1
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Xie R, Han Y, Luo W, Zhao Q, Li Y, Chen G. Palladium-Catalyzed C-H Olefination for Nucleic Acid Production. Curr Protoc 2023; 3:e829. [PMID: 37498139 DOI: 10.1002/cpz1.829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The palladium-catalyzed direct C-H olefination of unprotected uridine, 2'-deoxyuridine, uridine monophosphate, and uridine analogues are described here. This protocol provides an efficient, atom-economical, and environmentally friendly method for the introduction of an alkenyl group at the C5 position of the uracil without pre-functionalization. A series of C5-alkenylated uridine analogues, including some biologically significant compounds and potential pharmaceutical candidates, were synthesized with exposed hydroxyl groups on the ribose. © 2023 Wiley Periodicals LLC. Basic Protocol 1: The reaction of uridine, 2'-deoxyuridine, and sofosbuvir for the C-H olefination with methyl acrylate Basic Protocol 2: The reaction of uridine and 2'-deoxyuridine for the C-H olefination with styrene.
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Affiliation(s)
- Ruoqian Xie
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yunxi Han
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Wenhao Luo
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Qin Zhao
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yangyan Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Gang Chen
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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2
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Basran K, Bujalska A, Karimi A, Luedtke NW. Formal [4 + 2] Cycloadditions of Maleimides on Duplex DNA. Bioconjug Chem 2023; 34:977-982. [PMID: 37290129 DOI: 10.1021/acs.bioconjchem.3c00090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Near-quantitative DNA bioconjugation and detailed mechanistic investigations of reactions involving 5-(vinyl)-2'-deoxyuridine (VdU) and maleimides are reported. According to accelerated reaction rates in solvents with increasing polarity and trends in product stereochemistry, VdU-maleimide reactions proceed via a formal [4 + 2] stepwise cycloaddition. In contrast, 5-(1,3-butadienyl)-2'-deoxyuridine (BDdU) reacts with maleimides in a concerted [4 + 2] Diels-Alder cycloaddition. VdU-maleimide reactions enable high-yielding bioconjugation of duplex DNA in vitro (>90%) as well as metabolic labeling experiments in cells.
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Affiliation(s)
- Kaleena Basran
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Anna Bujalska
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ashkan Karimi
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Nathan W Luedtke
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
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3
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Zhao Q, Xie R, Zeng Y, Li W, Xiao G, Li Y, Chen G. Palladium-catalyzed C-H olefination of uridine, deoxyuridine, uridine monophosphate and uridine analogues. RSC Adv 2022; 12:24930-24934. [PMID: 36199883 PMCID: PMC9434382 DOI: 10.1039/d2ra03681a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/25/2022] [Indexed: 11/21/2022] Open
Abstract
The palladium-catalyzed oxidative C-H olefinations of uridine, deoxyuridine, uridine monophosphate and uridine analogues are reported herein. This protocol provides an efficient, atom-economic and environmentally friendly approach to the synthesis of biologically important C5-alkene modified uracil/uridine-containing derivatives and pharmaceutical candidates.
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Affiliation(s)
- Qin Zhao
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 People's Republic of China
| | - Ruoqian Xie
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 People's Republic of China
| | - Yuxiao Zeng
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 People's Republic of China
| | - Wanlu Li
- School of Chemistry and Chemical Engineering, Southeast University Nanjing 211189 People's Republic of China
| | - Guolan Xiao
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 People's Republic of China
| | - Yangyan Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 People's Republic of China
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering Yongzhou 425199 People's Republic of China
| | - Gang Chen
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 People's Republic of China
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4
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Loehr MO, Luedtke NW. A Kinetic and Fluorogenic Enhancement Strategy for Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2022; 61:e202112931. [PMID: 35139255 DOI: 10.1002/anie.202112931] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Indexed: 12/21/2022]
Abstract
Chemical modification of nucleic acids in living cells can be sterically hindered by tight packing of bioorthogonal functional groups in chromatin. To address this limitation, we report here a dual enhancement strategy for nucleic acid-templated reactions utilizing a fluorogenic intercalating agent capable of undergoing inverse electron-demand Diels-Alder (IEDDA) reactions with DNA containing 5-vinyl-2'-deoxyuridine (VdU) or RNA containing 5-vinyl-uridine (VU). Reversible high-affinity intercalation of a novel acridine-tetrazine conjugate "PINK" (KD =5±1 μM) increases the reaction rate of tetrazine-alkene IEDDA on duplex DNA by 60 000-fold (590 M-1 s-1 ) as compared to the non-templated reaction. At the same time, loss of tetrazine-acridine fluorescence quenching renders the reaction highly fluorogenic and detectable under no-wash conditions. This strategy enables live-cell dynamic imaging of acridine-modified nucleic acids in dividing cells.
