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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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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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Nakamura S, Ishino K, Fujimoto K. Photochemical RNA Editing of C to U by Using Ultrafast Reversible RNA Photo-crosslinking in DNA/RNA Duplexes. Chembiochem 2020; 21:3067-3070. [PMID: 32519413 DOI: 10.1002/cbic.202000269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/08/2020] [Indexed: 11/09/2022]
Abstract
RNA editing, which is used to edit nucleobases in RNA strands; is more feasible for use in medical applications than DNA editing. We previously reported the photochemical conversion of cytosine to uracil, which required photo-crosslinking, deamination, and photo-splitting. Here, we evaluated the influence of the bases surrounding the target cytosine on the conversion of cytosine to uracil in the RNA strand. The photo-crosslinker 3-carboxyvinylcarbazole(OHV K), which is more hydrophilic than 3-cyanovinylcarbazole(CNV K), 3-carboxyamidevinylcarbazole(NH2V K), and 3-methoxy carbonylvinylcarbazole(OMeV K), induced faster deamination of cytosine. Furthermore, inosine, which forms two hydrogen bonds with cytosine, was the most efficiently paired base for accelerating photochemical RNA editing. Upon evaluation of the conversion from cytosine to uracil in RNA, the use of oligodeoxynucleotides containing OHV K and inosine and the polarity of the bases surrounding the target cytosine were found to be crucial.
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Affiliation(s)
- Shigetaka Nakamura
- School of Advanced Science and Technology, Japan Advanced Institute Science and Technology, Asahi-dai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Kanako Ishino
- School of Advanced Science and Technology, Japan Advanced Institute Science and Technology, Asahi-dai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Kenzo Fujimoto
- School of Advanced Science and Technology, Japan Advanced Institute Science and Technology, Asahi-dai 1-1, Nomi, Ishikawa, 923-1292, Japan
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Sethi S, Honda N, Wan L, Nakamura S, Fujimoto K. Ultra-acceleration of Photochemical Cytosine Deamination by Using a 5'-Phosphate-Substituted Oligodeoxyribonucleotide Probe Containing a 3-Cyanovinylcarbazole Nucleotide at Its 5'-End. Chembiochem 2018; 19:2257-2261. [PMID: 30195263 DOI: 10.1002/cbic.201800384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Indexed: 01/18/2023]
Abstract
Genes are the blueprints for the architectures of living organisms, providing the backbone of the information required for formation of proteins. Changes in genes lead to disorders, and these disorders could be rectified by reversing the mutations that caused them. Photochemical methods currently in use for site-directed mutagenesis employ the photoactive 3-cyanovinylcarbazole (CNV K) nucleotide incorporated in the oligodeoxyribonucleotide (ODN) backbone. The major drawback of this method, the requirement for high temperature, has been addressed, and deamination has previously been achieved at 37 °C but with low efficiency. Here, efficient deamination has been accomplished under physiological conditions by using a short complementary photoactive ODN with a 5'-phosphate group in the -1 position with respect to the target cytosine. It is hypothesized that the free phosphate group affects the microenvironment around the target cytosine by activating the incoming nucleophile through hydrogen bonding with the water molecule, thus facilitating nucleophilic attack on the cytosine C-4 carbon. The degree of deamination observed in this technique is high and the effect of the phosphate group is to accelerate the deamination reaction.
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Affiliation(s)
- Siddhant Sethi
- Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Nozomi Honda
- Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Licheng Wan
- Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Shigetaka Nakamura
- Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Kenzo Fujimoto
- Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Nomi, Ishikawa, 923-1292, Japan
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Nakamura S, Nakajima R, Fujimoto K. DNA Photocrosslinking Using 3-Vinylcarbazole Derivatives in Two-color Detection of Methylcytosine. CHEM LETT 2018. [DOI: 10.1246/cl.180205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Shigetaka Nakamura
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Ryo Nakajima
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Kenzo Fujimoto
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
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Fujimoto K, Sasago S, Mihara J, Nakamura S. DNA Photo-cross-linking Using Pyranocarbazole and Visible Light. Org Lett 2018; 20:2802-2805. [DOI: 10.1021/acs.orglett.8b00593] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kenzo Fujimoto
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Shinobu Sasago
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Junichi Mihara
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Shigetaka Nakamura
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
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Sethi S, Nakamura S, Fujimoto K. Study of Photochemical Cytosine to Uracil Transition via Ultrafast Photo-Cross-Linking Using Vinylcarbazole Derivatives in Duplex DNA. Molecules 2018; 23:molecules23040828. [PMID: 29617316 PMCID: PMC6017022 DOI: 10.3390/molecules23040828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 12/14/2022] Open
Abstract
Gene therapies, including genome editing, RNAi, anti-sense technology and chemical DNA editing are becoming major methods for the treatment of genetic disorders. Techniques like CRISPR-Cas9, zinc finger nuclease (ZFN) and transcription activator-like effector-based nuclease (TALEN) are a few such enzymatic techniques. Most enzymatic genome editing techniques have their disadvantages. Thus, non-enzymatic and non-invasive technologies for nucleic acid editing has been reported in this study which might possess some advantages over the older methods of DNA manipulation. 3-cyanovinyl carbazole (CNVK) based nucleic acid editing takes advantage of photo-cross-linking between a target pyrimidine and the CNVK to afford deamination of cytosine and convert it to uracil. This method previously required the use of high temperatures but, in this study, it has been optimized to take place at physiological conditions. Different counter bases (inosine, guanine and cytosine) complementary to the target cytosine were used, along with derivatives of CNVK (NH2VK and OHVK) to afford the deamination at physiological conditions.
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Affiliation(s)
- Siddhant Sethi
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan.
| | - Shigetaka Nakamura
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan.
| | - Kenzo Fujimoto
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan.
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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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