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Leone D, Pohl R, Hubálek M, Kadeřábková M, Krömer M, Sýkorová V, Hocek M. Glyoxal‐Linked Nucleotides and DNA for Bioconjugations and Crosslinking with Arginine‐Containing Peptides and Proteins. Chemistry 2022; 28:e202104208. [DOI: 10.1002/chem.202104208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Marta Kadeřábková
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
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Konč J, Brown L, Whiten DR, Zuo Y, Ravn P, Klenerman D, Bernardes GJL. A Platform for Site‐Specific DNA‐Antibody Bioconjugation by Using Benzoylacrylic‐Labelled Oligonucleotides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Juraj Konč
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Libby Brown
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Daniel R. Whiten
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Yukun Zuo
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Peter Ravn
- AstraZeneca R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE) Milstein Building, Granta Park Cambridge CB21 6GH UK
- Current address: Department of Biotherapeutic Discovery H. Lundbeck A/S Ottiliavej 9, 2500 Valby Denmark
| | - David Klenerman
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- UK Dementia Research Institute University of Cambridge Cambridge CB2 0XY UK
| | - Gonçalo J. L. Bernardes
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
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Konč J, Brown L, Whiten DR, Zuo Y, Ravn P, Klenerman D, Bernardes GJL. A Platform for Site-Specific DNA-Antibody Bioconjugation by Using Benzoylacrylic-Labelled Oligonucleotides. Angew Chem Int Ed Engl 2021; 60:25905-25913. [PMID: 34555238 PMCID: PMC9297960 DOI: 10.1002/anie.202109713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Indexed: 12/27/2022]
Abstract
Many bioconjugation strategies for DNA oligonucleotides and antibodies suffer limitations, such as site-specificity, stoichiometry and hydrolytic instability of the conjugates, which makes them unsuitable for biological applications. Here, we report a new platform for the preparation of DNA-antibody bioconjugates with a simple benzoylacrylic acid pentafluorophenyl ester reagent. Benzoylacrylic-labelled oligonucleotides prepared with this reagent can be site-specifically conjugated to a range of proteins and antibodies through accessible cysteine residues. The homogeneity of the prepared DNA-antibody bioconjugates was confirmed by a new LC-MS protocol and the bioconjugate probes were used in fluorescence or super-resolution microscopy cell imaging experiments. This work demonstrates the versatility and robustness of our bioconjugation protocol that gives site-specific, well-defined and plasma-stable DNA-antibody bioconjugates for biological applications.
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Affiliation(s)
- Juraj Konč
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Libby Brown
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Daniel R Whiten
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Yukun Zuo
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Peter Ravn
- AstraZeneca, R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE), Milstein Building, Granta Park, Cambridge, CB21 6GH, UK.,Current address: Department of Biotherapeutic Discovery, H. Lundbeck A/S, Ottiliavej 9, 2500, Valby, Denmark
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,UK Dementia Research Institute, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Gonçalo J L Bernardes
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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Leone D, Hubálek M, Pohl R, Sýkorová V, Hocek M. 1,3-Diketone-Modified Nucleotides and DNA for Cross-Linking with Arginine-Containing Peptides and Proteins. Angew Chem Int Ed Engl 2021; 60:17383-17387. [PMID: 34107150 PMCID: PMC8362068 DOI: 10.1002/anie.202105126] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/27/2021] [Indexed: 12/28/2022]
Abstract
Linear or branched 1,3-diketone-linked thymidine 5'-O-mono- and triphosphate were synthesized through CuAAC click reaction of diketone-alkynes with 5-azidomethyl-dUMP or -dUTP. The triphosphates were good substrates for KOD XL DNA polymerase in primer extension synthesis of modified DNA. The nucleotide bearing linear 3,5-dioxohexyl group (HDO) efficiently reacted with arginine-containing peptides to form stable pyrimidine-linked conjugates, whereas the branched 2-acetyl-3-oxo-butyl (PDO) group was not reactive. Reaction with Lys or a terminal amino group formed enamine adducts that were prone to hydrolysis. This reactive HDO modification in DNA was used for bioconjugations and cross-linking with Arg-containing peptides or proteins (e.g. histones).
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Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
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Leone D, Hubálek M, Pohl R, Sýkorová V, Hocek M. 1,3‐Diketone‐Modified Nucleotides and DNA for Cross‐Linking with Arginine‐Containing Peptides and Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
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Zhang J, Peng J, Huang Y, Meng L, Li Q, Xiong F, Li X. Identification of Histone deacetylase (HDAC)‐Associated Proteins with DNA‐Programmed Affinity Labeling. Angew Chem Int Ed Engl 2020; 59:17525-17532. [DOI: 10.1002/anie.202001205] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/14/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Qingrong Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
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Zhang J, Peng J, Huang Y, Meng L, Li Q, Xiong F, Li X. Identification of Histone deacetylase (HDAC)‐Associated Proteins with DNA‐Programmed Affinity Labeling. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Qingrong Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
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