1
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Sethi S, Takashima Y, Nakamura S, Wan L, Honda N, Fujimoto K. Acceleration of the Deamination of Cytosine through Photo-Crosslinking. Curr Issues Mol Biol 2023; 45:4687-4700. [PMID: 37367047 DOI: 10.3390/cimb45060298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/18/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
Herein, we report the major factor for deamination reaction rate acceleration, i.e., hydrophilicity, by using various 5-substituted target cytosines and by carrying out deamination at high temperatures. Through substitution of the groups at the 5'-position of the cytosine, the effect of hydrophilicity was understood. It was then used to compare the various modifications of the photo-cross-linkable moiety as well as the effect of the counter base of the cytosine to edit both DNA and RNA. Furthermore, we were able to achieve cytosine deamination at 37 °C with a half-life in the order of a few hours.
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Affiliation(s)
- Siddhant Sethi
- Bioscience, Biotechnology, and Biomedical Engineering Research Area, Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Ishikawa, Nomi 923-1292, Japan
| | - Yasuharu Takashima
- Bioscience, Biotechnology, and Biomedical Engineering Research Area, Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Ishikawa, Nomi 923-1292, Japan
| | - Shigetaka Nakamura
- Bioscience, Biotechnology, and Biomedical Engineering Research Area, Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Ishikawa, Nomi 923-1292, Japan
| | - Licheng Wan
- Bioscience, Biotechnology, and Biomedical Engineering Research Area, Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Ishikawa, Nomi 923-1292, Japan
| | - Nozomi Honda
- Bioscience, Biotechnology, and Biomedical Engineering Research Area, Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Ishikawa, Nomi 923-1292, Japan
| | - Kenzo Fujimoto
- Bioscience, Biotechnology, and Biomedical Engineering Research Area, Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Ishikawa, Nomi 923-1292, Japan
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2
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Hirashima S, Sugiyama H, Park S. Characterization of 2-Fluoro-2'-deoxyadenosine in Duplex, G-quadruplex and I-motif. Chembiochem 2022; 23:e202200222. [PMID: 35438834 DOI: 10.1002/cbic.202200222] [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: 04/19/2022] [Indexed: 11/12/2022]
Abstract
Among various kinds of fluorine-substituted biomolecules, 2-fluoroadenine (2FA) and its derivatives have been actively investigated as therapeutic reagents, radio-sensitizers, and 19F-NMR probe. In spite of their excellent properties, DNA containing 2FA has not been studied well. Toward fundamental understanding and future applications to the development of functional nucleic acids, we characterized 2FA-containing oligonucleotides for canonical right-handed DNA duplex, G-quadruplex, and i-motif structures. Properties of 2FA were similar to native adenine due to the small size of fluorine atom, but it showed unique features caused by high electronegativity. This work provides useful information for future application of 2FA-modified DNA.
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Affiliation(s)
- Shingo Hirashima
- Kyoto University: Kyoto Daigaku, Chemistry, Kitashirakawa-oiwakecho, Sakyo-ku,, 606-8502, Kyoto, JAPAN
| | - Hiroshi Sugiyama
- Kyoto University: Kyoto Daigaku, Chemistry, Kitashirakawa-oiwakecho, Sakyo-ku, 606-8502, Kyoto, JAPAN
| | - Soyoung Park
- Osaka University: Osaka Daigaku, Immunology Research Frontier Center, 3-1 Ymadaoka Suita, 565-0871, Osaka, JAPAN
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3
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Aro-Heinilä A, Lepistö A, Äärelä A, Lönnberg TA, Virta P. 2-Trifluoromethyl-6-mercurianiline Nucleotide, a Sensitive 19F NMR Probe for Hg(II)-mediated Base Pairing. J Org Chem 2022; 87:137-146. [PMID: 34905374 PMCID: PMC8749955 DOI: 10.1021/acs.joc.1c02056] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 01/02/2023]
Abstract
A 2-trifluoromethylaniline C-nucleoside was synthesized, incorporated in the middle of an oligonucleotide, and mercurated. The affinity of the mercurated oligonucleotide toward complementary strands placing each of the canonical nucleobases opposite to the organomercury nucleobase analogue was examined by ultraviolet (UV), circular dichroism (CD), and 19F NMR spectroscopy analyses. According to the UV melting profile analysis, the organomercury nucleobase analogue showed increased affinities in the order T > G > C > A. The CD profiles indicated the typical B-type helix in each case. The 19F resonance signal proved sensitive for the local environmental changes, showing clearly distinct signals for the duplexes with different opposing nucleobases. Furthermore, valuable information on the mercurated oligonucleotide and its binding to complementary strands at varying temperature could be obtained by 19F NMR spectroscopy.
