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Montiel L, Spada F, Crisp A, Serdjukow S, Carell T, Frischmuth T. Divergent Synthesis of Ultrabright and Dendritic Xanthenes for Enhanced Click-Chemistry-Based Bioimaging. Chemistry 2023; 29:e202202633. [PMID: 36317813 PMCID: PMC10107433 DOI: 10.1002/chem.202202633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 12/13/2022]
Abstract
Biorthogonal labelling with fluorescent small molecules is an indispensable tool for diagnostic and biomedical applications. In dye-based 5-ethynyl-2'-deoxyuridine (EdU) cell proliferation assays, augmentation of the fluorescent signal entails an overall enhancement in the sensitivity and quality of the method. To this end, a rapid, divergent synthetic procedure that provides ready-to-click pH-insensitive rhodamine dyes exhibiting outstanding brightness was established. Compared to the shortest available synthesis of related high quantum-yielding rhodamines, two fewer synthetic steps are required. In a head-to-head imaging comparison involving copper(I)-catalyzed azide alkyne cycloaddition reactions with in vitro administered EdU, our new 3,3-difluoroazetidine rhodamine azide outperformed the popular 5-TAMRA-azide, making it among the best available choices when it comes to fluorescent imaging of DNA. In a further exploration of the fluorescence properties of these dyes, a set of bis-MPA dendrons carrying multiple fluorescein or rhodamine units was prepared by branching click chemistry. Fluorescence self-quenching of fluorescein- and rhodamine-functionalized dendrons limited the suitability of the dyes as labels in EdU-based experiments but provided new insights into these effects.
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Affiliation(s)
- Luis Montiel
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany.,Department of Chemistry, Institut für Chemische Epigenetik München (ICEM), Ludwig-Maximilians-Universität München (LMU), Butenandtstr. 5-13, 81377, Munich, Germany
| | - Fabio Spada
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany
| | - Antony Crisp
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany
| | - Sascha Serdjukow
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany
| | - Thomas Carell
- Department of Chemistry, Institut für Chemische Epigenetik München (ICEM), Ludwig-Maximilians-Universität München (LMU), Butenandtstr. 5-13, 81377, Munich, Germany
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Schönegger ES, Crisp A, Müller M, Fertl J, Serdjukow S, Croce S, Kollaschinski M, Carell T, Frischmuth T. Click Chemistry Enables Rapid Amplification of Full-Length Reverse Transcripts for Long-Read Third Generation Sequencing. Bioconjug Chem 2022; 33:1789-1795. [PMID: 36154005 DOI: 10.1021/acs.bioconjchem.2c00353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we describe the development of a novel click chemistry-based method for the generation and amplification of full-length cDNA libraries from total RNA, while avoiding the need for problematic template-switching (TS) reactions. Compared with prior efforts, our method involves neither random priming nor stochastic cDNA termination, thus enabling amplification of transcripts that were previously inaccessible via related click chemistry-based RNA sequencing techniques. A key modification involving the use of PCR primers containing two overhanging 3'-nucleotides substantially improved the read-through compatibility of the 1,4-disubstituted 1,2,3-triazole-containing cDNA, where such modifications typically hinder amplification. This allowed us to more than double the possible insert size compared with the state-of-the art click chemistry-based technique, PAC-seq. Furthermore, our method performed on par with a commercially available PCR-cDNA RNA sequencing kit, as determined by Oxford Nanopore sequencing. Given the known advantages of PAC-seq, namely, suppression of PCR artifacts, we anticipate that our contribution could enable diverse applications including improved analyses of mRNA splicing variants and fusion transcripts.
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Affiliation(s)
- Eva S Schönegger
- Ludwig-Maximilians-Universität München, Institute for Chemical Epigenetics Munich, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Antony Crisp
- baseclick GmbH, Floriansbogen 2-4, 82061 Neuried (Munich), Germany
| | - Markus Müller
- Ludwig-Maximilians-Universität München, Institute for Chemical Epigenetics Munich, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Jessica Fertl
- baseclick GmbH, Floriansbogen 2-4, 82061 Neuried (Munich), Germany
| | - Sascha Serdjukow
- baseclick GmbH, Floriansbogen 2-4, 82061 Neuried (Munich), Germany
| | - Stefano Croce
- baseclick GmbH, Floriansbogen 2-4, 82061 Neuried (Munich), Germany
| | | | - Thomas Carell
- Ludwig-Maximilians-Universität München, Institute for Chemical Epigenetics Munich, Butenandtstr. 5-13, 81377 Munich, Germany
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Croce S, Serdjukow S, Carell T, Frischmuth T. Chemoenzymatic Preparation of Functional Click-Labeled Messenger RNA. Chembiochem 2020; 21:1641-1646. [PMID: 31943671 DOI: 10.1002/cbic.201900718] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 12/23/2022]
Abstract
Synthetic mRNAs are promising candidates for a new class of transformative drugs that provide genetic information for patients' cells to develop their own cure. One key advancement to develop so-called druggable mRNAs was the preparation of chemically modified mRNAs, by replacing standard bases with modified bases, such as uridine with pseudouridine, which can ameliorate the immunogenic profile and translation efficiency of the mRNA. Thus the introduction of modified nucleobases was the foundation for the clinical use of such mRNAs. Herein we describe modular and simple methods to chemoenzymatically modify mRNA. Alkyne- and/or azide-modified nucleotides are enzymatically incorporated into mRNA and subsequently conjugated to fluorescent dyes using click chemistry. This allows visualization of the labeled mRNA inside cells. mRNA coding for the enhanced green fluorescent protein (eGFP) was chosen as a model system and the successful expression of eGFP demonstrated that our modified mRNA is accepted by the translation machinery.
