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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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2
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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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3
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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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4
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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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5
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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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6
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Schnieders R, Keyhani S, Schwalbe H, Fürtig B. More than Proton Detection-New Avenues for NMR Spectroscopy of RNA. Chemistry 2020; 26:102-113. [PMID: 31454110 PMCID: PMC6973061 DOI: 10.1002/chem.201903355] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleic acid oligonucleotides (RNAs) play pivotal roles in cellular function (riboswitches), chemical biology applications (SELEX-derived aptamers), cell biology and biomedical applications (transcriptomics). Furthermore, a growing number of RNA forms (long non-coding RNAs, circular RNAs) but also RNA modifications are identified, showing the ever increasing functional diversity of RNAs. To describe and understand this functional diversity, structural studies of RNA are increasingly important. However, they are often more challenging than protein structural studies as RNAs are substantially more dynamic and their function is often linked to their structural transitions between alternative conformations. NMR is a prime technique to characterize these structural dynamics with atomic resolution. To extend the NMR size limitation and to characterize large RNAs and their complexes above 200 nucleotides, new NMR techniques have been developed. This Minireview reports on the development of NMR methods that utilize detection on low-γ nuclei (heteronuclei like 13 C or 15 N with lower gyromagnetic ratio than 1 H) to obtain unique structural and dynamic information for large RNA molecules in solution. Experiments involve through-bond correlations of nucleobases and the phosphodiester backbone of RNA for chemical shift assignment and make information on hydrogen bonding uniquely accessible. Previously unobservable NMR resonances of amino groups in RNA nucleobases are now detected in experiments involving conformational exchange-resistant double-quantum 1 H coherences, detected by 13 C NMR spectroscopy. Furthermore, 13 C and 15 N chemical shifts provide valuable information on conformations. All the covered aspects point to the advantages of low-γ nuclei detection experiments in RNA.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Sara Keyhani
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
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7
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Nakamura S, Fujimoto K. Photo-cross-linking using trifluorothymidine and 3-cyanovinylcarbazole induced a large shifted (19)F MR signal. Chem Commun (Camb) 2016; 51:11765-8. [PMID: 26027537 DOI: 10.1039/c5cc02972d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Photo-cross-linking of trifluorothymidine ((TF)T) using 3-cyanovinylcarbazole ((CNV)K) clearly shifted its (19)F nuclear magnetic resonance (NMR) signal 8 ppm. This (CNV)K mediated ultrafast photo-cross-linking-induced shift can be utilized for miRNA detection by hybridization chain reaction (HCR) to detect 10 nM of a target in a sequence-specific manner.
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Affiliation(s)
- Shigetaka Nakamura
- Materials Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan.
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8
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Baraniak D, Baranowski D, Ruszkowski P, Boryski J. 3'-O- and 5'-O-Propargyl Derivatives of 5-Fluoro-2'-Deoxyuridine: Synthesis, Cytotoxic Evaluation and Conformational Analysis. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:178-94. [PMID: 26914155 DOI: 10.1080/15257770.2015.1122199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A series of new 3'-O- and 5'-O-propargyl derivatives of 5-fluoro-2'-deoxyuridine (1-4) was synthesized by means of propargyl reaction of properly blocked nucleosides (2,4), followed by the deprotection reaction with ammonium fluoride. The synthesized propargylated 5-fluoro-2'-deoxyuridine analogues (1-4) were evaluated for their cytotoxic activity in three human cancer cell lines: cervical (HeLa), oral (KB) and breast (MCF-7), using the sulforhodamine B (SRB) assay. The highest activity and the best SI coefficient in all of the investigated cancer cells were displayed by 3'-O-propargyl-5-fluoro-2'-deoxyuridine (1), and its activity was higher than that of the parent nucleoside. The other new compounds exhibited moderate activity in all of the used cell lines.