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Affiliation(s)
- Asmo Aro-Heinilä
- Department of Chemistry, University
of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Assi Lepistö
- Department of Chemistry, University
of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Antti Äärelä
- Department of Chemistry, University
of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | | | - Pasi Virta
- Department of Chemistry, University
of Turku, Henrikinkatu 2, 20500 Turku, Finland
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4
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Hori D, Yum JH, Sugiyama H, Park S. Tropylium Derivatives as New Entrants that Sense Quadruplex Structures. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daisuke Hori
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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5
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Wee WA, Yum JH, Hirashima S, Sugiyama H, Park S. Synthesis and application of a 19F-labeled fluorescent nucleoside as a dual-mode probe for i-motif DNAs. RSC Chem Biol 2021; 2:876-882. [PMID: 34458815 PMCID: PMC8382138 DOI: 10.1039/d1cb00020a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 11/21/2022] Open
Abstract
Because of their stable orientations and their minimal interference with native DNA interactions and folding, emissive isomorphic nucleoside analogues are versatile tools for the accurate analysis of DNA structural heterogeneity. Here, we report on a bifunctional trifluoromethylphenylpyrrolocytidine derivative (FPdC) that displays an unprecedented quantum yield and highly sensitive 19F NMR signal. This is the first report of a cytosine-based dual-purpose probe for both fluorescence and 19F NMR spectroscopic DNA analysis. FPdC and FPdC-containing DNA were synthesized and characterized; our robust dual probe was successfully used to investigate the noncanonical DNA structure, i-motifs, through changes in fluorescence intensity and 19F chemical shift in response to i-motif formation. The utility of FPdC was exemplified through reversible fluorescence switching of an FPdC-containing i-motif oligonucleotide in the presence of Ag(i) and cysteine.
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Affiliation(s)
- Wen Ann Wee
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Shingo Hirashima
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
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6
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The effect of 5-substituent in cytosine to the photochemical C to U transition in DNA strand. Bioorg Med Chem Lett 2021; 35:127812. [PMID: 33486052 DOI: 10.1016/j.bmcl.2021.127812] [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: 10/06/2020] [Revised: 01/05/2021] [Accepted: 01/17/2021] [Indexed: 11/21/2022]
Abstract
Nucleobase editing is a powerful tool in genetic disease therapy. We have reported the photochemical transition of cytosine to uracil using an ultrafast DNA photo-cross-linking. In this study, we used cytosine derivatives such as methylcytosine, hydroxymethylcytosine, and trifluoromethylcytosine to evaluate the effect of 5-position substitution of cytosine on deamination. The conversion of cytosine to uracil was the fastest, and the conversion of trifluoromethylcytosine to trifluoromethyluracil was the slowest. The order was correlated with the hydrophilicity of the double strand containing these cytosine derivatives.
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7
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Oweida TJ, Kim HS, Donald JM, Singh A, Yingling YG. Assessment of AMBER Force Fields for Simulations of ssDNA. J Chem Theory Comput 2021; 17:1208-1217. [PMID: 33434436 DOI: 10.1021/acs.jctc.0c00931] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Single-stranded DNA (ssDNA) plays an important role in biological processes and is used in DNA nanotechnology and other novel applications. Many important research questions can be addressed with molecular simulations of ssDNA molecules; however, no dedicated force field for ssDNA has been developed, and there is limited experimental information about ssDNA structures. This study assesses the accuracy and applicability of existing Amber force fields for all-atom simulations of ssDNA, such as ff99, bsc0, bsc1, and OL15, in implicit and explicit solvents via comparison to available experimental data, such as Forster resonance energy transfer and small angle X-ray scattering. We observed that some force fields agree better with experiments than others mainly due to the difference in parameterization of the propensity for hydrogen bonding and base stacking. Overall, the Amber ff99 force field in the IGB5 or IGB8 implicit solvent and the bsc1 force field in the explicit TIP3P solvent had the best agreement with experiment.
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Affiliation(s)
- Thomas J Oweida
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Ho Shin Kim
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Johnny M Donald
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Abhishek Singh
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yaroslava G Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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8
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Solodinin A, Gautrais A, Ollivier S, Yan H. 5-Fluoro-2'-deoxycytidine as a Probe for the Study of B/Z-DNA Transition by 19F NMR Spectroscopy. ACS OMEGA 2019; 4:19716-19722. [PMID: 31788603 PMCID: PMC6881825 DOI: 10.1021/acsomega.9b02461] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
5-Fluoro-2'-deoxycytidine was synthesized by treating 5-fluoro-2'-deoxyuridine with 2,4,6-trimethylphenol in the presence of 1-methylpyrrolidine and trifluoroacetic anhydride, followed by aminolysis. Among N-acetyl, pivaloyl, and benzoyl, N-acetyl was found to be suitable for the protection of the exocyclic amine of 5-fluoro-2'-deoxycytidine because of the stability of the N 4-protected nucleoside under acidic conditions and its ease of removal after solid-phase synthesis. This modified nucleoside was incorporated into d(CG)6 sequences through the phosphoramidite chemistry-based solid-phase synthesis. Circular dichroism experiments suggest that replacement of 2'-deoxycytidine with 5-fluoro-2'-deoxycytidine does not lead to detectable conformational changes, either in the B- or Z-form. 19F NMR spectroscopy of d(CG)6 containing 5-fluoro-2'-deoxycytidine revealed that B/Z-DNA transition induced by sodium chloride is likely initiated at terminal ends, leading to unwinding at the middle of duplexes, and eventual switch of handedness when sodium chloride concentration reaches a threshold value.
