1
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Khatik SY, Sudhakar S, Mishra S, Kalia J, Pradeepkumar PI, Srivatsan SG. Probing juxtaposed G-quadruplex and hairpin motifs using a responsive nucleoside probe: a unique scaffold for chemotherapy. Chem Sci 2023; 14:5627-5637. [PMID: 37265741 PMCID: PMC10231310 DOI: 10.1039/d3sc00519d] [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: 01/30/2023] [Accepted: 04/30/2023] [Indexed: 06/03/2023] Open
Abstract
Paucity of efficient probes and small molecule ligands that can distinguish different G-quadruplex (GQ) topologies poses challenges not only in understanding their basic structure but also in targeting an individual GQ form from others. Alternatively, G-rich sequences that harbour unique chimeric structural motifs (e.g., GQ-duplex or GQ-hairpin junctions) are perceived as new therapeutic hotspots. In this context, the epidermal growth factor receptor (EGFR) gene, implicated in many cancers, contains a 30 nucleotide G-rich segment in the promoter region, which adopts in vitro two unique architectures each composed of a GQ topology (parallel and hybrid-type) juxtaposed with a hairpin domain. Here, we report the use of a novel dual-app probe, C5-trifluoromethyl benzofuran-modified 2'-deoxyuridine (TFBF-dU), in the systematic analysis of EGFR GQs and their interaction with small molecules by fluorescence and 19F NMR techniques. Notably, distinct fluorescence and 19F NMR signals exhibited by the probe enabled the quantification of the relative population of random, parallel and hybrid-type GQ structures under different conditions, which could not be obtained by conventional CD and 1H NMR techniques. Using the fluorescence component, we quantified ligand binding properties of GQs, whereas the 19F label enabled the assessment of ligand-induced changes in GQ dynamics. Studies also revealed that mutations in the hairpin domain affected GQ formation and stability, which was further functionally verified in polymerase stop assay. We anticipate that these findings and useful properties of the nucleoside probe could be utilized in designing and evaluating binders that jointly target both GQ and hairpin domains for enhanced selectivity and druggability.
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Affiliation(s)
- Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road Pune 411008 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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Khatik SY, Srivatsan SG. Environment-Sensitive Nucleoside Probe Unravels the Complex Structural Dynamics of i-Motif DNAs. Bioconjug Chem 2022; 33:1515-1526. [PMID: 35819865 DOI: 10.1021/acs.bioconjchem.2c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although evidence for the existence and biological role of i-motif (iM) DNA structures in cells is emerging, probing their structural polymorphism and identifying physiologically active conformations using currently available tools remain a major challenge. Here, we describe the development of an innovative device to investigate the conformation equilibrium of different iMs formed by C-rich telomeric repeat and oncogenic B-raf promoter sequences using a new conformation-sensitive dual-purpose nucleoside probe. The nucleoside is composed of a trifluoromethyl-benzofuran-2-yl moiety at the C5 position of 2'-deoxyuridine, which functions as a responsive fluorescent and 19F NMR probe. While the fluorescent component is useful in monitoring and estimating the folding process, the 19F label provides spectral signatures for various iMs, thereby enabling a systematic analysis of their complex population equilibrium under different conditions (e.g., pH, temperature, metal ions, and cell lysate). Distinct 19F signals exhibited by the iMs formed by the human telomeric repeat helped in calculating their relative population. A battery of fluorescence and 19F NMR studies using native and mutated B-raf oligonucleotides gave valuable insights into the iM structure landscape and its dependence on environmental conditions and also helped in predicting the structure of the major iM conformation. Overall, our findings indicate that the probe is highly suitable for studying complex nucleic acid systems.
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Affiliation(s)
- Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
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3
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Xu Z, Gu S, Li Y, Wu J, Zhao Y. Recognition-Enabled Automated Analyte Identification via 19F NMR. Anal Chem 2022; 94:8285-8292. [PMID: 35622989 DOI: 10.1021/acs.analchem.2c00642] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nuclear magnetic resonance (NMR) is an indispensable tool for structural elucidation and noninvasive analysis. Automated identification of analytes with NMR is highly pursued in metabolism research and disease diagnosis; however, this process is often complicated by the signal overlap and the sample matrix. We herein report a detection scheme based on 19F NMR spectroscopy and dynamic recognition, which effectively simplifies the detection signal and mitigates the influence of the matrix on the detection. It is demonstrated that this approach can not only detect and differentiate capsaicin and dihydrocapsaicin in complex real-world samples but also quantify the ibuprofen content in sustained-release capsules. Based on the 19F signals obtained in the detection using a set of three 19F probes, automated analyte identification is achieved, effectively reducing the odds of misrecognition caused by structural similarity.