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Affiliation(s)
- Dagmara Baraniak
- a Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego St 12/14, 61-704 Poznań , Poland
| | - Daniel Baranowski
- a Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego St 12/14, 61-704 Poznań , Poland.,b Department of Pharmacology , Faculty of Pharmacy, Poznań University of Medical Sciences , Rokietnicka St 5a, 60-806 Poznań , Poland
| | - Piotr Ruszkowski
- b Department of Pharmacology , Faculty of Pharmacy, Poznań University of Medical Sciences , Rokietnicka St 5a, 60-806 Poznań , Poland
| | - Jerzy Boryski
- a Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego St 12/14, 61-704 Poznań , Poland
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9
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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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10
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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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11
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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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12
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Ingale SA, Leonard P, Tran QN, Seela F. Duplex DNA and DNA-RNA hybrids with parallel strand orientation: 2'-deoxy-2'-fluoroisocytidine, 2'-deoxy-2'-fluoroisoguanosine, and canonical nucleosides with 2'-fluoro substituents cause unexpected changes on the double helix stability. J Org Chem 2015; 80:3124-38. [PMID: 25742047 DOI: 10.1021/acs.joc.5b00040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligonucleotides with parallel or antiparallel strand orientation incorporating 2'-fluorinated 2'-deoxyribonucleosides with canonical nucleobases or 2'-deoxy-2'-fluoroisocytidine ((F)iCd, 1c) and 2'-deoxy-2'-fluoroisoguanosine ((F)iGd, 3c) were synthesized. To this end, the nucleosides 1c and 3c as well as the phosphoramidite building blocks 19 and 23 were prepared and employed in solid-phase oligonucleotide synthesis. Unexpectedly, (F)iCd is not stable during oligonucleotide deprotection (55 °C, aq NH3) and was converted to a cyclonucleoside (14). Side product formation was circumvented when oligonucleotides were deprotected under mild conditions (aq ammonia-EtOH, rt). Oligonucleotides containing 2'-fluoro substituents ((F)iCd, (F)iGd and fluorinated canonical 2'-deoxyribonucleosides) stabilize double-stranded DNA, RNA, and DNA-RNA hybrids with antiparallel strand orientation. Unexpected strong stability changes are observed for oligonucleotide duplexes with parallel chains. While fluorinated oligonucleotides form moderately stable parallel stranded duplexes with complementary DNA, they do not form stable hybrids with RNA. Furthermore, oligoribonucleotide duplexes with parallel strand orientation are extremely unstable. It is anticipated that nucleic acids with parallel chains might be too rigid to accept sugar residues in the N-conformation as observed for ribonucleosides or 2'-deoxy-2'-fluororibonucleosides. These observations might explain why nature has evolved the principle of antiparallel chain orientation and has not used the parallel chain alignment.
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Affiliation(s)
- Sachin A Ingale
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Quang Nhat Tran
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.,‡Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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Haque F, Guo P. Overview of methods in RNA nanotechnology: synthesis, purification, and characterization of RNA nanoparticles. Methods Mol Biol 2015; 1297:1-19. [PMID: 25895992 DOI: 10.1007/978-1-4939-2562-9_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
RNA nanotechnology encompasses the use of RNA as a construction material to build homogeneous nanostructures by bottom-up self-assembly with defined size, structure, and stoichiometry; this pioneering concept demonstrated in 1998 (Guo et al., Molecular Cell 2:149-155, 1998; featured in Cell) has emerged as a new field that also involves materials engineering and synthetic structural biology (Guo, Nature Nanotechnology 5:833-842, 2010). The field of RNA nanotechnology has skyrocketed over the last few years, as evidenced by the burst of publications in prominent journals on RNA nanostructures and their applications in nanomedicine and nanotechnology. Rapid advances in RNA chemistry, RNA biophysics, and RNA biology have created new opportunities for translating basic science into clinical practice. RNA nanotechnology holds considerable promise in this regard. Increased evidence also suggests that substantial part of the 98.5 % of human genome (Lander et al. Nature 409:860-921, 2001) that used to be called "junk DNA" actually codes for noncoding RNA. As we understand more on how RNA structures are related to function, we can fabricate synthetic RNA nanoparticles for the diagnosis and treatment of diseases. This chapter provides a brief overview of the field regarding the design, construction, purification, and characterization of RNA nanoparticles for diverse applications in nanotechnology and nanomedicince.
