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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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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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Huang Y, Li X. Recent Advances on the Selection Methods of DNA-Encoded Libraries. Chembiochem 2021; 22:2384-2397. [PMID: 33891355 DOI: 10.1002/cbic.202100144] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/23/2021] [Indexed: 12/15/2022]
Abstract
DNA-encoded libraries (DEL) have come of age and become a major technology platform for ligand discovery in both academia and the pharmaceutical industry. Technological maturation in the past two decades and the recent explosive developments of DEL-compatible chemistries have greatly improved the chemical diversity of DELs and fueled its applications in drug discovery. A relatively less-covered aspect of DELs is the selection method. Typically, DEL selection is considered as a binding assay and the selection is conducted with purified protein targets immobilized on a matrix, and the binders are separated from the non-binding background via physical washes. However, the recent innovations in DEL selection methods have not only expanded the target scope of DELs, but also revealed the potential of the DEL technology as a powerful tool in exploring fundamental biology. In this Review, we first cover the "classic" DEL selection methods with purified proteins on solid phase, and then we discuss the strategies to realize DEL selections in solution phase. Finally, we focus on the emerging approaches for DELs to interrogate complex biological targets.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong Science and Technology Parks, New Territories, Hong Kong SAR, China
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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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Ivancová I, Pohl R, Hubálek M, Hocek M. Squaramate-Modified Nucleotides and DNA for Specific Cross-Linking with Lysine-Containing Peptides and Proteins. Angew Chem Int Ed Engl 2019; 58:13345-13348. [PMID: 31328344 PMCID: PMC6771961 DOI: 10.1002/anie.201906737] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/12/2019] [Indexed: 01/31/2023]
Abstract
Squaramate-linked 2'-deoxycytidine 5'-O-triphosphate was synthesized and found to be good substrate for KOD XL DNA polymerase in primer extension or PCR synthesis of modified DNA. The resulting squaramate-linked DNA reacts with primary amines to form a stable diamide linkage. This reaction was used for bioconjugations of DNA with Cy5 and Lys-containing peptides. Squaramate-linked DNA formed covalent cross-links with histone proteins. This reactive nucleotide has potential for other bioconjugations of nucleic acids with amines, peptides or proteins without need of any external reagent.
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Affiliation(s)
- Ivana Ivancová
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 8CZ-12843Prague 2Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Martin Hubálek
- 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 8CZ-12843Prague 2Czech Republic
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Ivancová I, Pohl R, Hubálek M, Hocek M. Squaramate‐Modified Nucleotides and DNA for Specific Cross‐Linking with Lysine‐Containing Peptides and Proteins. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906737] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ivana Ivancová
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in Prague Hlavova 8 CZ-12843 Prague 2 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in Prague Hlavova 8 CZ-12843 Prague 2 Czech Republic
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Liszczak G, Muir TW. Barcoding mit Nukleinsäuren: Anwendung der DNA‐Sequenzierung als molekulares Zählwerk. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201808956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Glen Liszczak
- Department of ChemistryPrinceton University Princeton NJ 08544 USA
- Aktuelle Adresse: Department of BiochemistryUT Southwestern Medical Center Dallas TX 75390 USA
| | - Tom W. Muir
- Department of ChemistryPrinceton University Princeton NJ 08544 USA
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Liszczak G, Muir TW. Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter. Angew Chem Int Ed Engl 2019; 58:4144-4162. [PMID: 30153374 DOI: 10.1002/anie.201808956] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Indexed: 12/17/2022]
Abstract
The emergence of high-throughput DNA sequencing technologies sparked a revolution in the field of genomics that has rippled into many branches of the life and physical sciences. The remarkable sensitivity, specificity, throughput, and multiplexing capacity that are inherent to parallel DNA sequencing have since motivated its use as a broad-spectrum molecular counter. A key aspect of extrapolating DNA sequencing to non-traditional applications is the need to append nucleic-acid barcodes to entities of interest. In this review, we describe the chemical and biochemical approaches that have enabled nucleic-acid barcoding of proteinaceous and non-proteinaceous materials and provide examples of downstream technologies that have been made possible by DNA-encoded molecules. As commercially available high-throughput sequencers were first released less than 15 years ago, we believe related applications will continue to mature and close by proposing new frontiers to support this assertion.
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Affiliation(s)
- Glen Liszczak
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.,Present address: Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
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Zhang N, Bing T, Shen L, Song R, Wang L, Liu X, Liu M, Li J, Tan W, Shangguan D. Intercellular Connections Related to Cell-Cell Crosstalk Specifically Recognized by an Aptamer. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Nan Zhang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of the Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
| | - Luyao Shen
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of the Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Rusheng Song
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of the Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Linlin Wang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of the Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
| | - Meirong Liu
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
| | - Juan Li
- Department of Chemistry; Center for Research at the Bio/Nano Interface; Health Cancer Center; UF Genetics Institute; McKnight Brain Institute; University of Florida; Gainesville FL 32611-7200 USA
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Biology and College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P.R. China
| | - Weihong Tan
- Department of Chemistry; Center for Research at the Bio/Nano Interface; Health Cancer Center; UF Genetics Institute; McKnight Brain Institute; University of Florida; Gainesville FL 32611-7200 USA
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Biology and College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P.R. China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
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Zhang N, Bing T, Shen L, Song R, Wang L, Liu X, Liu M, Li J, Tan W, Shangguan D. Intercellular Connections Related to Cell-Cell Crosstalk Specifically Recognized by an Aptamer. Angew Chem Int Ed Engl 2016; 55:3914-8. [DOI: 10.1002/anie.201510786] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/26/2016] [Indexed: 01/23/2023]
Affiliation(s)
- Nan Zhang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of the Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
| | - Luyao Shen
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of the Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Rusheng Song
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of the Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Linlin Wang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of the Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
| | - Meirong Liu
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
| | - Juan Li
- Department of Chemistry; Center for Research at the Bio/Nano Interface; Health Cancer Center; UF Genetics Institute; McKnight Brain Institute; University of Florida; Gainesville FL 32611-7200 USA
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Biology and College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P.R. China
| | - Weihong Tan
- Department of Chemistry; Center for Research at the Bio/Nano Interface; Health Cancer Center; UF Genetics Institute; McKnight Brain Institute; University of Florida; Gainesville FL 32611-7200 USA
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Biology and College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P.R. China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
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Li G, Liu Y, Liu Y, Chen L, Wu S, Liu Y, Li X. Photoaffinity Labeling of Small-Molecule-Binding Proteins by DNA-Templated Chemistry. Angew Chem Int Ed Engl 2013; 52:9544-9. [DOI: 10.1002/anie.201302161] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/14/2013] [Indexed: 01/07/2023]
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12
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Li G, Liu Y, Liu Y, Chen L, Wu S, Liu Y, Li X. Photoaffinity Labeling of Small-Molecule-Binding Proteins by DNA-Templated Chemistry. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302161] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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