1
|
Spampinato A, Kužmová E, Pohl R, Sýkorová V, Vrábel M, Kraus T, Hocek M. trans-Cyclooctene- and Bicyclononyne-Linked Nucleotides for Click Modification of DNA with Fluorogenic Tetrazines and Live Cell Metabolic Labeling and Imaging. Bioconjug Chem 2023. [PMID: 36972479 PMCID: PMC10119924 DOI: 10.1021/acs.bioconjchem.3c00064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
A series of 2'-deoxyribonucleoside triphosphates (dNTPs) bearing 2- or 4-linked trans-cyclooctene (TCO) or bicyclononyne (BCN) tethered through a shorter propargylcarbamate or longer triethyleneglycol-based spacer were designed and synthesized. They were found to be good substrates for KOD XL DNA polymerase for primer extension enzymatic synthesis of modified oligonucleotides. We systematically tested and compared the reactivity of TCO- and BCN-modified nucleotides and DNA with several fluorophore-containing tetrazines in inverse electron-demand Diels-Alder (IEDDA) click reactions to show that the longer linker is crucial for efficient labeling. The modified dNTPs were transported into live cells using the synthetic transporter SNTT1, incubated for 1 h, and then treated with tetrazine conjugates. The PEG3-linked 4TCO and BCN nucleotides showed efficient incorporation into genomic DNA and good reactivity in the IEDDA click reaction with tetrazines to allow staining of DNA and imaging of DNA synthesis in live cells within time periods as short as 15 min. The BCN-linked nucleotide in combination with TAMRA-linked (TAMRA = carboxytetramethylrhodamine) tetrazine was also efficiently used for staining of DNA for flow cytometry. This methodology is a new approach for in cellulo metabolic labeling and imaging of DNA synthesis which is shorter, operationally simple, and overcomes several problems of previously used methods.
Collapse
Affiliation(s)
- Ambra Spampinato
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, Prague 6 CZ-16610, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2 12843, Czech Republic
| | - Erika Kužmová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, Prague 6 CZ-16610, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, Prague 6 CZ-16610, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, Prague 6 CZ-16610, Czech Republic
| | - Milan Vrábel
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, Prague 6 CZ-16610, Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, Prague 6 CZ-16610, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, Prague 6 CZ-16610, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2 12843, Czech Republic
| |
Collapse
|
2
|
Meher S, Gade CR, Sharma NK. Tropolone-Conjugated DNA: A Fluorescent Thymidine Analogue Exhibits Solvatochromism, Enzymatic Incorporation into DNA and HeLa Cell Internalization. Chembiochem 2023; 24:e202200732. [PMID: 36510378 DOI: 10.1002/cbic.202200732] [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: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022]
Abstract
Tropolone is a non-benzenoid aromatic scaffold with unique photophysical and metal-chelating properties. Recently, it has been conjugated with DNA, and the photophysical properties of this conjugate have been explored. Tropolonyl-deoxyuridine (tr-dU) is a synthetic fluorescent DNA nucleoside analogue that exhibits pH-dependent emissions. However, its solvent-dependent fluorescence properties are unexplored owing to its poor solubility in most organic solvents. It would be interesting to incorporate it into DNA primer enzymatically. This report describes the solvent-dependent fluorescence properties of the silyl-derivative, and enzymatic incorporation of its triphosphate analogue. For practical use, its cell-internalization and cytotoxicity are also explored. tr-dU nucleoside was found to be a potential analogue to design DNA probes and can be explored for various therapeutic applications in the future.
Collapse
Affiliation(s)
- Sagarika Meher
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatani, 752050, Odisha, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Chandrasekhar Reddy Gade
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatani, 752050, Odisha, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Nagendra K Sharma
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatani, 752050, Odisha, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Anushaktinagar, Mumbai, 400094, India
| |
Collapse
|
3
|
Kamińska E, Korytiaková E, Reichl A, Müller M, Carell T. Intragenomic Decarboxylation of 5-Carboxy-2'-deoxycytidine. Angew Chem Int Ed Engl 2021; 60:23207-23211. [PMID: 34432359 PMCID: PMC8596745 DOI: 10.1002/anie.202109995] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Indexed: 12/30/2022]
Abstract
Cellular DNA is composed of four canonical nucleosides (dA, dC, dG and T), which form two Watson-Crick base pairs. In addition, 5-methylcytosine (mdC) may be present. The methylation of dC to mdC is known to regulate transcriptional activity. Next to these five nucleosides, the genome, particularly of stem cells, contains three additional dC derivatives, which are formed by stepwise oxidation of the methyl group of mdC with the help of Tet enzymes. These are 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5-carboxy-dC (cadC). It is believed that fdC and cadC are converted back into dC, which establishes an epigenetic control cycle that starts with methylation of dC to mdC, followed by oxidation and removal of fdC and cadC. While fdC was shown to undergo intragenomic deformylation to give dC directly, a similar decarboxylation of cadC was postulated but not yet observed on the genomic level. By using metabolic labelling, we show here that cadC decarboxylates in several cell types, which confirms that both fdC and cadC are nucleosides that are directly converted back to dC within the genome by C-C bond cleavage.