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Affiliation(s)
- Morten O Loehr
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, Québec, H3A 0B8, Canada
| | - Nathan W Luedtke
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, Québec, H3A 0B8, Canada.,Department of Pharmacology and Therapeutics, McGill University, 3655 Prom. Sir William Osler, Montréal, Québec H3G 1Y6, Canada
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5
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Loehr MO, Luedtke NW. A Kinetic and Fluorogenic Enhancement Strategy for Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Morten O. Loehr
- Department of Chemistry McGill University 801 Sherbrooke St. West Montréal Québec, H3A 0B8 Canada
| | - Nathan W. Luedtke
- Department of Chemistry McGill University 801 Sherbrooke St. West Montréal Québec, H3A 0B8 Canada
- Department of Pharmacology and Therapeutics McGill University 3655 Prom. Sir William Osler Montréal Québec H3G 1Y6 Canada
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6
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Howlader H, Suzol SH, Blanco K, Martin‐Rafa L, Laverde EE, Liu Y, Wnuk SF. Purine Nucleosides with a Reactive (
β
‐Iodovinyl)sulfone or a (
β
‐Keto)sulfone Group at the C8 Position and Their Polymerase‐Catalyzed Incorporation into DNA. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202100764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hasan Howlader
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
| | - Sazzad H. Suzol
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
| | - Kevin Blanco
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
| | - Lilian Martin‐Rafa
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
| | - Eduardo E. Laverde
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
| | - Yuan Liu
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
- Biomolecular Sciences Institute Florida International University Miami Florida 33199 U.S.A
| | - Stanislaw F. Wnuk
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
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7
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Kawai K, Ikeda K, Sato A, Kabasawa A, Kojima M, Kokado K, Kakugo A, Sada K, Yoshino T, Matsunaga S. 1,2-Disubstituted 1,2-Dihydro-1,2,4,5-tetrazine-3,6-dione as a Dynamic Covalent Bonding Unit at Room Temperature. J Am Chem Soc 2022; 144:1370-1379. [PMID: 35040645 DOI: 10.1021/jacs.1c11665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dynamic covalent bonds are useful tools in a wide range of applications. Although various reversible chemical reactions have been studied for this purpose, the requirement for harsh conditions, such as high temperature and low or high pH, to activate generally stable covalent bonds limits their potential applications involving biomolecules or household utilization. Here, we report the design, synthesis, characterization, and dynamic covalent bonding properties of 1,2-disubstituted 1,2-dihydro-1,2,4,5-tetrazine-3,6-dione (TETRAD). Hetero-Diels-Alder reactions of TETRAD with furan derivatives and their retro-reactions proceeded rapidly at room temperature under neutral conditions, enabling a chemically induced sol-gel transition system.
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Affiliation(s)
- Kentaro Kawai
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kazuki Ikeda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Akane Sato
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Akira Kabasawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Japan
| | - Masahiro Kojima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kenta Kokado
- Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0020, Japan
| | - Akira Kakugo
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Japan
| | - Tatsuhiko Yoshino
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Shigeki Matsunaga
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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8
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Bujalska A, Basran K, Luedtke NW. [4+2] and [2+4] cycloaddition reactions on single- and double-stranded DNA: a dual-reactive nucleoside. RSC Chem Biol 2022; 3:698-701. [PMID: 35755194 PMCID: PMC9175100 DOI: 10.1039/d2cb00062h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/27/2022] [Indexed: 11/21/2022] Open
Abstract
Here we report dual reactivity of diene-modified duplex DNA containing 5-(1,3-butadienyl)-2'-deoxyuridine “BDdU”. Regular-electron demand [4+2] cycloaddition proceeded upon addition of a maleimide, whereas inversed-electron demand [2+4] cycloaddition occurred upon addition...
