1
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Akram F, Shah FI, Ibrar R, Fatima T, Haq IU, Naseem W, Gul MA, Tehreem L, Haider G. Bacterial thermophilic DNA polymerases: A focus on prominent biotechnological applications. Anal Biochem 2023; 671:115150. [PMID: 37054862 DOI: 10.1016/j.ab.2023.115150] [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: 01/14/2023] [Revised: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
DNA polymerases are the enzymes able to replicate the genetic information in nucleic acid. As a result, they are necessary to copy the complete genome of every living creature before cell division and sustain the integrity of the genetic information throughout the life of each cell. Any organism that uses DNA as its genetic information, whether unicellular or multicellular, requires one or more thermostable DNA polymerases to thrive. Thermostable DNA polymerase is important in modern biotechnology and molecular biology because it results in methods such as DNA cloning, DNA sequencing, whole genome amplification, molecular diagnostics, polymerase chain reaction, synthetic biology, and single nucleotide polymorphism detection. There are at least 14 DNA-dependent DNA polymerases in the human genome, which is remarkable. These include the widely accepted, high-fidelity enzymes responsible for replicating the vast majority of genomic DNA and eight or more specialized DNA polymerases discovered in the last decade. The newly discovered polymerases' functions are still being elucidated. Still, one of its crucial tasks is to permit synthesis to resume despite the DNA damage that stops the progression of replication-fork. One of the primary areas of interest in the research field has been the quest for novel DNA polymerase since the unique features of each thermostable DNA polymerase may lead to the prospective creation of novel reagents. Furthermore, protein engineering strategies for generating mutant or artificial DNA polymerases have successfully generated potent DNA polymerases for various applications. In molecular biology, thermostable DNA polymerases are extremely useful for PCR-related methods. This article examines the role and importance of DNA polymerase in a variety of techniques.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Fatima Iftikhar Shah
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan; The University of Lahore, Pakistan
| | - Ramesha Ibrar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Taseer Fatima
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan; Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Waqas Naseem
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Mahmood Ayaz Gul
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Laiba Tehreem
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ghanoor Haider
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
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2
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Liu D, Shu X, Xiang S, Li T, Huang C, Cheng M, Cao J, Hua Y, Liu J. N4 -allyldeoxycytidine: A New DNA Tag with Chemical Sequencing Power for Pinpointing Labelling Sites, Mapping Epigenetic Mark, and in situ Imaging. Chembiochem 2022; 23:e202200143. [PMID: 35438823 DOI: 10.1002/cbic.202200143] [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: 03/11/2022] [Revised: 04/18/2022] [Indexed: 11/08/2022]
Abstract
DNA tagging with base analogs has found numerous applications. To precisely record the DNA labelling information, it will be highly beneficial to develop chemical sequencing tags that can be encoded into DNA as regular bases and decoded as mutant bases upon a mild, efficient and bioorthognal chemical treatment. Here we reported such a DNA tag, N4-allyldeoxycytidine (a4dC), to label and identify DNA by in vitro assays. The iodination of a4dC led to fast and complete formation of 3, N4-cyclized deoxycytidine, which induced base misincorporation during DNA replication and thus could be located at single base resolution. We explored the applications of a4dC in pinpointing DNA labelling sites at single base resolution, mapping epigenetic mark N4-methyldeoxycytidine, and imaging nucleic acids in situ. In addition, mammalian cellular DNA could be metabolically labelled with a4dC. Together,our study sheds light on the design of next generation DNA tags with chemical sequencing power.
