR. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2014; 55:11.13.1-16. [PMID: 25631532 DOI: 10.1002/0471142700.nc1113s55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Unlike proteins, a given RNA sequence can adopt more than a single conformation. The two (or more) conformations are long-lived and have similar stabilities, but interconvert only slowly. Such bi- or multistability is often linked to the biological functions of the RNA. This unit describes how nuclear magnetic resonance (NMR) spectroscopy can be used to characterize the conformational dynamics of bistable RNAs.
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Affiliation(s)
- Boris Fürtig
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Frankfurt, Germany; Institute of Organic Chemistry and Chemical Biology, Cluster of Excellence Macromolecular Complexes, Johann Wolfgang Goethe University, Frankfurt, Germany
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47
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Gimenez Molina A, Jabgunde AM, Virta P, Lönnberg H. Solution phase synthesis of short oligoribonucleotides on a precipitative tetrapodal support. Beilstein J Org Chem 2014; 10:2279-85. [PMID: 25298795 PMCID: PMC4187100 DOI: 10.3762/bjoc.10.237] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/18/2014] [Indexed: 12/19/2022] Open
Abstract
An effective method for the synthesis of short oligoribonucleotides in solution has been elaborated. Novel 2'-O-(2-cyanoethyl)-5'-O-(1-methoxy-1-methylethyl) protected ribonucleoside 3'-phosphoramidites have been prepared and their usefulness as building blocks in RNA synthesis on a soluble support has been demonstrated. As a proof of concept, a pentameric oligoribonucleotide, 3'-UUGCA-5', has been prepared on a precipitative tetrapodal tetrakis(4-azidomethylphenyl)pentaerythritol support. The 3'-terminal nucleoside was coupled to the support as a 3'-O-(4-pentynoyl) derivative by Cu(I) promoted 1,3-dipolar cycloaddition. Couplings were carried out with 1.5 equiv of the building block. In each coupling cycle, the small molecular reagents and byproducts were removed by two quantitative precipitations from MeOH, one after oxidation and the second after the 5'-deprotection. After completion of the chain assembly, treatment with triethylamine, ammonia and TBAF released the pentamer in high yields.
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Affiliation(s)
- Alejandro Gimenez Molina
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Turku, FI-20014, Turku, Finland
| | - Amit M Jabgunde
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Turku, FI-20014, Turku, Finland
| | - Pasi Virta
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Turku, FI-20014, Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Turku, FI-20014, Turku, Finland
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48
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Charpentier J, Früh N, Togni A. Electrophilic trifluoromethylation by use of hypervalent iodine reagents. Chem Rev 2014; 115:650-82. [PMID: 25152082 DOI: 10.1021/cr500223h] [Citation(s) in RCA: 1182] [Impact Index Per Article: 118.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Julie Charpentier
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology , Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
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49
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Sára T, Schwarz TC, Kurzbach D, Wunderlich CH, Kreutz C, Konrat R. Magnetic resonance access to transiently formed protein complexes. ChemistryOpen 2014; 3:115-23. [PMID: 25050230 PMCID: PMC4101727 DOI: 10.1002/open.201402008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Indexed: 12/22/2022] Open
Abstract
Protein-protein interactions are of utmost importance to an understanding of biological phenomena since non-covalent and therefore reversible couplings between basic proteins leads to the formation of complex regulatory and adaptive molecular systems. Such systems are capable of maintaining their integrity and respond to external stimuli, processes intimately related to living organisms. These interactions, however, span a wide range of dissociation constants, from sub-nanomolar affinities in tight complexes to high-micromolar or even millimolar affinities in weak, transiently formed protein complexes. Herein, we demonstrate how novel NMR and EPR techniques can be used for the characterization of weak protein-protein (ligand) complexes. Applications to intrinsically disordered proteins and transiently formed protein complexes illustrate the potential of these novel techniques to study hitherto unobserved (and unobservable) higher-order structures of proteins.
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Affiliation(s)
- Tomáš Sára
- Department of Structural and Computational Biology Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna (Austria) E-mail:
| | - Thomas C Schwarz
- Department of Structural and Computational Biology Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna (Austria) E-mail:
| | - Dennis Kurzbach
- Department of Structural and Computational Biology Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna (Austria) E-mail:
| | - Christoph H Wunderlich
- Institute of Organic Chemistry and CMBI, University of Innsbruck Innrain 80/82, 6020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry and CMBI, University of Innsbruck Innrain 80/82, 6020 Innsbruck (Austria)
| | - Robert Konrat
- Department of Structural and Computational Biology Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna (Austria) E-mail:
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50
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Košutić M, Jud L, Da Veiga C, Frener M, Fauster K, Kreutz C, Ennifar E, Micura R. Surprising base pairing and structural properties of 2'-trifluoromethylthio-modified ribonucleic acids. J Am Chem Soc 2014; 136:6656-63. [PMID: 24766131 PMCID: PMC4021565 DOI: 10.1021/ja5005637] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The chemical synthesis of ribonucleic
acids (RNA) with novel chemical
modifications is largely driven by the motivation to identify eligible
functional probes for the various applications in life sciences. To
this end, we have a strong focus on the development of novel fluorinated
RNA derivatives that are powerful in NMR spectroscopic analysis of
RNA folding and RNA ligand interactions. Here, we report on the synthesis
of 2′-SCF3 pyrimidine nucleoside containing oligoribonucleotides
and the comprehensive investigation of their structure and base pairing
properties. While this modification has a modest impact on thermodynamic
stability when it resides in single-stranded regions, it was found
to be destabilizing to a surprisingly high extent when located in
double helical regions. Our NMR spectroscopic investigations on short
single-stranded RNA revealed a strong preference for C2′-endo
conformation of the 2′-SCF3 ribose unit. Together
with a recent computational study (L. Li, J. W. Szostak, J.
Am. Chem. Soc. 2014, 136, 2858–2865)
that estimated the extent of destabilization caused by a single C2′-endo
nucleotide within a native RNA duplex to amount to 6 kcal mol−1 because of disruption of the planar base pair structure,
these findings support the notion that the intrinsic preference for
C2′-endo conformation of 2′-SCF3 nucleosides
is most likely responsible for the pronounced destabilization of double
helices. Importantly, we were able to crystallize 2′-SCF3 modified RNAs and solved their X-ray structures at atomic
resolution. Interestingly, the 2′-SCF3 containing
nucleosides that were engaged in distinct mismatch arrangements, but
also in a standard Watson–Crick base pair, adopted the same
C3′-endo ribose conformations as observed in the structure
of the unmodified RNA. Likely, strong crystal packing interactions
account for this observation. In all structures, the fluorine atoms
made surprisingly close contacts to the oxygen atoms of the corresponding
pyrimidine nucleobase (O2), and the 2′-SCF3 moieties
participated in defined water-bridged hydrogen-bonding networks in
the minor groove. All these features allow a rationalization of the
structural determinants of the 2′-SCF3 nucleoside
modification and correlate them to base pairing properties.
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Affiliation(s)
- Marija Košutić
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , 6020 Innsbruck, Austria
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