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Affiliation(s)
- Zhenchuang Xu
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Siyi Gu
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yipeng Li
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Jian Wu
- Instrumental Analysis Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yanchuan Zhao
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 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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4
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Manna S, Sontakke VA, Srivatsan SG. Incorporation and Utility of a Responsive Ribonucleoside Analogue in Probing the Conformation of a Viral RNA Motif by Fluorescence and 19 F NMR Spectroscopy. Chembiochem 2021; 23:e202100601. [PMID: 34821449 DOI: 10.1002/cbic.202100601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/24/2021] [Indexed: 11/09/2022]
Abstract
Development of versatile probes that can enable the study of different conformations and recognition properties of therapeutic nucleic acid motifs by complementing biophysical techniques can greatly aid nucleic acid analysis and therapy. Here, we report the design, synthesis and incorporation of an environment-sensitive ribonucleoside analogue, which serves as a two-channel biophysical platform to investigate RNA structure and recognition by fluorescence and 19 F NMR spectroscopy techniques. The nucleoside analogue is based on a 5-fluorobenzofuran-uracil core and its fluorescence and 19 F NMR chemical shifts are highly sensitive to changes in solvent polarity and viscosity. Notably, the modified ribonucleotide and phosphoramidite substrates can be efficiently incorporated into RNA oligonucleotides (ONs) by in vitro transcription and standard solid-phase ON synthesis protocol, respectively. Fluorescence and 19 F readouts of the nucleoside incorporated into model RNA ONs are sensitive to the neighbouring base environment. The responsiveness of the probe was aptly utilized in detecting and quantifying the metal ion-induced conformational change in an internal ribosome entry site RNA motif of hepatitis C virus, which is an important therapeutic target. Taken together, our probe is a good addition to the nucleic acid analysis toolbox with the advantage that it can be used to study nucleic acid conformation and recognition simultaneously by two biophysical techniques.
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Affiliation(s)
- Sudeshna Manna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
| | - Vyankat A Sontakke
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
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5
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Majtnerova P, Capek J, Petira F, Handl J, Rousar T. Quantitative spectrofluorometric assay detecting nuclear condensation and fragmentation in intact cells. Sci Rep 2021; 11:11921. [PMID: 34099803 PMCID: PMC8184882 DOI: 10.1038/s41598-021-91380-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/21/2021] [Indexed: 12/17/2022] Open
Abstract
At present, nuclear condensation and fragmentation have been estimated also using Hoechst probes in fluorescence microscopy and flow cytometry. However, none of the methods used the Hoechst probes for quantitative spectrofluorometric assessment. Therefore, the aim of the present study was to develop a spectrofluorometric assay for detection of nuclear condensation and fragmentation in the intact cells. We used human hepatoma HepG2 and renal HK-2 cells cultured in 96-well plates treated with potent apoptotic inducers (i.e. cisplatin, staurosporine, camptothecin) for 6-48 h. Afterwards, the cells were incubated with Hoechst 33258 (2 µg/mL) and the increase of fluorescence after binding of the dye to DNA was measured. The developed spectrofluorometric assay was capable to detect nuclear changes caused by all tested apoptotic inducers. Then, we compared the outcomes of the spectrofluorometric assay with other methods detecting cell impairment and apoptosis (i.e. WST-1 and glutathione tests, TUNEL, DNA ladder, caspase activity, PARP-1 and JNKs expressions). We found that our developed spectrofluorometric assay provided results of the same sensitivity as the TUNEL assay but with the advantages of being fast processing, low-cost and a high throughput. Because nuclear condensation and fragmentation can be typical markers of cell death, especially in apoptosis, we suppose that the spectrofluorometric assay could become a routinely used method for characterizing cell death processes.
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Affiliation(s)
- Pavlina Majtnerova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10, Pardubice, Czech Republic
| | - Jan Capek
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10, Pardubice, Czech Republic
| | - Filip Petira
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10, Pardubice, Czech Republic
| | - Jiri Handl
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10, Pardubice, Czech Republic
| | - Tomas Rousar
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10, Pardubice, Czech Republic.
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6
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Sakamoto T, Qiu Z, Inagaki M, Fujimoto K. Simultaneous Amino Acid Analysis Based on 19F NMR Using a Modified OPA-Derivatization Method. Anal Chem 2019; 92:1669-1673. [PMID: 31886647 DOI: 10.1021/acs.analchem.9b05311] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
To provide alternative methods of analyzing amino acids without liquid chromatography, 19F NMR-based simultaneous and individual detection methods for amino acids using o-phthalaldehyde (OPA)-based 19F labeling have been developed. Since the chemical shifts of almost all 19F-labeled amino acids differ from each other, and they can be discriminated on the 19F NMR spectrum, simultaneous detection of amino acids has been successfully demonstrated. The discrimination pattern of the peak identical to that of the 19F-labeled amino acids was largely dependent on the chemical structure of the thiols having 19F nuclei, strongly suggesting that there is a large potential for clearer discrimination of amino acids by optimizing the thiol structure and/or combined use of thiols.