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Affiliation(s)
- Stefano Croce
- baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (bei München), Germany
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Sascha Serdjukow
- baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (bei München), Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Thomas Frischmuth
- baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (bei München), Germany
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Kollaschinski M, Sobotta J, Schalk A, Frischmuth T, Graf B, Serdjukow S. Efficient DNA Click Reaction Replaces Enzymatic Ligation. Bioconjug Chem 2020; 31:507-512. [PMID: 31874033 DOI: 10.1021/acs.bioconjchem.9b00805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report a chemical DNA-DNA ligation method based on copper-catalyzed azide-alkyne cycloaddition (CuAAC). We demonstrate that ion addition dramatically influences the efficiency of the so-called click reaction. Even without any further additions, such as typically splint oligonucleotides for preorganization, the "click ligation" yields up to ∼83% product without any byproducts. Additionally, purification of the desired product is straightforward. In comparison to enzymatic ligation methods used to introduce adapters into, e.g., mRNA library preparation, this targeted chemical ligation method exhibits several advantages: increased ligated product and no adapter or cDNA oligomers byproducts. The advantages of the click ligation method were demonstrated by incorporation of azide modified nucleotides by several enzymes as well as broad polymerase acceptance of the obtained triazole linkage in PCR.
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Affiliation(s)
| | | | | | | | - Birgit Graf
- Baseclick GmbH, Floriansbogen 2-4, 82061 Neuried, Germany
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Schröder AS, Parsa E, Iwan K, Traube FR, Wallner M, Serdjukow S, Carell T. 2'-(R)-Fluorinated mC, hmC, fC and caC triphosphates are substrates for DNA polymerases and TET-enzymes. Chem Commun (Camb) 2018; 52:14361-14364. [PMID: 27905578 DOI: 10.1039/c6cc07517g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A deeper investigation of the chemistry that occurs on the newly discovered epigenetic DNA bases 5-hydroxymethyl-(hmdC), 5-formyl-(fdC), and 5-carboxy-deoxycytidine (cadC) requires chemical tool compounds, which are able to dissect the different potential reaction pathways in cells. Here we report that the 2'-(R)-fluorinated derivatives F-hmdC, F-fdC, and F-cadC, which are resistant to removal by base excision repair, are good substrates for DNA polymerases and TET enzymes. This result shows that the fluorinated compounds are ideal tool substances to investigate potential C-C-bond cleaving reactions in the context of active demethylation.
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Affiliation(s)
- A S Schröder
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| | - E Parsa
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| | - K Iwan
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| | - F R Traube
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| | - M Wallner
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| | - S Serdjukow
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| | - T Carell
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
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Tomás-Gamasa M, Serdjukow S, Su M, Müller M, Carell T. "Post-it" type connected DNA created with a reversible covalent cross-link. Angew Chem Int Ed Engl 2014; 54:796-800. [PMID: 25446281 DOI: 10.1002/anie.201407854] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Indexed: 12/23/2022]
Abstract
We report the development of a new heterobase that is held together through reversible bonding. The so-formed cross-link adds strong stabilization to the DNA duplex. Despite this, the cross-link opens and closes through reversible imine bonding. Moreover, even enzymatic incorporation of the cross-link is possible. The new principle can be used to stabilize DNA duplexes and nanostructures that otherwise require high salt concentrations, which may hinder biological applications.
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Affiliation(s)
- María Tomás-Gamasa
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München (Germany) http://www.carellgroup.de
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Su M, Tomás-Gamasa M, Serdjukow S, Mayer P, Carell T. Synthesis and properties of a Cu(II) complexing pyrazole ligandoside in DNA. Chem Commun (Camb) 2014; 50:409-11. [PMID: 24263097 DOI: 10.1039/c3cc47561a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The development of metal base pairs is of immense importance for the construction of DNA nanostructures. Here we report the synthesis of a biaryl pyrazole-phenol nucleoside that forms in DNA a stable self-pair upon complexation of a Cu(II) ion. A sequence with five consecutive pyrazole nucleotides allows the complexation of five Cu(II) ions in a row.
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Affiliation(s)
- M Su
- Department of Chemistry, Ludwig-Maximilians University, Butenandtstraße 5-13, 81377, Munich, Germany.
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Serdjukow S, Kink F, Steigenberger B, Tomás-Gamasa M, Carell T. Synthesis of γ-labeled nucleoside 5'-triphosphates using click chemistry. Chem Commun (Camb) 2014; 50:1861-3. [PMID: 24402283 DOI: 10.1039/c3cc48937j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Real-time enzymatic studies are gaining importance as their chemical and technical instrumentation improves. Here we report the efficient synthesis of γ-alkyne modified triphosphate amidates that are converted into a variety of γ-fluorophore labeled triphosphates by Cu(I) catalyzed alkyne/azide click reactions. The synthesized triphosphates are incorporated into DNA by DNA polymerases.
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Affiliation(s)
- S Serdjukow
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
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Staudt H, Hoesl MG, Dreuw A, Serdjukow S, Oesterhelt D, Budisa N, Wachtveitl J, Grininger M. Directed manipulation of a flavoprotein photocycle. Angew Chem Int Ed Engl 2013; 52:8463-6. [PMID: 23818044 DOI: 10.1002/anie.201302334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Heike Staudt
- Institut für Physikalische and Theoretische Chemie, Exzellenzcluster Makromolekulare Komplexe, Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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Staudt H, Hoesl MG, Dreuw A, Serdjukow S, Oesterhelt D, Budisa N, Wachtveitl J, Grininger M. Gerichtete Manipulation des Photozyklus eines Flavoproteins. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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