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Affiliation(s)
- Anna Bujalska
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Kaleena Basran
- Department of Chemistry, McGill University 801 Sherbrooke St. West Montréal Québec H3A 0B8 Canada
| | - Nathan W Luedtke
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190 8057 Zurich Switzerland
- Department of Chemistry, McGill University 801 Sherbrooke St. West Montréal Québec H3A 0B8 Canada
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9
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Oligonucleotide conjugation by tyrosine‐click reaction. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Hanay SB, Fallah A, Senturk E, Yetim Z, Afghah F, Yilmaz H, Culha M, Koc B, Zarrabi A, Varma RS. Exploiting Urazole's Acidity for Fabrication of Hydrogels and Ion-Exchange Materials. Gels 2021; 7:261. [PMID: 34940320 PMCID: PMC8701905 DOI: 10.3390/gels7040261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 11/30/2022] Open
Abstract
In this study, the acidity of urazole (pKa 5-6) was exploited to fabricate a hydrogel in two simple and scalable steps. Commercially available poly(hexamethylene)diisocyanate was used as a precursor to synthesize an urazole containing gel. The formation of urazole was confirmed by FT-IR and 1H-NMR spectroscopy. The hydrogel was characterized by microscopy imaging as well as spectroscopic and thermo-gravimetric analyses. Mechanical analysis and cell viability tests were performed for its initial biocompatibility evaluation. The prepared hydrogel is a highly porous hydrogel with a Young's modulus of 0.91 MPa, has a swelling ratio of 87%, and is capable of exchanging ions in a medium. Finally, a general strategy was demonstrated to embed urazole groups directly into a crosslinked material.
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Affiliation(s)
- Saltuk B. Hanay
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul 34956, Turkey; (A.F.); (E.S.); (F.A.); (B.K.)
- Sabancı University Nanotechnology Research and Application Center—SUNUM, Istanbul 34956, Turkey; (H.Y.); (M.C.)
- Hanay Advanced Chemicals Inc., Hanay Ileri Kimya Arastirma Gelistirme ve Muhendislik AS, Istanbul 34413, Turkey
| | - Ali Fallah
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul 34956, Turkey; (A.F.); (E.S.); (F.A.); (B.K.)
- Sabancı University Nanotechnology Research and Application Center—SUNUM, Istanbul 34956, Turkey; (H.Y.); (M.C.)
- Integrated Manufacturing Technologies Research and Application Center, Sabanci University, Istanbul 34956, Turkey
| | - Efsun Senturk
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul 34956, Turkey; (A.F.); (E.S.); (F.A.); (B.K.)
- Hanay Advanced Chemicals Inc., Hanay Ileri Kimya Arastirma Gelistirme ve Muhendislik AS, Istanbul 34413, Turkey
| | - Zeliha Yetim
- Department of Histology and Embryology, Faculty of Medicine, Ataturk University, Erzurum 25240, Turkey;
| | - Ferdows Afghah
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul 34956, Turkey; (A.F.); (E.S.); (F.A.); (B.K.)
| | - Hulya Yilmaz
- Sabancı University Nanotechnology Research and Application Center—SUNUM, Istanbul 34956, Turkey; (H.Y.); (M.C.)
| | - Mustafa Culha
- Sabancı University Nanotechnology Research and Application Center—SUNUM, Istanbul 34956, Turkey; (H.Y.); (M.C.)
- Department of Internal Medicine and Ophthalmology, Morsani College of Medicine, The University of South Florida, Tampa, FL 33620, USA
| | - Bahattin Koc
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul 34956, Turkey; (A.F.); (E.S.); (F.A.); (B.K.)