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Affiliation(s)
- Takashi Sakamoto
- Faculty of Systems Engineering , Wakayama University , 930 Sakaedani , Wakayama 640-8510 , Japan
| | - Zhiyong Qiu
- Graduate School of Advanced Science and Technology , Japan Advanced Institute of Science and Technology , 1-1 Asahidai, Nomi , Ishikawa 923-1292 , Japan
| | - Miyu Inagaki
- Faculty of Systems Engineering , Wakayama University , 930 Sakaedani , Wakayama 640-8510 , Japan
| | - Kenzo Fujimoto
- Graduate School of Advanced Science and Technology , Japan Advanced Institute of Science and Technology , 1-1 Asahidai, Nomi , Ishikawa 923-1292 , Japan
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7
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Sakamoto T, Yamada R. Label‐Free in Situ Monitoring of the DNA Hybridization Chain Reaction by Using Sequence‐Selective Minor‐Groove‐Binding Fluorophores. Chembiochem 2019; 20:1242-1245. [DOI: 10.1002/cbic.201800738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Takashi Sakamoto
- Faculty of Systems EngineeringWakayama University 930 Sakaedani Wakayama 640-8510 Japan
| | - Rikuto Yamada
- Faculty of Systems EngineeringWakayama University 930 Sakaedani Wakayama 640-8510 Japan
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8
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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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9
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Dempsey ME, Marble HD, Shen TL, Fawzi NL, Darling EM. Synthesis and Characterization of a Magnetically Active 19F Molecular Beacon. Bioconjug Chem 2018; 29:335-342. [PMID: 29272914 DOI: 10.1021/acs.bioconjchem.7b00671] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Gene expression is used extensively to describe cellular characteristics and behaviors; however, most methods of assessing gene expression are unsuitable for living samples, requiring destructive processes such as fixation or lysis. Recently, molecular beacons have become a viable tool for live-cell imaging of mRNA molecules in situ. Historically, beacon-mediated imaging has been limited to fluorescence-based approaches. We propose the design and synthesis of a novel molecular beacon for magnetic resonance detection of any desired target nucleotide sequence. The biologically compatible synthesis incorporates commonly used bioconjugation reactions in aqueous conditions and is accessible for laboratories without extensive synthesis capabilities. The resulting beacon uses fluorine (19F) as a reporter, which is broadened, or turned "off", via paramagnetic relaxation enhancement from a stabilized nitroxide radical spin label when the beacon is not bound to its nucleic acid target. Therefore, the 19F NMR signal of the beacon is quenched in its hairpin conformation when the spin label and the 19F substituent are held in proximity, but the signal is recovered upon beacon hybridization to its specific complementary nucleotide sequence by physical separation of the radical from the 19F reporter. This study establishes a path for magnetic resonance-based assessment of specific mRNA expression, providing new possibilities for applying molecular beacon technology in living systems.
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Affiliation(s)
- Megan E Dempsey
- Center for Biomedical Engineering, ‡Department of Molecular Pharmacology, Physiology, and Biotechnology, §Department of Chemistry, ∥School of Engineering, and ⊥Department of Orthopaedics, Brown University , Providence, Rhode Island 02912, United States
| | - Hetal D Marble
- Center for Biomedical Engineering, ‡Department of Molecular Pharmacology, Physiology, and Biotechnology, §Department of Chemistry, ∥School of Engineering, and ⊥Department of Orthopaedics, Brown University , Providence, Rhode Island 02912, United States
| | - Tun-Li Shen
- Center for Biomedical Engineering, ‡Department of Molecular Pharmacology, Physiology, and Biotechnology, §Department of Chemistry, ∥School of Engineering, and ⊥Department of Orthopaedics, Brown University , Providence, Rhode Island 02912, United States
| | - Nicolas L Fawzi
- Center for Biomedical Engineering, ‡Department of Molecular Pharmacology, Physiology, and Biotechnology, §Department of Chemistry, ∥School of Engineering, and ⊥Department of Orthopaedics, Brown University , Providence, Rhode Island 02912, United States
| | - Eric M Darling
- Center for Biomedical Engineering, ‡Department of Molecular Pharmacology, Physiology, and Biotechnology, §Department of Chemistry, ∥School of Engineering, and ⊥Department of Orthopaedics, Brown University , Providence, Rhode Island 02912, United States
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10
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Sakamoto T, Hasegawa D, Fujimoto K. Disassembly-driven signal turn-on probes for bimodal detection of DNA with 19F NMR and fluorescence. Org Biomol Chem 2018; 16:7157-7162. [DOI: 10.1039/c8ob02218f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembling molecular probes that can detect DNA in a 19F NMR and fluorescence signal turn-on manner were successfully developed.
