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Zhu S, Song Y, Pei J, Xue F, Cui X, Xiong X, Li C. The application of photodynamic inactivation to microorganisms in food. Food Chem X 2021; 12:100150. [PMID: 34761205 PMCID: PMC8566761 DOI: 10.1016/j.fochx.2021.100150] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/09/2021] [Accepted: 10/25/2021] [Indexed: 12/27/2022] Open
Abstract
Nowadays, food safety issues have drawn increased attention due to the continual occurrence of infectious diseases caused by foodborne pathogens, which is an important factor causing food safety hazard. Meanwhile, the emergence of an increasing number of antibiotic-resistant pathogens is a worrisome phenomenon. Therefore, it is imperative to find new technologies with low-cost to inactivate pathogenic microorganisms and prevent cross-contamination. Compared with traditional preservatives, photodynamic inactivation (PDI) has emerged as a novel and promising strategy to eliminate foodborne pathogens with advantages such as non-toxic and low microbial resistance, which also meets the demand of current consumers for green treatment. Over the past few years, reports of using this technology for food safety have increased rapidly. This review summarizes recent progresses in the development of photodynamic inactivation of foodborne microorganisms. The mechanisms, factors influencing PDI and the application of different photosensitizers (PSs) in different food substrates are reviewed.
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Affiliation(s)
- Shengyu Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Yukang Song
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Jiliu Pei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Feng Xue
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Xiaowen Cui
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Xiaohui Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Chen Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
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2
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Elskens J, Madder A. Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection. RSC Chem Biol 2021; 2:410-422. [PMID: 34458792 PMCID: PMC8341421 DOI: 10.1039/d0cb00236d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/11/2021] [Indexed: 01/02/2023] Open
Abstract
Understanding the intricate interaction pattern of nucleic acids with other molecules is essential to gain further insight in biological processes and disease mechanisms. To this end, a multitude of hybridization-based assays have been designed that rely on the non-covalent recognition between complementary nucleic acid sequences. However, the ephemeral nature of these interactions complicates straightforward analysis as low efficiency and specificity are rule rather than exception. By covalently locking nucleic acid interactions by means of a crosslinking agent, the overall efficiency, specificity and selectivity of hybridization-based assays could be increased. In this mini-review we highlight methodologies that exploit the use of crosslinker-modified nucleic acid probes for interstrand nucleic acid crosslinking with the objective to study, detect and identify important targets as well as nucleic acid sequences that can be considered relevant biomarkers. We emphasize on the usefulness and advantages of crosslinking agents and elaborate on the chemistry behind the crosslinking reactions they induce.
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Affiliation(s)
- Joke Elskens
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
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3
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Yamayoshi A, Higuchi M, Sakai Y, Kobori A, Yamamoto T, Shibata T, Murakami A. Selective cross-linking behavior of oligodeoxyribonucleotides containing 2'- O-[ N-(4,5',8-trimethylpsoralen-4'-ylmethylcarbamoyl)]adenosine to mutant H-ras DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:119-130. [PMID: 31645189 DOI: 10.1080/15257770.2019.1677912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Point mutations are well characterized activators of oncogenes but are often indistinguishable using common gene technologies. In general, the precise sites of point-mutated oncogenes are difficult to distinguish under physiological conditions primarily because single nucleotide mismatch do not affect the annealing temperatures of DNA probes sufficiently. To address this limitation, we developed photo-responsive oligodeoxyribonucleotides containing 2'-O-[N-(4,5',8-trimethylpsoralen-4'-ylmethylcarbamoyl)]adenosine (Ps-amd-Oligo), which can be used to selectively manipulate and identify genes with point mutations. Here we present time course analyses of the photo-cross-linking efficiency of Ps-amd-Oligo with DNA and RNA and show promising selectivity for the oncogene H-ras.
