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Diafa S, Evéquoz D, Leumann CJ, Hollenstein M. Enzymatic Synthesis of 7',5'-Bicyclo-DNA Oligonucleotides. Chem Asian J 2017; 12:1347-1352. [PMID: 28371464 DOI: 10.1002/asia.201700374] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 03/30/2017] [Indexed: 01/06/2023]
Abstract
The selection of artificial genetic polymers with tailor-made properties for their application in synthetic biology requires the exploration of new nucleosidic scaffolds that can be used in selection experiments. Herein, we describe the synthesis of a bicyclo-DNA triphosphate (i.e., 7',5'-bc-TTP) and show its potential to serve for the generation of new xenonucleic acids (XNAs) based on this scaffold. 7',5'-bc-TTP is a good substrate for Therminator DNA polymerase, and up to seven modified units can be incorporated into a growing DNA chain. In addition, this scaffold sustains XNA-dependent DNA synthesis and potentially also XNA-dependent XNA synthesis. However, DNA-dependent XNA synthesis on longer templates is hampered by competitive misincorporation of deoxyadenosine triphosphate (dATP) caused by the slow rate of incorporation of 7',5'-bc-TTP.
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Affiliation(s)
- Stella Diafa
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Damien Evéquoz
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Marcel Hollenstein
- Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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2
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Hottin A, Betz K, Diederichs K, Marx A. Structural Basis for the KlenTaq DNA Polymerase Catalysed Incorporation of Alkene- versus Alkyne-Modified Nucleotides. Chemistry 2017; 23:2109-2118. [PMID: 27901305 DOI: 10.1002/chem.201604515] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Indexed: 01/12/2023]
Abstract
Efficient incorporation of modified nucleotides by DNA polymerases is essential for many cutting-edge biomolecular technologies. The present study compares the acceptance of either alkene- or alkyne-modified nucleotides by KlenTaq DNA polymerase and provides structural insights into how 7-deaza-adenosine and deoxyuridine with attached alkene-modifications are incorporated into the growing DNA strand. Thereby, we identified modified nucleotides that prove to be superior substrates for KlenTaq DNA polymerase compared with their natural analogues. The knowledge can be used to guide future design of functionalized nucleotide building blocks.
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Affiliation(s)
- Audrey Hottin
- Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Karin Betz
- Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Kay Diederichs
- Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
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Matyašovský J, Perlíková P, Malnuit V, Pohl R, Hocek M. 2-Substituted dATP Derivatives as Building Blocks for Polymerase-Catalyzed Synthesis of DNA Modified in the Minor Groove. Angew Chem Int Ed Engl 2016; 55:15856-15859. [PMID: 27879047 PMCID: PMC6680173 DOI: 10.1002/anie.201609007] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Indexed: 12/11/2022]
Abstract
2'-Deoxyadenosine triphosphate (dATP) derivatives bearing diverse substituents (Cl, NH2 , CH3 , vinyl, ethynyl, and phenyl) at position 2 were prepared and tested as substrates for DNA polymerases. The 2-phenyl-dATP was not a substrate for DNA polymerases, but the dATPs bearing smaller substituents were good substrates in primer-extension experiments, producing DNA substituted in the minor groove. The vinyl-modified DNA was applied in thiol-ene addition and the ethynyl-modified DNA was applied in a CuAAC click reaction to form DNA labelled with fluorescent dyes in the minor groove.
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Affiliation(s)
- Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Pavla Perlíková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Vincent Malnuit
- 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
| | - 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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4
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Matyašovský J, Perlíková P, Malnuit V, Pohl R, Hocek M. 2-Substituted dATP Derivatives as Building Blocks for Polymerase-Catalyzed Synthesis of DNA Modified in the Minor Groove. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Pavla Perlíková
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Vincent Malnuit
- 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
| | - 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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Welter M, Verga D, Marx A. Sequence-Specific Incorporation of Enzyme-Nucleotide Chimera by DNA Polymerases. Angew Chem Int Ed Engl 2016; 55:10131-5. [PMID: 27392211 DOI: 10.1002/anie.201604641] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Indexed: 02/06/2023]
Abstract
DNA polymerases select the right nucleotide for the growing polynucleotide chain based on the shape and geometry of the nascent nucleotide pairs and thereby ensure high DNA replication selectivity. High-fidelity DNA polymerases are believed to possess tight active sites that allow little deviation from the canonical structures. However, DNA polymerases are known to use nucleotides with small modifications as substrates, which is key for numerous core biotechnology applications. We show that even high-fidelity DNA polymerases are capable of efficiently using nucleotide chimera modified with a large protein like horseradish peroxidase as substrates for template-dependent DNA synthesis, despite this "cargo" being more than 100-fold larger than the natural substrates. We exploited this capability for the development of systems that enable naked-eye detection of DNA and RNA at single nucleotide resolution.
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Affiliation(s)
- Moritz Welter
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Daniela Verga
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany.
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Welter M, Verga D, Marx A. Sequenz-spezifischer Einbau von Enzym-Nukleotid-Chimären durch DNA-Polymerasen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Moritz Welter
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Daniela Verga
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Andreas Marx
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
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7
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Mačková M, Boháčová S, Perlíková P, Poštová Slavětínská L, Hocek M. Polymerase Synthesis and Restriction Enzyme Cleavage of DNA Containing 7-Substituted 7-Deazaguanine Nucleobases. Chembiochem 2015; 16:2225-36. [PMID: 26382079 DOI: 10.1002/cbic.201500315] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Indexed: 01/06/2023]
Abstract
Previous studies of polymerase synthesis of base-modified DNAs and their cleavage by restriction enzymes have mostly related only to 5-substituted pyrimidine and 7-substituted 7-deazaadenine nucleotides. Here we report the synthesis of a series of 7-substituted 7-deazaguanine 2'-deoxyribonucleoside 5'-O-triphosphates (dG(R) TPs), their use as substrates for polymerase synthesis of modified DNA and the influence of the modification on their cleavage by type II restriction endonucleases (REs). The dG(R) TPs were generally good substrates for polymerases but the PCR products could not be visualised on agarose gels by intercalator staining, due to fluorescence quenching. The presence of 7-substituted 7-deazaguanine residues in recognition sequences of REs in most cases completely blocked the cleavage.
