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Wang Y, Ji H, Ma J, Luo H, He Y, Tang X, Wu L. Reversible On-Off Photoswitching of DNA Replication Using a Dumbbell Oligodeoxynucleotide. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248992. [PMID: 36558127 PMCID: PMC9785685 DOI: 10.3390/molecules27248992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
In most organisms, DNA extension is highly regulated; however, most studies have focused on controlling the initiation of replication, and few have been done to control the regulation of DNA extension. In this study, we adopted a new strategy for azODNs to regulate DNA extension, which is based on azobenzene oligonucleotide chimeras regulated by substrate binding affinity, and the conformation of the chimera can be regulated by a light source with a light wavelength of 365 nm. The results showed that the primer was extended with Taq DNA polymerase after visible light treatment, and DNA extension could be effectively hindered with UV light treatment. We also verify the reversibility of the photoregulation of primer extension through photoswitching of dumbbell asODNs by alternate irradiation with UV and visible light. Our method has the advantages of fast and simple, green response and reversible operations, providing a new strategy for regulating gene replication.
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Affiliation(s)
- Yu Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heming Ji
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Zhejiang Institute of Mechanical and Electrical Technician, Yiwu 322000, China
| | - Jian Ma
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hang Luo
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Correspondence: (X.T.); (L.W.)
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Zhejiang Institute of Mechanical and Electrical Technician, Yiwu 322000, China
- Correspondence: (X.T.); (L.W.)
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2
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Synthesis of azobenzenes with high reactivity towards reductive cleavage: Enhancing the repertoire of hypersensitive azobenzenes and examining their dissociation behavior. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.152018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Bhilare S, Shet H, Sanghvi YS, Kapdi AR. Discovery, Synthesis, and Scale-up of Efficient Palladium Catalysts Useful for the Modification of Nucleosides and Heteroarenes. Molecules 2020; 25:E1645. [PMID: 32260100 PMCID: PMC7181029 DOI: 10.3390/molecules25071645] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 03/25/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid derivatives are imperative biomolecules and are involved in life governing processes. The chemical modification of nucleic acid is a fascinating area for researchers due to the potential activity exhibited as antiviral and antitumor agents. In addition, these molecules are also of interest toward conducting useful biochemical, pharmaceutical, and mutagenic study. For accessing such synthetically useful structures and features, transition-metal catalyzed processes have been proven over the years to be an excellent tool for carrying out the various transformations with ease and under mild reaction conditions. Amidst various transition-metal catalyzed processes available for nucleoside modification, Pd-catalyzed cross-coupling reactions have proven to be perhaps the most efficient, successful, and broadly applicable reactions in both academia and industry. Pd-catalyzed C-C and C-heteroatom bond forming reactions have been widely used for the modification of the heterocyclic moiety in the nucleosides, although a single catalyst system that could address all the different requirements for nucleoside modifications isvery rare or non-existent. With this in mind, we present herein a review showcasing the recent developments and improvements from our research groups toward the development of Pd-catalyzed strategies including drug synthesis using a single efficient catalyst system for the modification of nucleosides and other heterocycles. The review also highlights the improvement in conditions or the yield of various bio-active nucleosides or commercial drugs possessing the nucleoside structural core. Scale ups wherever performed (up to 100 g) of molecules of commercial importance have also been disclosed.
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Affiliation(s)
- Shatrughn Bhilare
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh Road, Matunga, Mumbai 400019, India;
| | - Harshita Shet
- Department of Chemistry, Institute of Chemical Technology-Indian Oil Odisha Campus, IIT Kharagpur Extension Centre, MouzaSamantpuri, Bhubaneswar 751013, Odisha, India;
| | - Yogesh S. Sanghvi
- Rasayan Inc., 2802, Crystal Ridge Road, Encinitas, CA 92024-6615, USA;
| | - Anant R. Kapdi
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh Road, Matunga, Mumbai 400019, India;
- Department of Chemistry, Institute of Chemical Technology-Indian Oil Odisha Campus, IIT Kharagpur Extension Centre, MouzaSamantpuri, Bhubaneswar 751013, Odisha, India;
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4
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Eom T, Khan A. Hypersensitive azobenzenes: facile synthesis of clickable and cleavable azo linkers with tunable and high reducibility. Org Biomol Chem 2020; 18:420-424. [PMID: 31904038 DOI: 10.1039/c9ob02515d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The aim of this work is to show that by increasing the number of donor substituents in a donor/acceptor system, the sensitivity of the azobenzene linkage towards a reductive cleavage reaction can be enhanced to unprecedented high levels. For instance, in a triple-donor system, less than a second constitutes the half-life of the azo (N[double bond, length as m-dash]N) bond. Synthetic access to such redox active scaffolds is highly practical and requires only 1-2 synthetic steps. The fundamental molecular design is also adaptable. This is demonstrated through scaffold functionalization by azide, tetraethylene glycol, and biotin groups. The availability of the azide group is shown in a copper-free 'click' reaction suitable in context with protein conjugation and proteomics application. Finally, the clean nature of the scission process is demonstrated with the help of liquid chromatography coupled with mass analysis. This work, therefore, describes development of cleavable azobenzene linkers that can be accessed with synthetic ease, can be multiply functionalized, and show a clean and rapid response to mild reducing conditions.
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Affiliation(s)
- Taejun Eom
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-Ro, Seongbuk-Gu, Seoul 02841, Korea.
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Liu Y, Zhou P, Da H, Jia H, Bai F, Hu G, Zhang B, Fang J. An Azo Coupling Strategy for Protein 3-Nitrotyrosine Derivatization. Chemistry 2019; 25:11228-11232. [PMID: 31241789 DOI: 10.1002/chem.201901828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/09/2019] [Indexed: 11/11/2022]
Abstract
Herein, a strategy for the selective derivatization of 3-nitrotyrosine-containing proteins using the classic azo coupling reaction as the key step is described. This novel approach featured multiple advantages and was successfully applied to detect picomole levels of protein tyrosine nitration in biological samples.
