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Griffiths OM, Esteves HA, Chen Y, Sowa K, May OS, Morse P, Blakemore DC, Ley SV. Photoredox-Catalyzed Dehydrogenative Csp 3-Csp 2 Cross-Coupling of Alkylarenes to Aldehydes in Flow. J Org Chem 2021; 86:13559-13571. [PMID: 34524825 DOI: 10.1021/acs.joc.1c01621] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Executing photoredox reactions in flow offers solutions to frequently encountered issues regarding reproducibility, reaction time, and scale-up. Here, we report the transfer of a photoredox-catalyzed benzylic coupling of alkylarenes to aldehydes to a flow chemistry setting leading to improvements in terms of higher concentration, shorter residence times, better yields, ease of catalyst preparation, and enhanced substrate scope. Its applicability has been demonstrated by a multi-gram-scale reaction using high-power light-emitting diodes (LEDs), late-stage functionalization of selected active pharmaceutical ingredients (APIs), and also a photocatalyst recycling method.
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Affiliation(s)
- Oliver M Griffiths
- Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, U.K
| | - Henrique A Esteves
- Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, U.K
| | - Yiding Chen
- Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, U.K
| | - Karin Sowa
- Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, U.K.,Department of Chemistry, University of Münster, 48149 Münster, Germany
| | - Oliver S May
- Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, U.K
| | - Peter Morse
- Medicine Design, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - David C Blakemore
- Medicine Design, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Steven V Ley
- Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, U.K
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2
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Balasubramaniyam T, Oh KI, Jin HS, Ahn HB, Kim BS, Lee JH. Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides. Int J Mol Sci 2021; 22:9552. [PMID: 34502459 PMCID: PMC8430589 DOI: 10.3390/ijms22179552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.
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Affiliation(s)
- Thananjeyan Balasubramaniyam
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Kwnag-Im Oh
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Ho-Seong Jin
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Hye-Bin Ahn
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Byeong-Seon Kim
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
- Department of Chemistry Education, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Joon-Hwa Lee
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
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3
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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4
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Seio K, Yamaguchi K, Yamazaki A, Kanamori T, Masaki Y. Transcription of DNA duplex containing deoxypseudouridine and deoxypseudoisocytidine, and inhibition of transcription by triplex forming oligonucleotide that recognizes the modified duplex. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:892-904. [PMID: 32126878 DOI: 10.1080/15257770.2020.1714652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
We developed new DNA triplexes that contain four base triads T-A·T, A-ψ·CBr, G-PIC·YO, and C-G·Py+, where CBr, YO, Py, ψ, and PIC are 5-bromocytosine, 5-methyl-4-pyrimidone, 2-aminopyridine, the aglycons of deoxypseudouridine, and deoxypseudoisocytidine, respectively. DNA duplex incorporating T-A, A-ψ, G-PIC, and C-G, and triplex forming oligonucleotide incorporating T, CBr, YO, and Py formed the triplex as evaluated by Tm measurements. The triplex formation was successfully applied to the inhibition of transcription of the DNA duplex incorporating T7-promoter sequence modified by the above modified bases.
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Affiliation(s)
- Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kei Yamaguchi
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ayano Yamazaki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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Gorczak N, Fujii T, Mishra AK, Houtepen AJ, Grozema FC, Lewis FD. Mechanism and Dynamics of Electron Injection and Charge Recombination in DNA. Dependence on Neighboring Pyrimidines. J Phys Chem B 2015; 119:7673-80. [DOI: 10.1021/jp512113w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Natalie Gorczak
- Department of Chemical
Engineering, Delft University of Technology, 2628 BL Delft, The Netherlands
| | - Taiga Fujii
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ashutosh Kumar Mishra
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Arjan J. Houtepen
- Department of Chemical
Engineering, Delft University of Technology, 2628 BL Delft, The Netherlands
| | - Ferdinand C. Grozema
- Department of Chemical
Engineering, Delft University of Technology, 2628 BL Delft, The Netherlands
| | - Frederick D. Lewis
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
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Gyssels E, Carrette LLG, Vercruysse E, Stevens K, Madder A. Triplex crosslinking through furan oxidation requires perturbation of the structured triple-helix. Chembiochem 2015; 16:651-8. [PMID: 25630588 DOI: 10.1002/cbic.201402602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Indexed: 01/08/2023]
Abstract
Short oligonucleotides can selectively recognize duplexes by binding in the major groove thereby forming triplexes. Based on the success of our recently developed strategy for furan-based crosslinking in DNA duplexes, we here investigated for the first time the use of the furan-oxidation crosslink methodology for the covalent locking of triplex structures by an interstrand crosslink. It was shown that in a triplex context, although crosslinking yields are surprisingly low (to nonexistent) when targeting fully complementary duplexes, selective crosslinking can be achieved towards mismatched duplex sites at the interface of triplex to duplex structures. We show the promising potential of furan-containing probes for the selective detection of single-stranded regions within nucleic acids containing a variety of structural motifs.
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Affiliation(s)
- Ellen Gyssels
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, 9000 Gent (Belgium)
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Kanamori T, Ohzeki H, Masaki Y, Ohkubo A, Takahashi M, Tsuda K, Ito T, Shirouzu M, Kuwasako K, Muto Y, Sekine M, Seio K. Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation. Chembiochem 2014; 16:167-76. [PMID: 25469677 DOI: 10.1002/cbic.201402346] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 12/16/2022]
Abstract
We developed fluorescent turn-on probes containing a fluorescent nucleoside, 5-(benzofuran-2-yl)deoxyuridine (dU(BF)) or 5-(3-methylbenzofuran-2-yl)deoxyuridine (dU(MBF)), for the detection of single-stranded DNA or RNA by utilizing DNA triplex formation. Fluorescence measurements revealed that the probe containing dU(MBF) achieved superior fluorescence enhancement than that containing dU(BF). NMR and fluorescence analyses indicated that the fluorescence intensity increased upon triplex formation partly as a consequence of a conformational change at the bond between the 3-methylbenzofuran and uracil rings. In addition, it is suggested that the microenvironment around the 3-methylbenzofuran ring contributed to the fluorescence enhancement. Further, we developed a method for detecting RNA by rolling circular amplification in combination with triplex-induced fluorescence enhancement of the oligonucleotide probe containing dU(MBF).
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Affiliation(s)
- Takashi Kanamori
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501 (Japan)
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Crossey K, Hardacre C, Migaud ME. Nucleoside phosphitylation using ionic liquid stabilised phosphorodiamidites and mechanochemistry. Chem Commun (Camb) 2013; 48:11969-71. [PMID: 23128063 DOI: 10.1039/c2cc36367d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A range of nucleoside phosphoramidites incorporating small amino substituents have been readily synthesised using ionic liquid stabilised phosphorodiamidites coupled with mechanochemistry.
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Affiliation(s)
- Kerri Crossey
- QUILL/School of Chemistry and Chemical Engineering, Queen's University, Belfast, UK
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