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Affiliation(s)
- Donghong Liu
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Xiao Shu
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Siying Xiang
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Tengwei Li
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Chenyang Huang
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Mohan Cheng
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Jie Cao
- Zhejiang University, Life Sciences Institute; Department of Polymer Science and Engineering, CHINA
| | - Yuejin Hua
- Zhejiang University, he MOE Key Laboratory of Biosystems Homeostasis & Protection; Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, CHINA
| | - Jianzhao Liu
- Zhejiang University, Department of Polymer Science and Engineering, Zheda road 38, 310007, hangzhou, CHINA
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3
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Medžiūnė J, Kapustina Ž, Žeimytė S, Jakubovska J, Sindikevičienė R, Čikotienė I, Lubys A. Advanced preparation of fragment libraries enabled by oligonucleotide-modified 2',3'-dideoxynucleotides. Commun Chem 2022; 5:34. [PMID: 36697673 PMCID: PMC9814608 DOI: 10.1038/s42004-022-00649-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/07/2022] [Indexed: 02/01/2023] Open
Abstract
The ever-growing demand for inexpensive, rapid, and accurate exploration of genomes calls for refinement of existing sequencing techniques. The development of next-generation sequencing (NGS) was a revolutionary milestone in genome analysis. While modified nucleotides already were inherent tools in sequencing and imaging, further modification of nucleotides enabled the expansion into even more diverse applications. Herein we describe the design and synthesis of oligonucleotide-tethered 2',3'-dideoxynucleotide (ddONNTP) terminators bearing universal priming sites attached to the nucleobase, as well as their enzymatic incorporation and performance in read-through assays. In the context of NGS library preparation, the incorporation of ddONNTP fulfills two requirements at once: the fragmentation step is integrated into the workflow and the obtained fragments are readily labeled by platform-specific adapters. DNA polymerases can incorporate ddONNTP nucleotides, as shown by primer extension assays. More importantly, reading through the unnatural linkage during DNA synthesis was demonstrated, with 25-30% efficiency in single-cycle extension.
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Affiliation(s)
- Justina Medžiūnė
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania ,grid.6441.70000 0001 2243 2806Faculty of Chemistry and Geosciences, Vilnius University, Vilnius, LT-03225 Lithuania
| | - Žana Kapustina
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania ,grid.6441.70000 0001 2243 2806Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, LT-10257 Lithuania
| | - Simona Žeimytė
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania
| | - Jevgenija Jakubovska
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania
| | - Rūta Sindikevičienė
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania
| | - Inga Čikotienė
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania ,grid.6441.70000 0001 2243 2806Faculty of Chemistry and Geosciences, Vilnius University, Vilnius, LT-03225 Lithuania
| | - Arvydas Lubys
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania
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4
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Ishaqat A, Herrmann A. Polymers Strive for Accuracy: From Sequence-Defined Polymers to mRNA Vaccines against COVID-19 and Polymers in Nucleic Acid Therapeutics. J Am Chem Soc 2021; 143:20529-20545. [PMID: 34841867 DOI: 10.1021/jacs.1c08484] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Unquestionably, polymers have influenced the world over the past 100 years. They are now more crucial than ever since the COVID-19 pandemic outbreak. The pandemic paved the way for certain polymers to be in the spotlight, namely sequence-defined polymers such as messenger ribonucleic acid (mRNA), which was the first type of vaccine to be authorized in the U.S. and Europe to protect against the SARS-CoV-2 virus. This rise of mRNA will probably influence scientific research concerning nucleic acids in general and RNA therapeutics in specific. In this Perspective, we highlight the recent trends in sequence-controlled and sequence-defined polymers. Then we discuss mRNA vaccines as an example to illustrate the need of ultimate sequence control to achieve complex functions such as specific activation of the immune system. We briefly present how mRNA vaccines are produced, the importance of modified nucleotides, the characteristic features, and the advantages and challenges associated with this class of vaccines. Finally, we discuss the chances and opportunities for polymer chemistry to provide solutions and contribute to the future progress of RNA-based therapeutics. We highlight two particular roles of polymers in this context. One represents conjugation of polymers to nucleic acids to form biohybrids. The other is concerned with advanced polymer-based carrier systems for nucleic acids. We believe that polymers can help to address present problems of RNA-based therapeutic technologies and impact the field beyond the COVID-19 pandemic.
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Affiliation(s)
- Aman Ishaqat
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany.,Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Andreas Herrmann
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany.,Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
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5
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Butterworth A, Pratibha P, Marx A, Corrigan DK. Electrochemical Detection of Oxacillin Resistance using Direct-Labeling Solid-Phase Isothermal Amplification. ACS Sens 2021; 6:3773-3780. [PMID: 34595928 DOI: 10.1021/acssensors.1c01688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Isothermal amplification reactions represent an important and exciting approach to achieve widespread, low cost, and easily implemented molecular diagnostics. This work presents a modified recombinase polymerase amplification (RPA) reaction, which can be directly coupled to a simple electrochemical measurement to ultimately allow development of a nucleic acid-based assay for antibiotic resistance genes. It is shown that use of reagents from a standard RPA reaction kit allows incorporation of horse radish peroxidase-labeled thymine nucleotides into amplified DNA strands, which can be detected via an amperometric signal readout for detection of important gene sequences. The assay is exemplified through detection of fragments of the oxacillin resistance gene in Escherichia coli cells bearing a drug resistance plasmid, achieving a potential limit of detection of 319 cfus/mL and an unoptimized time to result of 60 min. This work serves as a suitable demonstration of the potential for a system to deliver detection of key drug resistance genes at clinically relevant levels.