- Sabancı University Nanotechnology Research and Application Center—SUNUM, Istanbul 34956, Turkey; (H.Y.); (M.C.)
- Integrated Manufacturing Technologies Research and Application Center, Sabanci University, Istanbul 34956, Turkey
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul 34396, Turkey;
| | - Rajender S. Varma
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University in Olomouc, 78371 Olomouc, Czech Republic
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11
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Zheng Y, Zhou Y, Zhang Y, Deng P, Zhao X, Jiang S, Du G, Shen X, Xie X, Su Z, Yu Z. Water-Involved Ring-Opening of 4-Phenyl-1,2,4-triazoline-3,5-dione for "Photo-Clicked" Access to Carbamoyl Formazan Photoswitches In Situ. Chem Asian J 2021; 17:e202101239. [PMID: 34851039 DOI: 10.1002/asia.202101239] [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: 10/28/2021] [Revised: 11/23/2021] [Indexed: 11/08/2022]
Abstract
Cyclic azodicarbonyl derivatives, particularly 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD), commonly serve as arenophile, dienophile, enophile and electrophile. Perplexed by its instability in aqueous environment, there are few studies focused on the transient intermediate produced by hydrolysis of PTAD to achieve synthetic significance. Herein, we describe a "photo-click" method that involves nitrile imine (NI) from diarylsydnone to capture the diazenecarbonyl-phenyl-carbamic acid (DACPA) generated by water-promoted ring-opening of PTAD. DFT calculation reveal that H-bonding interactions between PTAD and water are vital to form DACPA which exhibited an umpolung effect during ligation by nature bond orbit (NBO) analysis. The ultra-fast ligation resulted in carbamoyl formazans, as a unique Z↔E photo-switchable linker on target molecules, including peptide and drugs, with excellent anti-fatigue performance. This strategy is showcased to construct highly functionalized carbamoyl formazans in situ for photo-pharmacology and material studies, which also expands the chemistry of PTAD in aqueous media.
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Affiliation(s)
- Yuanqin Zheng
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Yuqiao Zhou
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Yan Zhang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Pengchi Deng
- Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Xiaohu Zhao
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Shichao Jiang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Guangxi Du
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Xin Shen
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Xinyu Xie
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Zhishan Su
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
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12
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Ravi Kumara GS, Pandith A, Seo YJ. Direct and selective metal-free N 6-arylation of adenosine residues for simple fluorescence labeling of DNA and RNA. Chem Commun (Camb) 2021; 57:5450-5453. [PMID: 33950062 DOI: 10.1039/d1cc02069b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have developed an unprecedented transition metal-free approach for the direct fluorescence turn-on labeling of natural oligonucleotides through selective N6-arylation of adenosine moieties. This method allows the simple and direct fluorescence labeling of natural unmodified DNA and RNA, but is dependent on the secondary structure, favoring single-stranded structures.
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Affiliation(s)
| | - Anup Pandith
- Department of Chemistry, Jeonbuk National University, Jeonju 561-756, South Korea.
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 561-756, South Korea.
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13
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Ito Y, Hayashi H, Fuchi Y, Hari Y. Post-synthetic modification of oligonucleotides containing 5-mono- and 5-di-fluoromethyluridines. Tetrahedron 2021. [DOI: 10.1016/j.tet.2020.131769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Walunj MB, Srivatsan SG. Nucleic Acid Conformation Influences Postsynthetic Suzuki-Miyaura Labeling of Oligonucleotides. Bioconjug Chem 2020; 31:2513-2521. [PMID: 33089687 PMCID: PMC7611128 DOI: 10.1021/acs.bioconjchem.0c00466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemoselective transformations that work under physiological conditions have emerged as powerful tools to label nucleic acids in cell-free and cellular environments. However, detailed studies investigating the influence of nucleic acid conformation on the performance of such chemoselective nucleic labeling methods are less explored. Given that nucleic acids adopt complex structures, it is highly important to study the scope of the chemical modification method in the context of nucleic acid conformations. Here we report a systematic study on the effect of local conformation on the postsynthetic Suzuki-Miyaura functionalization of human telomeric (H-Telo) DNA repeat oligonucleotide (ON) sequences, which form multiple G-quadruplex (GQ) structures. 5-Iodo-2'-deoxyuridine (IdU)-modified H-Telo ONs were synthesized by the solid-phase method, and when subjected to Suzuki-Miyaura cross-coupling reaction, its efficiency was found to depend on the type of conformation and the position of IdU label in different loops of the GQ structure. IdU-labeled GQs gave better yields as compared to single-stranded random coil structures. However, the IdU-labeled duplex under different ionic conditions did not undergo the coupling reaction. Further, using this method, we directly installed an environment-sensitive fluorescent probe, which photophysically reported the formation as well as distinguished different GQ topologies of telomeric repeat. Collectively, this systematic study underscores the influence of nucleic acid conformation, which has to be taken into account when establishing postsynthetic chemoselective functionalization strategies.