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Affiliation(s)
- Yuxin Liu
- State Key Laboratory of Applied Organic Chemistry &, College of Chemistry and Chemical Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou, 730000, China
| | - Pengcheng Zhou
- College of Chemistry & Materials Science, South-Central University for Nationalities, No. 708 Minyuan Road, Wuhan, 430074, China
| | - Honghong Da
- State Key Laboratory of Applied Organic Chemistry &, College of Chemistry and Chemical Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou, 730000, China
| | - Huiyi Jia
- State Key Laboratory of Applied Organic Chemistry &, College of Chemistry and Chemical Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou, 730000, China
| | - Feifei Bai
- State Key Laboratory of Applied Organic Chemistry &, College of Chemistry and Chemical Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou, 730000, China
| | - Guodong Hu
- State Key Laboratory of Applied Organic Chemistry &, College of Chemistry and Chemical Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou, 730000, China
| | - Baoxin Zhang
- State Key Laboratory of Applied Organic Chemistry &, College of Chemistry and Chemical Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou, 730000, China
| | - Jianguo Fang
- State Key Laboratory of Applied Organic Chemistry &, College of Chemistry and Chemical Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou, 730000, China
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6
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Batule BS, Lee CY, Park KS, Park HG. Polymerization-sensitive switch-on monomer for terminal transferase activity assay. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:256-259. [PMID: 30688096 DOI: 10.1080/21691401.2018.1552593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We herein describe a simple but efficient method for the determination of terminal transferase (TdT) activity, which relies on our finding that Fe(III)-quenched boron-dipyrromethene (BODIPY)-ATP is utilized as a switch-on monomer for polymerization and enables the facile synthesis of fluorescence oligonucleotides without additional, post-processing steps. As TdT carries out the synthesis of DNA by adding the monomers into growing chains, Fe(III) is displaced from BODIPY with the release of pyrophosphate group, which consequently leads to the generation of highly fluorescent long oligonucleotides. With this strategy, we selectively detected the TdT activity with high sensitivity. In addition, its practical applicability was successfully demonstrated by determining TdT activities in human serum.
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Affiliation(s)
- Bhagwan S Batule
- a Department of Chemical and Biomolecular Engineering (BK21+ Program) , KAIST , Daejeon , Republic of Korea
| | - Chang Yeol Lee
- a Department of Chemical and Biomolecular Engineering (BK21+ Program) , KAIST , Daejeon , Republic of Korea
| | - Ki Soo Park
- b Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , Republic of Korea
| | - Hyun Gyu Park
- a Department of Chemical and Biomolecular Engineering (BK21+ Program) , KAIST , Daejeon , Republic of Korea
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7
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Crystal structures of ternary complexes of archaeal B-family DNA polymerases. PLoS One 2017; 12:e0188005. [PMID: 29211756 PMCID: PMC5718519 DOI: 10.1371/journal.pone.0188005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/30/2017] [Indexed: 01/04/2023] Open
Abstract
Archaeal B-family polymerases drive biotechnology by accepting a wide substrate range of chemically modified nucleotides. By now no structural data for archaeal B-family DNA polymerases in a closed, ternary complex are available, which would be the basis for developing next generation nucleotides. We present the ternary crystal structures of KOD and 9°N DNA polymerases complexed with DNA and the incoming dATP. The structures reveal a third metal ion in the active site, which was so far only observed for the eukaryotic B-family DNA polymerase δ and no other B-family DNA polymerase. The structures reveal a wide inner channel and numerous interactions with the template strand that provide space for modifications within the enzyme and may account for the high processivity, respectively. The crystal structures provide insights into the superiority over other DNA polymerases concerning the acceptance of modified nucleotides.
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8
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Tan L, Liu Y, Li X, Wu XY, Gong B, Shen YM, Shao Z. Synthesis and evaluations of an acid-cleavable, fluorescently labeled nucleotide as a reversible terminator for DNA sequencing. Chem Commun (Camb) 2016; 52:2549-52. [PMID: 26744748 DOI: 10.1039/c5cc09578f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An acid-cleavable linker based on a dimethylketal moiety was synthesized and used to connect a nucleotide with a fluorophore to produce a 3'-OH unblocked nucleotide analogue as an excellent reversible terminator for DNA sequencing by synthesis.
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Affiliation(s)
- Lianjiang Tan
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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Li J, Liu G, Zhou J, Wang A, Wang J, Jin R. Redox activity of lignite and its accelerating effects on the chemical reduction of azo dye by sulfide. RSC Adv 2016. [DOI: 10.1039/c6ra11930a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Redox active lignite can act as a mediator to accelerate azo dye decolorization through enhancing electron transfer from sulfide to the azo dye.
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Affiliation(s)
- Juanjuan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering
- Ministry of Education
- School of Environmental Science and Technology
- Dalian University of Technology
- Dalian 116024
| | - Guangfei Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering
- Ministry of Education
- School of Environmental Science and Technology
- Dalian University of Technology
- Dalian 116024
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering
- Ministry of Education
- School of Environmental Science and Technology
- Dalian University of Technology
- Dalian 116024
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering
- Ministry of Education
- School of Environmental Science and Technology
- Dalian University of Technology
- Dalian 116024
| | - Ruofei Jin
- Key Laboratory of Industrial Ecology and Environmental Engineering
- Ministry of Education
- School of Environmental Science and Technology
- Dalian University of Technology
- Dalian 116024
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