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Affiliation(s)
- Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center, Departmentof Pharmaceutical Sciences, University of Kentucky, 789 S Limestone Ave, 576 Biopharm Complex, Lexington, KY, 40536, USA,
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Kukhanova MK, Korovina AN, Sharkin YA, Azhayev AV, Kochetkov SN. 2′-Fluoronucleotides as substrates of viral replicative polymerases. Mol Biol 2014. [DOI: 10.1134/s0026893314050082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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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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Shu Y, Pi F, Sharma A, Rajabi M, Haque F, Shu D, Leggas M, Evers BM, Guo P. Stable RNA nanoparticles as potential new generation drugs for cancer therapy. Adv Drug Deliv Rev 2014; 66:74-89. [PMID: 24270010 DOI: 10.1016/j.addr.2013.11.006] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 10/11/2013] [Accepted: 11/13/2013] [Indexed: 12/13/2022]
Abstract
Human genome sequencing revealed that only ~1.5% of the DNA sequence coded for proteins. More and more evidence has uncovered that a substantial part of the 98.5% so-called "junk" DNAs actually code for noncoding RNAs. Two milestones, chemical drugs and protein drugs, have already appeared in the history of drug development, and it is expected that the third milestone in drug development will be RNA drugs or drugs that target RNA. This review focuses on the development of RNA therapeutics for potential cancer treatment by applying RNA nanotechnology. A therapeutic RNA nanoparticle is unique in that its scaffold, ligand, and therapeutic component can all be composed of RNA. The special physicochemical properties lend to the delivery of siRNA, miRNA, ribozymes, or riboswitches; imaging using fluogenenic RNA; and targeting using RNA aptamers. With recent advances in solving the chemical, enzymatic, and thermodynamic stability issues, RNA nanoparticles have been found to be advantageous for in vivo applications due to their uniform nano-scale size, precise stoichiometry, polyvalent nature, low immunogenicity, low toxicity, and target specificity. In vivo animal studies have revealed that RNA nanoparticles can specifically target tumors with favorable pharmacokinetic and pharmacodynamic parameters without unwanted accumulation in normal organs. This review summarizes the key studies that have led to the detailed understanding of RNA nanoparticle formation as well as chemical and thermodynamic stability issue. The methods for RNA nanoparticle construction, and the current challenges in the clinical application of RNA nanotechnology, such as endosome trapping and production costs, are also discussed.
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Affiliation(s)
- Yi Shu
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Fengmei Pi
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Ashwani Sharma
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Mehdi Rajabi
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Farzin Haque
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Dan Shu
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Markos Leggas
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - B Mark Evers
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Peixuan Guo
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
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Fauster K, Kreutz C, Micura R. 2'-SCF3 uridine-a powerful label for probing structure and function of RNA by 19F NMR spectroscopy. Angew Chem Int Ed Engl 2012; 51:13080-4. [PMID: 23161779 PMCID: PMC3555429 DOI: 10.1002/anie.201207128] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Indexed: 12/20/2022]
Abstract
Fluorishing: the Togni reagent allows efficient synthetic access to fluorine-labeled RNA molecules. These are in turn highly useful for NMR spectroscopic analyses of secondary and tertiary structures, RNA-protein interactions, and functionality of riboswitch modules.
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Affiliation(s)
- Katja Fauster
- Institute of Organic Chemistry (IOC) and Center for Molecular Biosciences (CMBI), University of Innsbruck, Center for Chemistry and Biomedicine (CCB)020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry (IOC) and Center for Molecular Biosciences (CMBI), University of Innsbruck, Center for Chemistry and Biomedicine (CCB)020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry (IOC) and Center for Molecular Biosciences (CMBI), University of Innsbruck, Center for Chemistry and Biomedicine (CCB)020 Innsbruck (Austria)
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18
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Fauster K, Kreutz C, Micura R. 2′-SCF3Uridine-A Powerful Label for Probing Structure and Function of RNA by19F NMR Spectroscopy. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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19