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Affiliation(s)
- Asako Yamayoshi
- Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,PRSTO, JST, Kawaguchi, Saitama, Japan
| | - Maiko Higuchi
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Kyoto, Japan
| | - Yui Sakai
- Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Akio Kobori
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Kyoto, Japan
| | - Tsuyoshi Yamamoto
- Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Takayuki Shibata
- Graduate School of Health Sciences, Gunma University, Gunma, Japan
| | - Akira Murakami
- Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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4
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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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5
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Sakamoto T, Ooe M, Fujimoto K. Critical Effect of Base Pairing of Target Pyrimidine on the Interstrand Photo-Cross-Linking of DNA via 3-Cyanovinylcarbazole Nucleoside. Bioconjug Chem 2015; 26:1475-8. [PMID: 26190032 DOI: 10.1021/acs.bioconjchem.5b00352] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To evaluate the effect of base pairing of the target pyrimidine on the interstrand photo-cross-linking reaction of DNA via 3-cyanovinylcarbazole nucleoside ((CNV)K), a complementary base of target pyrimidine was substituted with noncanonical purine bases or 1,3-propandiol (S). As the decrease of the hydrogen bonds in the base pairing of target C accelerated the photo-cross-linking reaction markedly (3.6- to 7.7-fold), it can be concluded that the number of hydrogen bonds in the base pairing, i.e., the stability of base pairing, of the target pyrimidine plays a critical role in the interstrand photo-cross-linking reaction. In the case of G to S substitution, the highest photoreactivity toward C was observed, whose photoreaction rate constant (k = 2.0 s(-1)) is comparable to that of (CNV)K toward T paired with A (k = 3.5 s(-1)). This is the most reactive photo-cross-linking reaction toward C in the sequence specific interstrand photo-cross-linking. This might facilitate the design of the photo-cross-linkable oligodeoxyribonucleotides for various target sequences.
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Affiliation(s)
- Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Minako Ooe
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
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6
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Sakamoto T, Tanaka Y, Fujimoto K. DNA photo-cross-linking using 3-cyanovinylcarbazole modified oligonucleotide with threoninol linker. Org Lett 2015; 17:936-9. [PMID: 25654759 DOI: 10.1021/acs.orglett.5b00035] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
3-Cyanovinylcarbazole modified D-threoninol ((CNV)D) was incorporated in oligodeoxyribonucleotide and tested for a photo-cross-linking reaction with complementary oligodeoxyribonucleotide. The photoreactivity was 1.8- to 8-fold greater than that of 3-cyanovinylcarbazole modified deoxyribose ((CNV)K) previously reported. From the results of melting analysis and circular dichroism spectroscopy of the duplexes, the relatively flexible structure of (CNV)D compared with (CNV)K might be advantageous for [2 + 2] photocycloaddition between the cyanovinyl group on the (CNV)D and pyrimidine base in the complementary strand.
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Affiliation(s)
- Takashi Sakamoto
- School of Materials Science, ‡Research Center for Bio-architecture, Japan Advanced Institute of Science and Technology , 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
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7
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Capobianco ML, Marchesi E, Perrone D, Navacchia ML. Labeling deoxyadenosine for the preparation of functional conjugated oligonucleotides. Bioconjug Chem 2014; 24:1398-407. [PMID: 23883134 DOI: 10.1021/bc400243q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Herein we present a versatile synthetic method for the 8-thioalkylation of (deoxy)adenosine with a short carbon linker having on the other side a variety of molecules (psoralen, acridine) and functional groups (alkyne). After conventional protections, the modified adenosine can be phosphytylated and inserted into an oligonucleotide without affecting the standard protocols for supported oligonucleotide synthesis. The hybridization properties of a generic oligonucleotide containing the above conjugated moieties toward both DNA and RNA are evaluated both in the case of a perfectly complementary strand and in the case of a single mismatch. This methodology is suitable for the preparation of several types of derivatives and—through the alkynyl moiety—provides fast access to click-chemistry transformations.