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Affiliation(s)
- Adrian Butterworth
- Department of Biomedical Engineering, Wolfson Centre, University of Strathclyde, 106 Rottenrow East, Glasgow G1 1XQ, U.K
| | - Pratibha Pratibha
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Damion K. Corrigan
- Department of Biomedical Engineering, Wolfson Centre, University of Strathclyde, 106 Rottenrow East, Glasgow G1 1XQ, U.K
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6
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Espinasse A, Lembke HK, Cao AA, Carlson EE. Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications. RSC Chem Biol 2020; 1:333-351. [PMID: 33928252 PMCID: PMC8081287 DOI: 10.1039/d0cb00078g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Modified nucleoside triphosphates (NTPs) are invaluable tools to probe bacterial enzymatic mechanisms, develop novel genetic material, and engineer drugs and proteins with new functionalities. Although the impact of nucleobase alterations has predominantly been studied due to their importance for protein recognition, sugar and phosphate modifications have also been investigated. However, NTPs are cell impermeable due to their negatively charged phosphate tail, a major hurdle to achieving live bacterial studies. Herein, we review the recent advances made to investigate and evolve bacteria and their processes with the use of modified NTPs by exploring alterations in one of the three moieties: the nucleobase, the sugar and the phosphate tail. We also present the innovative methods that have been devised to internalize NTPs into bacteria for in vivo applications.
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Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Hannah K. Lembke
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Angela A. Cao
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
- Department of Medicinal Chemistry, University of Minnesota208 Harvard Street SEMinneapolisMinnesota 55454USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota321 Church St SEMinneapolisMinnesota 55454USA
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7
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Flamme M, Levi-Acobas F, Hensel S, Naskar S, Röthlisberger P, Sarac I, Gasser G, Müller J, Hollenstein M. Enzymatic Construction of Artificial Base Pairs: The Effect of Metal Shielding. Chembiochem 2020; 21:3398-3409. [PMID: 32673442 DOI: 10.1002/cbic.202000402] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/16/2020] [Indexed: 12/12/2022]
Abstract
Th formation of metal base pairs is a versatile method for the introduction of metal cations into nucleic acids that has been used in numerous applications including the construction of metal nanowires, development of energy, charge-transfer devices and expansion of the genetic alphabet. As an alternative, enzymatic construction of metal base pairs is an alluring strategy that grants access to longer sequences and offers the possibility of using such unnatural base pairs (UBPs) in SELEX experiments for the identification of functional nucleic acids. This method remains rather underexplored, and a better understanding of the key parameters in the design of efficient nucleotides is required. We have investigated the effect of methylation of the imidazole nucleoside (dImnMe TP) on the efficiency of the enzymatic construction of metal base pairs. The presence of methyl substituents on dImTP facilitates the polymerase-driven formation of dIm4Me -AgI -dIm and dIm2Me TP-CrIII -dIm base pairs. Steric factors rather than the basicity of the imidazole nucleobase appear to govern the enzymatic formation of such metal base pairs. We also demonstrate the compatibility of other metal cations rarely considered in the construction of artificial metal bases by enzymatic DNA synthesis under both primer extension reaction and PCR conditions. These findings open up new directions for the design of nucleotide analogues for the development of metal base pairs.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France.,Université Paris Descartes, Sorbonne Paris Cité, 12 rue de l'École de Médecine, 75006, Paris, France.,Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 11, rue Pierre et Marie Curie, 75005, Paris, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Susanne Hensel
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 30, 48149, Münster, Germany
| | - Shuvankar Naskar
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 30, 48149, Münster, Germany
| | - Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 11, rue Pierre et Marie Curie, 75005, Paris, France
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 30, 48149, Münster, Germany
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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8
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Duffy K, Arangundy-Franklin S, Holliger P. Modified nucleic acids: replication, evolution, and next-generation therapeutics. BMC Biol 2020; 18:112. [PMID: 32878624 PMCID: PMC7469316 DOI: 10.1186/s12915-020-00803-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs.