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Patra A, Paolillo M, Charisse K, Manoharan M, Rozners E, Egli M. 2'-Fluoro RNA shows increased Watson-Crick H-bonding strength and stacking relative to RNA: evidence from NMR and thermodynamic data. Angew Chem Int Ed Engl 2012; 51:11863-6. [PMID: 23055396 PMCID: PMC3757553 DOI: 10.1002/anie.201204946] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/21/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Amritraj Patra
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146 (USA)
| | - Michael Paolillo
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902 (USA)
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142 (USA)
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142 (USA)
| | - Eriks Rozners
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902 (USA)
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146 (USA)
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Patra A, Paolillo M, Charisse K, Manoharan M, Rozners E, Egli M. 2′-Fluoro RNA Shows Increased Watson-Crick H-Bonding Strength and Stacking Relative to RNA: Evidence from NMR and Thermodynamic Data. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204946] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Sharma GV, Reddy PS, Chatterjee D, Kunwar AC. Investigation of folding patterns in homo-oligomers of (R)-β2,2-amino acids with carbohydrate side chain. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.02.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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22
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Nucleic Acid Based Fluorinated Derivatives: New Tools for Biomedical Applications. APPLIED SCIENCES-BASEL 2012. [DOI: 10.3390/app2020245] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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23
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Bundgaard Jensen T, Pasternak A, Stahl Madsen A, Petersen M, Wengel J. Synthesis and structural characterization of 2'-fluoro-α-L-RNA-modified oligonucleotides. Chembiochem 2011; 12:1904-11. [PMID: 21728225 DOI: 10.1002/cbic.201100161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Indexed: 11/07/2022]
Abstract
We describe the synthesis and binding properties of oligonucleotides that contain one or more 2'-fluoro-α-L-RNA thymine monomer(s). Incorporation of 2'-fluoro-α-L-RNA thymine into oligodeoxynucleotides decreased thermal binding stability slightly upon hybridization with complementary DNA and RNA with the smallest destabilization towards RNA. Thermodynamic data show that the duplex formation with 2'-fluoro-α-L-RNA nucleotides is enthalpically disfavored but entropically favored. 2'-Fluoro-α-L-RNA nucleotides exhibit very good base pairing specificity following Watson--Crick rules. The 2'-fluoro-α-L-RNA monomer was designed as a monocyclic mimic of the bicyclic α-L-LNA, and molecular modeling showed that this indeed is the case as the 2'-fluoro monomer adopts a C3'-endo/C2'-exo sugar pucker. Molecular modeling of modified duplexes show that the 2'-fluoro-α-L-RNA nucleotides partake in Watson--Crick base pairing and nucleobase stacking when incorporated in duplexes while the unnatural α-L-ribo configured geometry of the sugar is absorbed by changes in the sugar-phosphate backbone torsion angles. The duplex behavior of our new nucleotide follows that of α-L-LNA, by and large.
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Affiliation(s)
- Troels Bundgaard Jensen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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24
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Liu J, Guo S, Cinier M, Shu Y, Chen C, Shen G, Guo P. Fabrication of stable and RNase-resistant RNA nanoparticles active in gearing the nanomotors for viral DNA packaging. ACS NANO 2011; 5:237-46. [PMID: 21155596 PMCID: PMC3026857 DOI: 10.1021/nn1024658] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Both DNA and RNA can serve as powerful building blocks for bottom-up fabrication of nanostructures. A pioneering concept proposed by Ned Seeman 30 years ago has led to an explosion of knowledge in DNA nanotechnology. RNA can be manipulated with simplicity characteristic of DNA, while possessing noncanonical base-pairing, versatile function, and catalytic activity similar to proteins. However, standing in awe of the sensitivity of RNA to RNase degradation has made many scientists flinch away from RNA nanotechnology. Here we report the construction of stable RNA nanoparticles resistant to RNase digestion. The 2'-F (2'-fluoro) RNA retained its property for correct folding in dimer formation, appropriate structure in procapsid binding, and biological activity in gearing the phi29 nanomotor to package viral DNA and producing infectious viral particles. Our results demonstrate that it is practical to produce RNase-resistant, biologically active, and stable RNA for application in nanotechnology.