Collapse
Affiliation(s)
- Ewelina Kamińska
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Eva Korytiaková
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Andreas Reichl
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Markus Müller
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Thomas Carell
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| |
Collapse
|
4
|
Kamińska E, Korytiaková E, Reichl A, Müller M, Carell T. Intragenomische Decarboxylierung von 5‐Carboxy‐2′‐desoxycytidin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ewelina Kamińska
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Eva Korytiaková
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Andreas Reichl
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Markus Müller
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Thomas Carell
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| |
Collapse
|
5
|
Güixens-Gallardo P, Hocek M. Acetophenyl-thienyl-aniline-Linked Nucleotide for Construction of Solvatochromic Fluorescence Light-Up DNA Probes Sensing Protein-DNA Interactions. Chemistry 2021; 27:7090-7093. [PMID: 33769635 DOI: 10.1002/chem.202100575] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Indexed: 12/20/2022]
Abstract
The synthesis of 2'-deoxycytidine and its 5'-O-triphosphate bearing solvatochromic acetophenyl-thienyl-aniline fluorophore was developed using the Sonogashira cross-coupling reaction as the key step. The triphosphate was used for polymerase synthesis of labelled DNA. The labelled nucleotide or DNA exerted weak red fluorescence when excited at 405 nm, but a significant colour change (to yellow or green) and light-up (up to 20 times) was observed when the DNA probes interacted with proteins or lipids.
Collapse
Affiliation(s)
- Pedro Güixens-Gallardo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
| |
Collapse
|
6
|
Kuba M, Kraus T, Pohl R, Hocek M. Nucleotide-Bearing Benzylidene-Tetrahydroxanthylium Near-IR Fluorophore for Sensing DNA Replication, Secondary Structures and Interactions. Chemistry 2020; 26:11950-11954. [PMID: 32633433 PMCID: PMC7361531 DOI: 10.1002/chem.202003192] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Indexed: 12/16/2022]
Abstract
Thymidine triphosphate bearing benzylidene-tetrahydroxanthylium near-IR fluorophore linked to the 5-methyl group via triazole was synthesized through the CuAAC reaction and was used for polymerase synthesis of labelled DNA probes. The fluorophore lights up upon incorporation to DNA (up to 348-times) presumably due to interactions in major groove and the fluorescence further increases in the single-stranded oligonucleotide. The labelled dsDNA senses binding of small molecules and proteins by a strong decrease of fluorescence. The nucleotide was used as a light-up building block in real-time PCR for detection of SARS-CoV-2 virus.
Collapse
Affiliation(s)
- Miroslav Kuba
- 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
| | - Tomáš Kraus
- 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
| | - 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
| |
Collapse
|
7
|
Ming Z, Pang Y, Liu J. Mechanical Deformation Mediated Transmembrane Transport. Macromol Rapid Commun 2019; 41:e1900518. [PMID: 31885137 DOI: 10.1002/marc.201900518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/06/2019] [Indexed: 12/15/2022]
Abstract
Transmembrane transport is essential and plays critical roles for molecule exchange for cell survival. Methods capable of mimicking and regulating transmembrane transport have transformed the ability to create biosensors, separation membranes, and drug carriers. However, artificial channels have been largely restricted by their complicated chemical fabrication and inefficiency to dynamically manipulate the transport process. Here, a novel approach to regulate transmembrane transport is described by simply adjusting the mechanical deformation of liposomal bilayers which are covalently embedded in a crosslinked hydrogel network. This new approach is able to dynamically control transmembrane transport by stretching and loosening. The transmembrane diffusion of molecules can be switched on and off, and precisely tuned by varying strain. A potential of this method to programmably regulate cell growth is demonstrated by tuning external mechanical force. Given its unique characteristics, this method allows the development of innovative systems for controlled transmembrane transport of molecules.
Collapse
Affiliation(s)
- Zunzhen Ming
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Institute of Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yan Pang
- Department of Ophthalmology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200011, China
| | - Jinyao Liu
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Institute of Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| |
Collapse
|
8
|
McStay N, Reilly AM, Gathergood N, Kellett A. Efficient DNA Condensation by a C3‐Symmetric Codeine Scaffold. Chempluschem 2018; 84:38-42. [DOI: 10.1002/cplu.201800480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/12/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Natasha McStay
- School of Chemical Sciencesand National Institute for Cellular BiotechnologyDublin City University Glasnevin Dublin 9 Ireland
| | - Anthony M. Reilly
- School of Chemical SciencesDublin City University Glasnevin Dublin 9 Ireland
- Synthesis and Solid-State Pharmaceutical CentreSchool of Chemical SciencesDublin City University Glasnevin Dublin 9 Ireland
| | - Nicholas Gathergood
- Department of Chemistry and BiotechnologyTallinn University of Technology Akadeemia tee 15 12618 Tallinn Estonia
| | - Andrew Kellett
- School of Chemical Sciencesand National Institute for Cellular BiotechnologyDublin City University Glasnevin Dublin 9 Ireland
- Synthesis and Solid-State Pharmaceutical CentreSchool of Chemical SciencesDublin City University Glasnevin Dublin 9 Ireland
| |
Collapse
|