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Affiliation(s)
- Manisha B. Walunj
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Seergazhi G. Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411008, India
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15
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George JT, Srivatsan SG. Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state. Chem Commun (Camb) 2020; 56:12307-12318. [PMID: 33026365 PMCID: PMC7611129 DOI: 10.1039/d0cc05228k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To understand the structure and ensuing function of RNA in various cellular processes, researchers greatly rely on traditional as well as contemporary labeling technologies to devise efficient biochemical and biophysical platforms. In this context, bioorthogonal chemistry based on chemoselective reactions that work under biologically benign conditions has emerged as a state-of-the-art labeling technology for functionalizing biopolymers. Implementation of this technology on sugar, protein, lipid and DNA is fairly well established. However, its use in labeling RNA has posed challenges due to the fragile nature of RNA. In this feature article, we provide an account of bioorthogonal chemistry-based RNA labeling techniques developed in our lab along with a detailed discussion on other technologies put forward recently. In particular, we focus on the development and applications of covalent methods to label RNA by transcription and posttranscription chemo-enzymatic approaches. It is expected that existing as well as new bioorthogonal functionalization methods will immensely advance our understanding of RNA and support the development of RNA-based diagnostic and therapeutic tools.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pune 411008, India.
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16
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Tera M, Luedtke NW. Cross-linking cellular nucleic acids via a target-directing double click reagent. Methods Enzymol 2020; 641:433-457. [PMID: 32713534 DOI: 10.1016/bs.mie.2020.04.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bioorthogonal ligation reactions are powerful tools for characterizing DNA metabolism, DNA-protein binding interactions, and they even provide new leads for therapeutic strategies. Nucleoside analogs can deliver bioorthogonal functional groups into chromatin via cellular metabolic pathways, however, insufficient phosphorylation by endogenous kinases often limits the efficiency of their incorporation. Even when successfully metabolized into biopolymers, steric hindrance of the modified nucleotide by chromatin can inhibit subsequent click reactions. In this chapter, we describe methods that overcome these limitations. Nucleotide monophosphate triesterers can bypass the need for cellular nucleoside kinase activity and thereby enable efficient incorporation of azide groups into cellular DNA. Steric access to and modification of the azide groups within natively folded chromatin can then be accomplished using a bioorthogonal "intercalating reagent" comprised of a cationic Sondheimer diyne that reversibly intercalates into duplexes where it undergoes tandem, strain-promoted cross-linking of two azides to give DNA-DNA interstrand crosslinks or DNA-fluorophore conjugation, depending on the relative number and spatial orientation of the azide groups in the DNA.
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Affiliation(s)
- Masayuki Tera
- Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan.