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Affiliation(s)
- Jing Liu
- Department of Biomedical Engineering, College of Engineering & College of Medicine, University of Cincinnati, Cincinnati, OH 45267
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology
| | | | - Mathieu Cinier
- Department of Biomedical Engineering, College of Engineering & College of Medicine, University of Cincinnati, Cincinnati, OH 45267
| | - Yi Shu
- Department of Biomedical Engineering, College of Engineering & College of Medicine, University of Cincinnati, Cincinnati, OH 45267
| | - Chaoping Chen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523
| | - Guanxin Shen
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology
| | - Peixuan Guo
- Department of Biomedical Engineering, College of Engineering & College of Medicine, University of Cincinnati, Cincinnati, OH 45267
- Address correspondence to: Peixuan Guo, 3125 Eden Ave. Rm#1436, Vontz Center for Molecular Studies, University of Cincinnati, Cincinnati, OH 45267, Phone: (513)558-0041, Fax: (513)558-6079,
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Puffer B, Kreutz C, Rieder U, Ebert MO, Konrat R, Micura R. 5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy. Nucleic Acids Res 2010; 37:7728-40. [PMID: 19843610 PMCID: PMC2794194 DOI: 10.1093/nar/gkp862] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
19F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondary structure equilibria were chosen as model systems and analyzed by 1D 19F and 1H NMR spectroscopy. A comparison with the unmodified analogs revealed that the equilibrium characteristics of the bistable DNA and RNA oligonucleotides were hardly affected upon fluorine substitution at C5 of pyrimidines. This observation was in accordance with UV spectroscopic melting experiments which demonstrated that single 5-fluoro substitutions in double helices lead to comparable thermodynamic stabilities. Thus, 5-fluoro pyrimidine labeling of DNA and RNA can be reliably applied for NMR based nucleic acid secondary structure evaluation. Furthermore, we developed a facile synthetic route towards 5-fluoro cytidine phosphoramidites that enables their convenient site-specific incorporation into oligonucleotides by solid-phase synthesis.
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Affiliation(s)
- Barbara Puffer
- Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020 Innsbruck, Austria, Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland and Max Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
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Seela F, Xu K. DNA with stable fluorinated dA and dG substitutes: syntheses, base pairing and 19F-NMR spectra of 7-fluoro-7-deaza-2'-deoxyadenosine and 7-fluoro-7-deaza-2'-deoxyguanosine. Org Biomol Chem 2008; 6:3552-60. [PMID: 19082156 DOI: 10.1039/b806145a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fluorinated DNA containing stable fluorine substituents in the "purine" base were synthesized for the first time. For this, the phosphoramidites of 7-fluoro-7-deaza-2'-deoxyadenosine and 7-fluoro-7-deaza-2'-deoxyguanosine were prepared and oligonucleotides were synthesized. The 7-fluoro substitution leads to increased duplex stability and more selective base pairing compared to the non-functionalized 7-deazapurine oligonucleotides. (19)F NMR spectra of fluorinated nucleosides, single stranded oligonucleotides and DNA duplex show only a single signal for one fluorine modification. The NMR sensitive (19)F spin or the positron emitting (18)F isotope make these compounds applicable for DNA detection or imaging in vitro and in vivo.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.
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27
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Hennig M, Munzarova ML, Bermel W, Scott LG, Sklenar V, Williamson JR. Measurement of long-range 1H-19F scalar coupling constants and their glycosidic torsion dependence in 5-fluoropyrimidine-substituted RNA. J Am Chem Soc 2007; 128:5851-8. [PMID: 16637654 PMCID: PMC2556634 DOI: 10.1021/ja060165t] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long-range scalar 5J(H1',F) couplings were observed in 5-fluoropyrimidine-substituted RNA. We developed a novel S3E-19F-alpha,beta-edited NOESY experiment for quantitation of these long-range scalar 5J(H1',F) couplings, where the J-couplings can be extracted from inspection of intraresidual (H1',H6) NOE cross-peaks. Quantum chemical calculations were exploited to investigate the relation between scalar couplings and conformations around the glycosidic bond in oligonucleotides. The theoretical dependence of the observed 5J(H1',F) couplings on the torsion angle chi can be described by a generalized Karplus relationship. The corresponding density functional theory (DFT) analysis is outlined. Additional NMR experiments facilitating the resonance assignments of 5-fluoropyrimidine-substituted RNAs are described, and chemical shift changes due to altered shielding in the presence of fluorine-19 (19F) are presented.