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Affiliation(s)
- Takashi Sakamoto
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510
- Japan
| | - Daisaku Hasegawa
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi
- Japan
| | - Kenzo Fujimoto
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi
- Japan
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11
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Xu M, Guo C, Hu G, Xu S, Wang L. Organic Nanoprobes for Fluorescence and 19
F Magnetic Resonance Dual-Modality Imaging. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201700382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Minmin Xu
- State Key Laboratory of Chemical Resource Engineering; Beijing University of Chemical Technology; Beijing 100029 China
| | - Chang Guo
- State Key Laboratory of Chemical Resource Engineering; Beijing University of Chemical Technology; Beijing 100029 China
| | - Gaofei Hu
- State Key Laboratory of Chemical Resource Engineering; Beijing University of Chemical Technology; Beijing 100029 China
| | - Suying Xu
- State Key Laboratory of Chemical Resource Engineering; Beijing University of Chemical Technology; Beijing 100029 China
| | - Leyu Wang
- State Key Laboratory of Chemical Resource Engineering; Beijing University of Chemical Technology; Beijing 100029 China
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12
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Synthesis and Applicability of Base-Discriminating DNA-Triplex-Forming19F NMR Probes. European J Org Chem 2017. [DOI: 10.1002/ejoc.201701110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Yang Q, Jia C, Chen Q, Du W, Wang Y, Zhang Q. A NIR fluorescent probe for the detection of fluoride ions and its application in in vivo bioimaging. J Mater Chem B 2017; 5:2002-2009. [DOI: 10.1039/c6tb03193e] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A near-infrared fluorescent probe has been developed, which is available for visualizing exogenous fluoride ions in vitro and in vivo.
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Affiliation(s)
- Qiuyun Yang
- Hainan Provincial Key Lab of Fine Chemistry
- Hainan University
- Haikou
- China
| | - Chunman Jia
- Hainan Provincial Key Lab of Fine Chemistry
- Hainan University
- Haikou
- China
- Key Study Center of the National Ministry of Education for Tropical Resources Utilization
| | - Qing Chen
- Hainan Provincial Key Lab of Fine Chemistry
- Hainan University
- Haikou
- China
| | - Wei Du
- Hainan Provincial Key Lab of Fine Chemistry
- Hainan University
- Haikou
- China
| | - Yile Wang
- Hainan Provincial Key Lab of Fine Chemistry
- Hainan University
- Haikou
- China
| | - Qi Zhang
- Hainan Provincial Key Lab of Fine Chemistry
- Hainan University
- Haikou
- China
- Key Study Center of the National Ministry of Education for Tropical Resources Utilization
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14
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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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15
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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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16
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Sakamoto T, Hasegawa D, Fujimoto K. Simultaneous detection of single-nucleotide polymorphisms in a DNA bulge structure using a fluorine-modified bisbenzimide derivative. Analyst 2016; 141:1214-7. [DOI: 10.1039/c5an02389k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-nucleotide polymorphisms on the bulged-out nucleobase in dsDNA can be detected simultaneously in a 19F NMR spectrum using 3,5-bis(trifluoromethyl)benzene-modified bisbenzimide H33258.
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Affiliation(s)
- Takashi Sakamoto
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi
- Japan
| | - Daisaku Hasegawa
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi
- Japan
| | - Kenzo Fujimoto
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi
- Japan
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17
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Ke B, Wu W, Wei L, Wu F, Chen G, He G, Li M. Cell and in vivo imaging of fluoride ion with highly selective bioluminescent probes. Anal Chem 2015; 87:9110-3. [PMID: 26329828 DOI: 10.1021/acs.analchem.5b02237] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Two rapid bioluminescent probes for the detection of fluoride ion were developed on the basis of F-Si bond formation herein. It should be noted that probe 1 exhibited highly selective and sensitive detection toward fluoride ion over other anions and has been successfully applied in imaging fluoride ion in both living cells and animals.
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Affiliation(s)
- Bowen Ke
- Department of Anaesthesiology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University , Chengdu, Sichuan 610041, China
| | - Wenxiao Wu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University , Jinan, Shandong 250012, China
| | - Liu Wei
- Department of Anaesthesiology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University , Chengdu, Sichuan 610041, China
| | - Fengbo Wu
- Department of Anaesthesiology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University , Chengdu, Sichuan 610041, China
| | - Guo Chen
- Department of Anaesthesiology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University , Chengdu, Sichuan 610041, China
| | - Gu He
- Department of Anaesthesiology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University , Chengdu, Sichuan 610041, China
| | - Minyong Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University , Jinan, Shandong 250012, China
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