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17
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Tera M, Luedtke NW. Three-Component Bioorthogonal Reactions on Cellular DNA and RNA. Bioconjug Chem 2019; 30:2991-2997. [DOI: 10.1021/acs.bioconjchem.9b00630] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Masayuki Tera
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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18
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Liu HS, Ishizuka T, Kawaguchi M, Nishii R, Kataoka H, Xu Y. A Nucleoside Derivative 5-Vinyluridine (VrU) for Imaging RNA in Cells and Animals. Bioconjug Chem 2019; 30:2958-2966. [DOI: 10.1021/acs.bioconjchem.9b00643] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hong-shan Liu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Makiko Kawaguchi
- Section of Oncopathology and Regenerative Biology, Department of Pathology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Ryuichi Nishii
- Department of Molecular Imaging and Theranostics, National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Hiroaki Kataoka
- Section of Oncopathology and Regenerative Biology, Department of Pathology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
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19
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Xie S, Zhou J, Chen X, Kong N, Fan Y, Zhang Y, Hammer G, Castner DG, Ramström O, Yan M. A Versatile Catalyst-Free Perfluoroaryl Azide-Aldehyde-Amine Conjugation Reaction. MATERIALS CHEMISTRY FRONTIERS 2019; 3:251-256. [PMID: 31543961 PMCID: PMC6754110 DOI: 10.1039/c8qm00516h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A tri-component reaction, involving an electrophilically-activated perfluoroaryl azide, an enolizable aldehyde and an amine, reacts readily at room temperature without any catalysts in solvents including aqueous conditions to yield a stable amidine conjugate. The versatility of this reaction is demonstrated in the conjugation of an amino acid without prior protection of the carboxyl group, and in the synthesize antibiotic-nanoparticle conjugates.
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Affiliation(s)
- Sheng Xie
- Department of Chemistry, KTH-Royal Institute of Technology, Stockholm, Sweden
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Juan Zhou
- Department of Chemistry, KTH-Royal Institute of Technology, Stockholm, Sweden
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Xuan Chen
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854, USA. E-mail: ,
| | - Na Kong
- Department of Chemistry, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Yanmiao Fan
- Department of Chemistry, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Yang Zhang
- Department of Chemistry, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Gerry Hammer
- Departments of Bioengineering and Chemical Engineering, National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, Washington, USA
| | - David G Castner
- Departments of Bioengineering and Chemical Engineering, National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, Washington, USA
| | - Olof Ramström
- Department of Chemistry, KTH-Royal Institute of Technology, Stockholm, Sweden
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854, USA. E-mail: ,
- Department of Chemistry and Biomedical Sciences, Linnaeus University, SE-39182 Kalmar, Sweden
| | - Mingdi Yan
- Department of Chemistry, KTH-Royal Institute of Technology, Stockholm, Sweden
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854, USA. E-mail: ,
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20
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Wu K, He M, Khan I, Asare Okai PN, Lin Q, Fuchs G, Royzen M. Bio-orthogonal chemistry-based method for fluorescent labelling of ribosomal RNA in live mammalian cells. Chem Commun (Camb) 2019; 55:10456-10459. [DOI: 10.1039/c9cc05346h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A bio-orthogonal chemistry-based approach for fluorescent labelling of ribosomal RNA is described.
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Affiliation(s)
- K. Wu
- University at Albany
- SUNY
- Department of Chemistry
- Albany
- USA
| | - M. He
- University at Albany
- SUNY
- Department of Chemistry
- Albany
- USA
| | - I. Khan
- University at Albany
- SUNY
- Department of Chemistry
- Albany
- USA
| | - P. N. Asare Okai
- University of Delaware
- Department of Chemistry and Biochemistry
- Brown Labs
- Newark
- USA
| | - Q. Lin
- University at Albany
- SUNY
- Department of Chemistry
- Albany
- USA
| | - G. Fuchs
- University at Albany
- SUNY
- Department of Chemistry
- Albany
- USA
| | - M. Royzen
- University at Albany
- SUNY
- Department of Chemistry
- Albany
- USA
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21
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Ito Y, Matsuo M, Yamamoto K, Yamashita W, Osawa T, Hari Y. Post-synthetic modification of oligonucleotides containing 5-trifluoromethylpyrimidine bases. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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22
