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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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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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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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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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