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8
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Kobori A, Yamayoshi A, Murakami A. Synthesis of Oligonucleotides Containing 4,5',8-Trimethylpsoralen at the 2'-O Position and Their Cross-Linking Properties with RNAs. ACTA ACUST UNITED AC 2014; 58:5.15.1-15. [PMID: 25199638 DOI: 10.1002/0471142700.nc0515s58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
4,5',8-Trimethylpsoralen-conjugated oligonucleotides have been used in the study of photo-cross-linking with target oligonucleotides and in the field of the photodynamic therapy. This unit describes synthetic procedures for oligonucleotides using 2'-O-methylphosphoramidite units and an adenosine phosphoramidite unit containing a 4,5',8-trimethylpsoralen derivative attached at the 2' position of an adenosine sugar moiety via an ethoxymethylene linkage. Procedures for obtaining the photo-cross-linking efficiency of 2'-O-methyloligonucleotides containing a 4,5',8-trimethylpsoralen derivative with a target oligonucleotide under UV irradiation conditions are also described, together with the procedure for preparation of (32)P-radiolabeled RNA.
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Affiliation(s)
- Akio Kobori
- Kyoto Institute of Technology, Graduate School of Science and Technology, Department of Biomolecular Engineering, Matsugasaki, Sakyo-ku, Kyoto, Japan
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9
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Nowak-Karnowska J, Chebib Z, Milecki J, Franzen S, Skalski B. Highly efficient fluorescent interstrand photo-crosslinking of DNA duplexes labeled with 5-fluoro-4-thio-2'-o-methyluridine. Chembiochem 2014; 15:2045-9. [PMID: 25111776 DOI: 10.1002/cbic.201402182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Indexed: 02/03/2023]
Abstract
The formation of a fluorescent photoadduct between 5-fluoro-4-thiouridine ((FS) U), in the sequence context 5'-A(FS) UA-3' and incorporated into a synthetic oligonucleotide either at its 3'- or 5'-end, and one of the thymines of the TAT motif in a complementary target DNA strand led to photo-crosslinking of the two strands for several oligonucleotide constructs. Enzymatic digestion, MS, UV, and fluorescence spectral analyses of the interstrand crosslinked oligonucleotides revealed the identity of the thymidine that participates in the photo-crosslinking reaction as well as the diastereomeric structures of the crosslinks. The proposed pathways of interstrand photo-crosslinking are supported by experiments with isotopically labeled oligonucleotide constructs and visualized by means of molecular dynamics simulations.
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Affiliation(s)
- Joanna Nowak-Karnowska
- Centre of Advanced Technology, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznań (Poland)
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10
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Yamayoshi A, Matsuyama Y, Kushida M, Kobori A, Murakami A. Novel photodynamic effect of a psoralen-conjugated oligonucleotide for the discrimination of the methylation of cytosine in DNA. Photochem Photobiol 2014; 90:716-22. [PMID: 24372306 DOI: 10.1111/php.12232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/17/2013] [Indexed: 12/11/2022]
Abstract
DNA methylation and demethylation significantly affect the deactivation and activation processes of gene expression significantly. In particular, C-5-methylation of cytosine in the CpG islands is important for the epigenetic modification in genes, which plays a key role in regulating gene expression. The determination of the location and frequency of DNA methylation is important for the elucidation of the mechanisms of cell differentiation and carcinogenesis. Here we designed a psoralen-conjugated oligonucleotide (PS-oligo) for the discrimination of 5-methylcytosine (5-mC) in DNA. The cross-linking behavior of psoralen derivatives with pyrimidine bases, such as thymine, uracil and cytosine has been well discussed, but there are no reports which have examined whether cross-linking efficiency of psoralen with cytosine would be changed with or without C-5 methylation. We found that the cross-linking efficiency of PS-oligo with target-DNA containing 5-mC was greatly increased compared to the case of target-DNA without 5-mC, approximately seven-fold higher. Here we report a new aspect of the photocross-linking behavior of psoralen with 5-mC that is applicable to a simple, sequence-specific and quantitative analysis for the discrimination of 5-mC in DNA, which can be applicable to study the epigenetic behavior of gene expressions.