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Kaiser D, Winne JM, Ortiz-Soto ME, Seibel J, Le TA, Engels B. Mechanistical Insights into the Bioconjugation Reaction of Triazolinediones with Tyrosine. J Org Chem 2018; 83:10248-10260. [PMID: 30005167 DOI: 10.1021/acs.joc.8b01445] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The bioconjugation at tyrosine residues using cyclic diazodicarboxamides, especially 4-substituted 3 H-1,2,4-triazole-3,5(4 H)-dione (PTAD), is a highly enabling synthetic reaction because it can be employed for orthogonal and site-selective (multi)functionalizations of native peptides and proteins. Despite its importance, the underlying mechanisms have not been thoroughly investigated. The reaction can proceed along four distinctive pathways: (i) the SEAr path, (ii) along a pericyclic group transfer pathway (a classical ene reaction), (iii) along a stepwise reaction path, or (iv) along an unusual higher order concerted pericyclic mechanism. The product mixtures obtained from reactions of PTAD with 2,4-unsubstituted phenolate support the SEAr mechanism, but it remains unclear if other mechanisms also take place. In the present work, the various mechanisms are compared using high-level quantum chemistry approaches for the model reaction of 4 H,3 H-1,2,4-triazole-3,5(4 H)-dione (HTAD) with p-cresol and p-cresolate. In a protic solvent (water), the barriers of the SEAr mechanism and the ene reaction are similar but still too high to explain the available experimental observations. This is only possible if the SEAr reaction of cresolate with HTAD is taken into account for which nearly vanishing barriers are computed. This satisfactorily explains measured conversion rates in buffered aqueous solutions and the strong activation effects observed upon addition of bases.
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Affiliation(s)
- Dustin Kaiser
- Institute of Physical and Theoretical Chemistry , Julius-Maximilians Universität Würzburg , Emil-Fischer-Str. 42 , Würzburg 97074 , Germany
| | - Johan M Winne
- Department of Organic and Macromolecular Chemistry , Ghent University , Krijgslaan 281-S4 , B-9000 Ghent , Germany
| | - Maria Elena Ortiz-Soto
- Institute of Organic Chemistry , Julius-Maximilians Universität Würzburg , Am Hubland , Würzburg 97074 , Germany
| | - Jürgen Seibel
- Institute of Organic Chemistry , Julius-Maximilians Universität Würzburg , Am Hubland , Würzburg 97074 , Germany
| | - Thien A Le
- Institute of Physical and Theoretical Chemistry , Julius-Maximilians Universität Würzburg , Emil-Fischer-Str. 42 , Würzburg 97074 , Germany
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry , Julius-Maximilians Universität Würzburg , Emil-Fischer-Str. 42 , Würzburg 97074 , Germany
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23
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Qin LH, Hu W, Long YQ. Bioorthogonal chemistry: Optimization and application updates during 2013–2017. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.04.058] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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24
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Suzol S, Howlader AH, Wen Z, Ren Y, Laverde EE, Garcia C, Liu Y, Wnuk SF. Pyrimidine Nucleosides with a Reactive (β-Chlorovinyl)sulfone or (β-Keto)sulfone Group at the C5 Position, Their Reactions with Nucleophiles and Electrophiles, and Their Polymerase-Catalyzed Incorporation into DNA. ACS OMEGA 2018; 3:4276-4288. [PMID: 29732453 PMCID: PMC5928487 DOI: 10.1021/acsomega.8b00584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 04/05/2018] [Indexed: 05/28/2023]
Abstract
Transition-metal-catalyzed chlorosulfonylation of 5-ethynylpyrimidine nucleosides provided (E)-5-(β-chlorovinyl)sulfones A, which undergo nucleophilic substitution with amines or thiols affording B. The treatment of vinyl sulfones A with ammonia followed by acid-catalyzed hydrolysis of the intermediary β-sulfonylvinylamines gave 5-(β-keto)sulfones C. The latter reacts with electrophiles, yielding α-carbon-alkylated or -sulfanylated analogues D. The 5'-triphosphates of A and C were incorporated into double-stranded DNA, using open and one-nucleotide gap substrates, by human or Escherichia coli DNA-polymerase-catalyzed reactions.
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Affiliation(s)
- Sazzad
H. Suzol
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - A. Hasan Howlader
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Zhiwei Wen
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Yaou Ren
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Eduardo E. Laverde
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Carol Garcia
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Yuan Liu
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Stanislaw F. Wnuk
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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