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9
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Nakamura S, Takashima Y, Fujimoto K. Multiplexed detection of nucleic acids using 19F NMR chemical shift changes based on DNA photo-cross-linking of 3-vinylcarbazole derivatives. Org Biomol Chem 2018; 16:891-894. [PMID: 29340411 DOI: 10.1039/c7ob03008h] [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
The detection methodology for nucleic acids is a useful tool for the analysis of biological systems and diagnosis of diseases. We demonstrated the feasibility of the detection of any nucleic acids based on large chemical shifts via ultrafast DNA photo-cross-linking and the effects of substitution by 3-vinylcarbazole derivatives. These chemical shifts enable the sequence-specific detection of any strand using hybridization chain reaction.
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Affiliation(s)
- Shigetaka Nakamura
- Department of Advanced Science and Technology, Japan Advanced Institute Science and Technology, Asahi-dai, Nomi, Ishikawa 923-1292, Japan.
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10
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Vorobyeva DV, Vinogradov MM, Nelyubina YV, Loginov DA, Peregudov AS, Osipov SN. Rhodium(iii)-catalyzed CF3-carbenoid C–H functionalization of 6-arylpurines. Org Biomol Chem 2018; 16:2966-2974. [PMID: 29623337 DOI: 10.1039/c8ob00645h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An expedient route to access a new family of fluorine-containing purine derivatives via chelation-controlled rhodium(iii)-catalyzed carbenoid C–H functionalization has been developed.
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Affiliation(s)
- Daria V. Vorobyeva
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - Mikhail M. Vinogradov
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - Yulia V. Nelyubina
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - Dmitry A. Loginov
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - Alexander S. Peregudov
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - Sergey N. Osipov
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
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11
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Kubyshkin V, Budisa N. Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models. Beilstein J Org Chem 2017; 13:2442-2457. [PMID: 29234471 PMCID: PMC5704756 DOI: 10.3762/bjoc.13.241] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/19/2017] [Indexed: 12/17/2022] Open
Abstract
Fluorinated moieties are highly valuable to chemists due to the sensitive NMR detectability of the 19F nucleus. Fluorination of molecular scaffolds can also selectively influence a molecule's polarity, conformational preferences and chemical reactivity, properties that can be exploited for various chemical applications. A powerful route for incorporating fluorine atoms in biomolecules is last-stage fluorination of peptide scaffolds. One of these methods involves esterification of the C-terminus of peptides using a diazomethane species. Here, we provide an investigation of the physicochemical consequences of peptide esterification with partially fluorinated ethyl groups. Derivatives of N-acetylproline are used to model the effects of fluorination on the lipophilicity, hydrolytic stability and on conformational properties. The conformational impact of the 2,2-difluoromethyl ester on several neutral and charged oligopeptides was also investigated. Our results demonstrate that partially fluorinated esters undergo variable hydrolysis in biologically relevant buffers. The hydrolytic stability can be tailored over a broad pH range by varying the number of fluorine atoms in the ester moiety or by introducing adjacent charges in the peptide sequence.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin 10623, Germany
| | - Nediljko Budisa
- Biocatalysis group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin 10623, Germany
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12
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Ito Y, Matsuo M, Osawa T, Hari Y. Triplex- and Duplex-Forming Abilities of Oligonucleotides Containing 2'-Deoxy-5-trifluoromethyluridine and 2'-Deoxy-5-trifluoromethylcytidine. Chem Pharm Bull (Tokyo) 2017; 65:982-988. [PMID: 28966282 DOI: 10.1248/cpb.c17-00530] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A facile synthesis of 2'-deoxy-5-trifluoromethyluridine and 2'-deoxy-5-trifluoromethylcytidine phosphoramidites from commercially available 2'-deoxyuridine and 2'-deoxycytidine was achieved, respectively. The obtained phosphoramidites were incorporated into oligonucleotides, and their binding affinity to double-stranded DNA (dsDNA) and single-stranded RNA (ssRNA) was evaluated by UV-melting experiments. The triplex-forming abilities of oligonucleotides including 5-trifluoromethylpyrimidine nucleobases with dsDNA were decreased. Especially, the stability of the triplex containing a trifluoromethylcytosine (CF3C)-GC base triplet was low, likely due to the low pKa of protonated CF3C by the electron-withdrawing trifluoromethyl group. A slight decrease in stability of the duplex formed with ssRNA by oligonucleotides including 5-trifluoromethylpyrimidine nucleobases was only observed, suggesting that they might be applicable to various ssRNA-targeted technologies using features of fluorine atoms.
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Affiliation(s)
- Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University
| | - Misaki Matsuo
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University
| | - Takashi Osawa
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University
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