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Affiliation(s)
- Asako Yamayoshi
- Department of Biomolecular Engineering, Kyoto Institute of Technology, Matsugasaki, Sakuo-ku, Kyoto, Japan
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11
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Fujimoto K, Yamada A, Yoshimura Y, Tsukaguchi T, Sakamoto T. Details of the Ultrafast DNA Photo-Cross-Linking Reaction of 3-Cyanovinylcarbazole Nucleoside: Cis–Trans Isomeric Effect and the Application for SNP-Based Genotyping. J Am Chem Soc 2013; 135:16161-7. [DOI: 10.1021/ja406965f] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | - Tadashi Tsukaguchi
- Faculty
of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
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12
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Fujimoto K, Kishi S, Sakamoto T. Geometric Effect on the Photocrosslinking Reaction between 3-Cyanovinylcarbazole Nucleoside and Pyrimidine Base in DNA/RNA Heteroduplex. Photochem Photobiol 2013; 89:1095-9. [DOI: 10.1111/php.12118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/16/2013] [Indexed: 11/30/2022]
Affiliation(s)
| | - Satomi Kishi
- School of Materials Science; Japan Advanced Institute of Science and Technology; Nomi-shi; Japan
| | - Takashi Sakamoto
- School of Materials Science; Japan Advanced Institute of Science and Technology; Nomi-shi; Japan
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13
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Hagihara S, Lin WC, Kusano S, Chao XG, Hori T, Imoto S, Nagatsugi F. The Crosslink formation of 2'-OMe oligonucleotide containing 2-amino-6-vinylpurine protects mRNA from miRNA-mediated silencing. Chembiochem 2013; 14:1427-9. [PMID: 23893865 DOI: 10.1002/cbic.201300382] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Indexed: 12/21/2022]
Abstract
Masking the miRNA binding site: Crosslink-forming oligonucleotide (CFO) was used for target gene-specific inhibition of microRNA (miRNA) functions. This method can interfere with specific miRNA-mRNA interactions by recognizing sequences unique to the 3'-UTR that are inherent in each mRNA.
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Affiliation(s)
- Shinya Hagihara
- Institute of Transformative Bio-molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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14
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Nishimoto A, Jitsuzaki D, Onizuka K, Taniguchi Y, Nagatsugi F, Sasaki S. 4-vinyl-substituted pyrimidine nucleosides exhibit the efficient and selective formation of interstrand cross-links with RNA and duplex DNA. Nucleic Acids Res 2013; 41:6774-81. [PMID: 23778430 PMCID: PMC3711451 DOI: 10.1093/nar/gkt197] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The formation of interstrand cross-links in nucleic acids can have a strong impact on biological function of nucleic acids; therefore, many cross-linking agents have been developed for biological applications. Despite numerous studies, there remains a need for cross-linking agents that exhibit both efficiency and selectivity. In this study, a 4-vinyl-substituted analog of thymidine (T-vinyl derivative) was designed as a new cross-linking agent, in which the vinyl group is oriented towards the Watson–Crick face to react with the amino group of an adenine base. The interstrand cross-link formed rapidly and selectively with a uridine on the RNA substrate at the site opposite to the T-vinyl derivative. A detailed analysis of cross-link formation while varying the flanking bases of the RNA substrates indicated that interstrand cross-link formation is preferential for the adenine base on the 5′-side of the opposing uridine. In the absence of a 5′-adenine, a uridine at the opposite position underwent cross-linking. The oligodeoxynucleotides probe incorporating the T-vinyl derivative efficiently formed interstrand cross-links in parallel-type triplex DNA with high selectivity for dA in the homopurine strand. The efficiency and selectivity of the T-vinyl derivative illustrate its potential use as a unique tool in biological and materials research.
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Affiliation(s)
- Atsushi Nishimoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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15
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Imoto S, Chikuni T, Kansui H, Kunieda T, Nagatsugi F. Fast DNA interstrand cross-linking reaction by 6-vinylpurine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2013; 31:752-62. [PMID: 23067126 DOI: 10.1080/15257770.2012.726756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Oligonucleotides that incorporate a reactive moiety to form an interstrand cross-link have been widely studied for their potential toward inhibiting gene expression or as basic tools for chemical biology studies. The 6-vinylpurine (2) newly designed in the current study serves well as a new purine-base moiety for increasing cross-link reactivity to target cytosine. Thus, oligonucleotides containing 6-vinylpurine exhibit a more selective and much smoother DNA cross-linking ability to cytosine than the oligonucleotide analogs derived from 2-amino-6-vinylpurine (1) previously explored.