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Affiliation(s)
- Mirko Hennig
- Department of Molecular Biology and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, MB 33, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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Chakraborty TK, Koley D, Ravi R, Kunwar AC. Synthesis and structural studies of peptides containing a mannose-derived furanoid sugar amino acid. Org Biomol Chem 2007; 5:3713-6. [DOI: 10.1039/b712365p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Engels JW, Scherr M, Ganser A, Grez M, Wittmann V. Modified Hammerhead Ribozymes as Potential Therapeutics. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Joachim W. Engels
- a Institut fur Organische Chemie, Johann Wolfgang Goethe-Universität , Marie-Curie-Str. 11, D-60439 , Frankfurt amMain , Germany
| | - Michaela Scherr
- a Institut fur Organische Chemie, Johann Wolfgang Goethe-Universität , Marie-Curie-Str. 11, D-60439 , Frankfurt amMain , Germany
| | - Arnold Ganser
- b Medizinische Hochschule Hannover , 30625 , Hannover , Germany
| | - Manuel Grez
- c Georg-Speyer-Haus , 60596 , Frankfurt am Main , Germany
| | - Valentin Wittmann
- a Institut fur Organische Chemie, Johann Wolfgang Goethe-Universität , Marie-Curie-Str. 11, D-60439 , Frankfurt amMain , Germany
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Kreutz C, Kählig H, Konrat R, Micura R. A General Approach for the Identification of Site-Specific RNA Binders by19F NMR Spectroscopy: Proof of Concept. Angew Chem Int Ed Engl 2006; 45:3450-3. [PMID: 16622887 DOI: 10.1002/anie.200504174] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Christoph Kreutz
- Leopold Franzens University, Institute of Organic Chemistry, Center for Molecular Biosciences, Innrain 52a, 6020 Innsbruck, Austria
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31
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Kreutz C, Kählig H, Konrat R, Micura R. Ein allgemeiner Ansatz zur Identifizierung ortsspezifisch bindender RNA-Liganden mittels19F-NMR-Spektroskopie – Bestätigung des Konzepts. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504174] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
Bovine dentin phosphophoryn (BDP), a protein rich in aspartyl (Asp) and o-phosphoseryl [Ser(P)] residues, is synthesized by odontoblasts and believed to be involved in matrix-mediated biomineralization of dentin. The elucidation of the structure-function relationship of phosphophoryn has been a challenge because of its high-molecular weight, high negative charge, repetitive sequence, and lability. We have used the dynamic behavior of the (1)H NMR signal at 600 MHz to provide insight into the molecular dynamics of phosphophoryn. Our results indicate that phosphophoryn is a molecule of uniformly high mobility, thus belonging to a recently identified class of intrinsically disordered proteins that are characterized by sequences of low complexity and rich in polar and charged residues. The significance of our results is that phosphophoryn, because of its uniform nature has the potential to be replaced by biomimetic synthetic peptide analogs that together with amorphous calcium phosphate may lead to the development of novel, nontoxic, apatite-based dental restorative materials.
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Affiliation(s)
- K J Cross
- Cooperative Research Centre for Oral Health Science, School of Dental Science, The University of Melbourne, Melbourne, Australia
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Luy B, Barchi JJ, Marino JP. S(3)E-E.COSY methods for the measurement of (19)F associated scalar and dipolar coupling constants. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 152:179-184. [PMID: 11531377 DOI: 10.1006/jmre.2001.2386] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A (1)H-(19)F spin state selective excitation (S(3)E) pulse sequence element has been applied in combination with (1)H homonuclear mixing to create E.COSY-type experiments designed to measure scalar J(HF2') and J(HH2') and residual dipolar D(HF2') and D(HH2') couplings in 2'-deoxy-2'-fluoro-sugars. The (1)H-(19)F S(3)E pulse sequence element, which resembles a simple INEPT sequence, achieves spin-state-selective correlation between geminal (1)H-(19)F spin pairs by linear combination of in-phase (19)F magnetization and anti-phase magnetization evolved from (1)H. Since the S(3)E sequence converts both (19)F and (1)H steady-state polarization into observable coherences, an approximately twofold signal increase is observed for fully relaxed (1)H-(19)F spin pairs with respect to a standard (1)H coupled (19)F 1D experiment. The improved sensitivity and resolution afforded by the use of (1)H-(19)F S(3)E E.COSY-type experiments for measuring couplings is demonstrated on the nucleoside 9-(2',3'-dideoxy-2'-fluoro-beta-D-threo-pentofuranosyl)adenine (beta-FddA) and on a selectively 2'-fluorine labeled 21mer RNA oligonucleotide.