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Affiliation(s)
- Michaela Mačková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Pavla Perlíková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 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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8
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Simonova A, Balintová J, Pohl R, Havran L, Fojta M, Hocek M. Methoxyphenol and Dihydrobenzofuran as Oxidizable Labels for Electrochemical Detection of DNA. Chempluschem 2014. [DOI: 10.1002/cplu.201402194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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9
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Kielkowski P, Fanfrlík J, Hocek M. 7-Aryl-7-deazaadenine 2′-Deoxyribonucleoside Triphosphates (dNTPs): Better Substrates for DNA Polymerases than dATP in Competitive Incorporations. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404742] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Kielkowski P, Fanfrlík J, Hocek M. 7-Aryl-7-deazaadenine 2'-deoxyribonucleoside triphosphates (dNTPs): better substrates for DNA polymerases than dATP in competitive incorporations. Angew Chem Int Ed Engl 2014; 53:7552-5. [PMID: 24890276 DOI: 10.1002/anie.201404742] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Indexed: 01/31/2023]
Abstract
A series of 7-substituted 7-deazaadenine and 5-substituted cytosine 2'-deoxyribonucleoside triphosphates (dNTPs) were tested for their competitive incorporations (in the presence of dATP and dCTP) into DNA by several DNA polymerases by using analysis based on cleavage by restriction endonucleases. 7-Aryl-7-deazaadenine dNTPs were more efficient substrates than dATP because of their higher affinity for the active site of the enzyme, as proved by kinetic measurements and calculations.
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Affiliation(s)
- Pavel Kielkowski
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic) http://www.uochb.cas.cz/hocekgroup
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Lercher L, McGouran JF, Kessler BM, Schofield CJ, Davis BG. DNA modification under mild conditions by Suzuki-Miyaura cross-coupling for the generation of functional probes. Angew Chem Int Ed Engl 2013; 52:10553-8. [PMID: 23943570 PMCID: PMC3823066 DOI: 10.1002/anie.201304038] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/26/2013] [Indexed: 12/23/2022]
Abstract
Quick and clean: A method for Pd-catalyzed Suzuki-Miyaura cross-coupling to iododeoxyuridine (IdU) in DNA is described. Key to the reactivity is the choice of the ligand and the buffer. A covalent [Pd]-DNA intermediate was isolated and characterized. Photocrosslinking probes were generated to trap proteins that bind to epigenetic DNA modifications.
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Affiliation(s)
- Lukas Lercher
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryMansfield Road, Oxford OX1 3TA (UK)
| | - Joanna F McGouran
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Henry Wellcome Building for Molecular PhysiologyRoosevelt Drive, Oxford OX3 7FZ (UK)
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Henry Wellcome Building for Molecular PhysiologyRoosevelt Drive, Oxford OX3 7FZ (UK)
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryMansfield Road, Oxford OX1 3TA (UK)
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryMansfield Road, Oxford OX1 3TA (UK)
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Lercher L, McGouran JF, Kessler BM, Schofield CJ, Davis BG. DNA Modification under Mild Conditions by Suzuki-Miyaura Cross-Coupling for the Generation of Functional Probes. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304038] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Bergen K, Betz K, Welte W, Diederichs K, Marx A. Structures of KOD and 9°N DNA polymerases complexed with primer template duplex. Chembiochem 2013; 14:1058-62. [PMID: 23733496 DOI: 10.1002/cbic.201300175] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Indexed: 12/29/2022]
Abstract
Replicate it: Structures of KOD and 9°N DNA polymerases, two enzymes that are widely used to replicate DNA with highly modified nucleotides, were solved at high resolution in complex with primer/template duplex. The data elucidate substrate interaction of the two enzymes and pave the way for further optimisation of the enzymes and substrates.
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Affiliation(s)
- Konrad Bergen
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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14
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Holzberger B, Strohmeier J, Siegmund V, Diederichsen U, Marx A. Enzymatic synthesis of 8-vinyl- and 8-styryl-2'-deoxyguanosine modified DNA--novel fluorescent molecular probes. Bioorg Med Chem Lett 2012; 22:3136-9. [PMID: 22483394 DOI: 10.1016/j.bmcl.2012.03.056] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 03/12/2012] [Accepted: 03/14/2012] [Indexed: 12/19/2022]
Abstract
Fluorescent analogs of the natural nucleobases are widely used as molecular probes for investigating DNA hybridization and topology. In this study the guanosine analogs 8-vinyl- and 8-styryl-2'-deoxyguanosine were synthesized and converted into the corresponding 5'-triphosphates. These C8 modified nucleotides were processed by various DNA polymerases to create fluorescent DNA. Whereas the 8-styryl modified nucleotide somewhat hampers DNA synthesis 8-vinyl-2'-deoxyguanosine is processed by DNA polymerases emphasizing the broad applicability as a molecular probe for fluorescence spectroscopy.
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Affiliation(s)
- Bastian Holzberger
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
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