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Affiliation(s)
- Shuhei Imoto
- Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto-city, Kumamoto, Japan.
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16
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Kobori A, Kohji T, Nagae Y, Yamayoshi A, Murakami A. Synthesis and Crosslinking Activity of 4-N-(4,5′,8-Trimethylpsoralen-4′-ylmethyl)-2′-deoxycytidine-containing Oligodeoxyribonucleotides. CHEM LETT 2012. [DOI: 10.1246/cl.2012.804] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Akio Kobori
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology
| | - Tomita Kohji
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology
| | - Yuko Nagae
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology
| | - Asako Yamayoshi
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology
| | - Akira Murakami
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology
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17
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Kobori A, Yamauchi T, Nagae Y, Yamayoshi A, Murakami A. Novel photoresponsive cross-linking oligodeoxyribonucleotides having a caged α-chloroaldehyde. Bioorg Med Chem 2012; 20:5071-6. [PMID: 22871262 DOI: 10.1016/j.bmc.2012.07.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/13/2012] [Accepted: 07/13/2012] [Indexed: 01/06/2023]
Abstract
We have developed photoresponsive cross-linking oligodeoxyribonucleotides (ODNs) for sequence-selective interstrand covalent bond formation toward target nucleotides. A phosphoramidite derivative of α-chloroaldehyde whose carbonyl group was converted to a bis(2-nitrobenzyl)acetal group was prepared for the synthesis of photoresponsive α-chloroaldehyde (PCA)-conjugated ODN. The bis(2-nitrobenzyl)acetal group of a PCA-thymidine conjugate was completely removed by UV irradiation at 365 nm (400 mW/cm(2)) for 1 min. Photo-cross-linking studies revealed that PCA-ODN selectively reacted with the target nucleotides having an adenine or a cytosine moiety at the frontal position of the α-chloroaldehyde group.
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Affiliation(s)
- Akio Kobori
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
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18
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Sasaki S, Onizuka K, Taniguchi Y. The oligodeoxynucleotide probes for the site-specific modification of RNA. Chem Soc Rev 2011; 40:5698-706. [PMID: 21647493 DOI: 10.1039/c1cs15066a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As the knowledge of the biological functions of RNA expands, the demand for research tools to investigate intracellular RNA is increasing. Oligonucleotides can be rationally designed for the target RNA sequence, and therefore, have become a reliable platform for the development of specific molecules for RNA. The chemical modification of RNA has a strong impact on RNA research; the fluorescent labeling of RNA is useful to monitor RNA production, processing, relocation in the cell, interaction with other intracellular components and degradation, etc. Chemical modification may affect the RNA function through a variety of pathways, and therefore, would be potentially useful for biological research, therapeutic approach and artificial manipulation of the RNA function. This tutorial review starts with an introduction of the biological relevance of modified RNA, and focuses on the recent progress of the oligodeoxynucleotide probes for the covalent modifications of RNA. The prospects of this new technology are also discussed.
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Affiliation(s)
- Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan.
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19
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Nagatsugi F, Imoto S. Induced cross-linking reactions to target genes using modified oligonucleotides. Org Biomol Chem 2011; 9:2579-85. [PMID: 21373696 DOI: 10.1039/c0ob00819b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Synthetic oligonucleotides (ONs) are valuable tools that interfere with gene expression by specifically binding to target genes in a sequence-specific manner. Reactive ONs containing cross-linking agents are expected to induce efficient inhibition because they bind covalently to target genes. In recent years, researchers have reported several cross-linking reactions that target DNA induced by external stimuli. This short review highlights recently developed novel cross-linking reactions, focusing particularly on nucleoside derivatives developed by our group.
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Affiliation(s)
- Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, Miyagi 980-8577, Japan.