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Affiliation(s)
- B Luy
- Center for Advanced Research in Biotechnology, University of Maryland and the National Institute for Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
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Tennilä T, Azhayeva E, Vepsäläinen J, Laatikainen R, Azhayev A, Mikhailopulo IA. Oligonucleotides containing 9-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-adenine and -guanine: synthesis, hybridization and antisense properties. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:1861-84. [PMID: 11200279 DOI: 10.1080/15257770008045466] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Synthesis of 9-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-adenine (7, ara-A2'F) and -guanine (12, ara-G2'F) was accomplished via the condensation of 2,6-dichloropurine (1) with 2-deoxy-2-fluoro-1,3,5-tri-O-benzoyl-alpha-D-arabinofuranose (2) as a key chemical step. Condensation of silylated N6-benzoyladenine (6) with 2 gave, after deblocking and chromatographic separation, ara-A2'F (7) (14%), it's alpha-anomer 8 (14%) and N7-alpha-isomer 9 (25%). The PSEUROT analysis of N9-betaD-arabinosides 7 and 12 manifested slight preference for the S rotamer (64%) for the former, and an equal population of the N and S rotamers for the latter. The arabinosides 7 and 12 were used for the preparation of the respective phosphoamidite building blocks 13 and 14 for automated oligonucleotide synthesis. Four 15-mer oligonucleotides (ONs) complementary to the initiation codon region of firefly luciferase mRNA were prepared: unmodified 2'-deoxy-ON (AS 1) and containing (i) ara-A2'F instead of the only A (AS2), (ii) ara-G2'F vs. 3-G from the 5'-terminus (AS3), and (iii) both arabinosides at the same positions (AS4). All these ONs display practically the same (i) affinity to both complementary DNA and RNA, and (ii) ability to inhibit a luciferase gene expression in a cell-free transcription-translation system.
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Affiliation(s)
- T Tennilä
- Department of Pharmaceutical Chemistry, University of Kuopio, Finland
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Abstract
Recent advances in structural and conformational analysis of fluorinated carbohydrates by NMR spectroscopy are reviewed. Characteristic 1H, 13C, and 19F NMR chemical shifts and coupling constants for selected examples are given and the spectral data of a series of fluorinated carbohydrates were collected in continuation of the review of Csuk and Glänzer [Adv. Carbohydr. Chem. Biochem., 46 (1988) 73-177].
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Affiliation(s)
- M Michalik
- Institut für Organische Katalyseforschung an der Universität Rostock eV, Germany.
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Abstract
The dynamics of RNA hairpin tetraloops of the GNRA type [sequence G- any ribonucleotide (N)-purine (R)-A] was analyzed by fluorescence spectroscopy and by fluorescence-detected temperature-jump relaxation, using RNA oligomers with 2-aminopurine (2AP) substituted in two different positions of the loop sequence, Gp2APpApA (HP1) and GpAp2APpA (HP2), as indicator. The fluorescence of HP1 is much higher than that of HP2, indicating a lower degree of 2AP-stacking in HP1. Addition of Mg(2+) or Ca(2+) ions leads to an increase of fluorescence in HP1, whereas a decrease of fluorescence is observed in HP2. In both cases at least two ion-binding equilibria are required to fit titration data. T-jump experiments using fluorescence detection show a relaxation process with a time constant of 22 micros for HP1, whereas two relaxation processes with time constants 5 and 41 micros, are found for HP2. These results clearly demonstrate the existence of more than the single conformation state detected by NMR analysis. The T-jump amplitudes decrease with increasing bivalent ion concentration, indicating that one of the states is favored in the presence of bivalent ions. The loop relaxation processes are slower than standard stacking processes, probably because of activation barriers imposed by a restricted mobility of loop residues, and are assigned to a stacking rearrangement, probably between the 5' and the 3'-side. A similar process has been observed previously for the anticodon loop of tRNA(Phe). The rate constants of the transition are in the range of 10(4) s(-1) in the case of HP1. The data demonstrate the existence of structures that are not resolved by standard NMR because of fast exchange and are not found by X-ray analysis because of restrictions by crystal packing.
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Affiliation(s)
- M Menger
- Max-Planck-Institut für biophysikalische Chemie, D-37077 Göttingen, Germany
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Vincent SP, Burkart MD, Tsai CY, Zhang Z, Wong CH. Electrophilic Fluorination−Nucleophilic Addition Reaction Mediated by Selectfluor: Mechanistic Studies and New Applications. J Org Chem 1999; 64:5264-5279. [DOI: 10.1021/jo990686h] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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