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20
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Higuchi M, Yamayoshi A, Kato K, Kobori A, Wake N, Murakami A. Specific regulation of point-mutated K-ras-immortalized cell proliferation by a photodynamic antisense strategy. Oligonucleotides 2010; 20:37-44. [PMID: 20038252 DOI: 10.1089/oli.2008.0173] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
It has been reported that point mutations in genes are responsible for various cancers, and the selective regulation of gene expression is an important factor in developing new types of anticancer drugs. To develop effective drugs for the regulation of point-mutated genes, we focused on photoreactive antisense oligonucleotides. Previously, we reported that photoreactive oligonucleotides containing 2'-O-psoralenylmethoxyethyl adenosine (2'-Ps-eom) showed drastic photoreactivity in a strictly sequence-specific manner. Here, we demonstrated the specific gene regulatory effects of 2'-Ps-eom on [(12)Val]K-ras mutant (GGT --> GTT). Photo-cross-linking between target mRNAs and 2'-Ps-eom was sequence-specific, and the effect was UVA irradiation-dependent. Furthermore, 2'-Ps-eom was able to inhibit K-ras-immortalized cell proliferation (K12V) but not Vco cells that have the wild-type K-ras gene. These results suggest that the 2'-Ps-eom will be a powerful nucleic acid drug to inhibit the expression of disease-causing point mutation genes, and has great therapeutic potential in the treatment of cancer.
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Affiliation(s)
- Maiko Higuchi
- Department of Biomolecular Engineering, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan
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Kobori A, Takaya K, Higuchi M, Yamayoshi A, Murakami A. Synthesis and Photoinduced Cross-linking Reactions of 4,5′,8-Trimethylpsoralen-incorporated Oligodeoxyribonucleotide. CHEM LETT 2009. [DOI: 10.1246/cl.2009.272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Synthesis of antisense oligonucleotides containing 2'-O-psoralenylmethoxyalkyl adenosine for photodynamic regulation of point mutations in RNA. Bioorg Med Chem 2008; 17:475-83. [PMID: 19135379 DOI: 10.1016/j.bmc.2008.12.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 12/01/2008] [Accepted: 12/02/2008] [Indexed: 12/30/2022]
Abstract
2'-O-psoralen-conjugated antisense oligonucleotide was able to recognize a point mutation of mRNA. It had outstanding ability to photo-cross-link only to oligoribonucleotides (ORN) having a point mutation. This type of antisense molecule is the only one of its kind so far. To give high photo-cross-linking efficiency and sequence selectivity to antisense molecules, we synthesized novel photo-reactive oligonucleotides (2'-Ps-xom) containing psoralen at the 2'-O-position adenosine via an ethoxymethylene (2'-Ps-eom), propoxymethylene (2'-Ps-pom) and butoxymethylene (2'-Ps-bom) linker, respectively. We evaluated the photo-cross-linking efficiency and sequence selectivity in photo-cross-linking of 2'-Ps-xom to the complementary ORN and to an ORN having a mismatch base. Among them, 2'-Ps-eom exhibited superior photo-cross-linking efficiency with high sequence selectivity.
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Ali MM, Oishi M, Nagatsugi F, Mori K, Nagasaki Y, Kataoka K, Sasaki S. Intracellular inducible alkylation system that exhibits antisense effects with greater potency and selectivity than the natural oligonucleotide. Angew Chem Int Ed Engl 2007; 45:3136-40. [PMID: 16572503 DOI: 10.1002/anie.200504441] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Md Monsur Ali
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Higuchi M, Yamayoshi A, Yamaguchi T, Iwase R, Yamaoka T, Kobori A, Murakami A. Selective photo-cross-linking of 2'-O-psoralen-conjugated oligonucleotide with RNAs having point mutations. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 26:277-90. [PMID: 17454737 DOI: 10.1080/15257770701257434] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
It has been reported that point mutations in genes are responsible for various cancers and the selective regulation of the gene expression is an important issue to develop a new type of anticancer drugs. In this report, we present a new type of antisense molecule that photo-cross-links to an oligoribonucleotide having a point mutation site in a sequence specific manner. 2'-O-psoralen-conjugated adenosine was synthesized in four steps from adenosine and introduced in the middle of an oligodeoxyribonucleotide (2'-Ps-oligo). Compared with 5'-O-psoralen-conjugated oligodeoxyribonucleotide (5'-Ps-oligo), which has a psoralen at the 5'-end, 2'-Ps-oligo more selectively photo-cross-linked to a pyrimidine base of the site of alteration from purine to pyrimidine in the oligoribonucleotide.
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Affiliation(s)
- Maiko Higuchi
- Department of Biomolecular Engineering, Kyoto Institute of Technology, Matsugasaki, Kyoto, Japan
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25
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Yamayoshi A, Kato K, Suga S, Ichinoe A, Arima T, Matsuda T, Kato H, Murakami A, Wake N. Specific apoptosis induction in human papillomavirus-positive cervical carcinoma cells by photodynamic antisense regulation. Oligonucleotides 2007; 17:66-79. [PMID: 17461764 DOI: 10.1089/oli.2006.0047] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Human papillomavirus type 18 (HPV18) is frequently detected in cervical cancer cells. The viral proteins E6 and E7 are expressed consistently and have oncogenic activities. The E7 protein binds to a tumor suppressor, the retinoblastoma gene product (pRB), however, leading to the stabilization of tumor suppressor, p53 protein. On the other hand, another viral product, E6, forms complexes with p53 and abrogates its function, resulting in tumor progression. These facts imply that the E6 oncogene is one of the ideal targets for directed gene therapy in HPV-positive cervical cancer. In this study, we tried photodynamic antisense regulation of the antiapoptotic E6 expression using a photocross-linking reagent, 4,5',8-trimethylpsoralen, conjugated oligo(nucleoside phosphorothioate) (Ps-S-Oligo). This photodynamic antisense strategy effectively elicited the apoptotic death of HPV18-positive cervical cancer cells through the selective repression of E6 mRNA and consequent stabilization of p53 protein. E7-mediated signals potentially activated the p53 function and mobilized the p53 pathway to deliver pro-apoptotic signals to the cancer cells, leading to the suppression of in vivo tumorigenesis. An extremely low concentration of cisplatin in addition to Ps-S-Oligos further up-regulated p53 activity, provoking massive apoptotic induction. These results suggest that the photodynamic antisense strategy has the great therapeutic potential in HPV-positive cervical cancers.
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Affiliation(s)
- Asako Yamayoshi
- Department of Molecular Genetics, Division of Molecular and Cell Therapeutics, Kyushu University, Maidashi, Fukuoka 812-8582, Japan
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Ali MM, Oishi M, Nagatsugi F, Mori K, Nagasaki Y, Kataoka K, Sasaki S. Intracellular Inducible Alkylation System That Exhibits Antisense Effects with Greater Potency and Selectivity than the Natural Oligonucleotide. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kawasaki T, Nagatsugi F, Ali MM, Maeda M, Sugiyama K, Hori K, Sasaki S. Hybridization-promoted and cytidine-selective activation for cross-linking with the use of 2-amino-6-vinylpurine derivatives. J Org Chem 2005; 70:14-23. [PMID: 15624902 DOI: 10.1021/jo048298p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, we have proposed a new concept for cross-linking agents with inducible reactivity, in which the highly reactive cross-linking agent, the 2-amino-6-vinylpurine nucleoside analogue (1), can be regenerated in situ from its stable precursors, the phenylsulfide (4) and the phenylsulfoxide (3) derivatives, by a hybridization-promoted activation process with selectivity to cytidine. The phenylsulfide precursor (4) exhibited cross-linking ability despite its high stability toward strong nucleophiles such as amines and thiols. In this study, we investigated the substituent effects of the phenylsulfide group on the cross-linking reaction, and determined the 2-carboxy substituent of the phenylsulfide derivative (11k) as an efficient cross-linking agent with inducible reactivity. Detailed investigations have shown that the phenylsulfoxide (3) and phenylsulfide (4) precursors produce the 2-amino-6-vinylpurine nucleoside (1) as the common reactive species. It has been concluded that the nature of the inducible reactivity of the precursors (3 and 4) is acceleration of their elimination to the 2-amino-6-vinylpurine nucleoside (1) through the selective process in the duplex with the ODN having cytidine at the target site.
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Affiliation(s)
- Takeshi Kawasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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