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Affiliation(s)
- Karen Duffy
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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9
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Combining the Sensitivity of LAMP and Simplicity of Primer Extension via a DNA-Modified Nucleotide. CHEMISTRY 2020. [DOI: 10.3390/chemistry2020029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
LAMP is an approach for isothermal nucleic acids diagnostics with increasing importance but suffers from the need of tedious systems design and optimization for every new target. Here, we describe an approach for its simplification based on a single nucleoside-5′-O-triphosphate (dNTP) that is covalently modified with a DNA strand. We found that the DNA-modified dNTP is a substrate for DNA polymerases in versatile primer extension reactions despite its size and that the incorporated DNA indeed serves as a target for selective LAMP analysis.
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10
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Diafa S, Evéquoz D, Leumann CJ, Hollenstein M. Synthesis and Enzymatic Characterization of Sugar-Modified Nucleoside Triphosphate Analogs. Methods Mol Biol 2019; 1973:1-13. [PMID: 31016692 DOI: 10.1007/978-1-4939-9216-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical modification of nucleic acids can be achieved by the enzymatic polymerization of modified nucleoside triphosphates (dN*TPs). This approach obviates some of the requirements and drawbacks imposed by the more traditional solid-phase synthesis of oligonucleotides. Here, we describe the protocol that is necessary to synthesize dN*TPs and evaluate their substrate acceptance by polymerases for their subsequent use in various applications including selection experiments to identify aptamers. The protocol is exemplified for a sugar-constrained nucleoside analog, 7',5'-bc-TTP.
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Affiliation(s)
- Stella Diafa
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Damien Evéquoz
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Marcel Hollenstein
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, Institut Pasteur, Paris, France.
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11
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Jakubovska J, Tauraite D, Birštonas L, Meškys R. N4-acyl-2'-deoxycytidine-5'-triphosphates for the enzymatic synthesis of modified DNA. Nucleic Acids Res 2019; 46:5911-5923. [PMID: 29846697 PMCID: PMC6158702 DOI: 10.1093/nar/gky435] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/08/2018] [Indexed: 02/06/2023] Open
Abstract
A huge diversity of modified nucleobases is used as a tool for studying DNA and RNA. Due to practical reasons, the most suitable positions for modifications are C5 of pyrimidines and C7 of purines. Unfortunately, by using these two positions only, one cannot expand a repertoire of modified nucleotides to a maximum. Here, we demonstrate the synthesis and enzymatic incorporation of novel N4-acylated 2′-deoxycytidine nucleotides (dCAcyl). We find that a variety of family A and B DNA polymerases efficiently use dCAcylTPs as substrates. In addition to the formation of complementary CAcyl•G pair, a strong base-pairing between N4-acyl-cytosine and adenine takes place when Taq, Klenow fragment (exo–), Bsm and KOD XL DNA polymerases are used for the primer extension reactions. In contrast, a proofreading phi29 DNA polymerase successfully utilizes dCAcylTPs but is prone to form CAcyl•A base pair under the same conditions. Moreover, we show that terminal deoxynucleotidyl transferase is able to incorporate as many as several hundred N4-acylated-deoxycytidine nucleotides. These data reveal novel N4-acylated deoxycytidine nucleotides as beneficial substrates for the enzymatic synthesis of modified DNA, which can be further applied for specific labelling of DNA fragments, selection of aptamers or photoimmobilization.
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Affiliation(s)
- Jevgenija Jakubovska
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Daiva Tauraite
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Lukas Birštonas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
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12
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Finke A, Schneider A, Spreng A, Leist M, Niemeyer CM, Marx A. Functionalized DNA Hydrogels Produced by Polymerase-Catalyzed Incorporation of Non-Natural Nucleotides as a Surface Coating for Cell Culture Applications. Adv Healthc Mater 2019; 8:e1900080. [PMID: 30861332 DOI: 10.1002/adhm.201900080] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Indexed: 12/17/2022]
Abstract
Cells from most mammalian tissues require an extracellular matrix (ECM) for attachment and proper functioning. In vitro cell cultures therefore must be supplied with an ECM that satisfies both the biological needs of cells used and the technical demands of the experimental setup. The latter include matrix functionalization for cell attachment, favorable microscopic properties, and affordable production costs. Here, modified DNA materials are therefore developed as an ECM mimic. The material is prepared by chemical cross-linking of commonly available salmon sperm DNA. To render the material cell-compatible, it is enzymatically modified by DNA polymerase I to provide versatile attachment points for peptides, proteins, or antibodies via a modular strategy. Different cells specifically attach to the material, even from mixed populations. They can be mildly released for further cell studies by DNase I-mediated digestion of the DNA material. Additionally, neural stem cells not only attach and survive on the material but also differentiate to a neural lineage when prompted. Furthermore, the DNA material can be employed to capture and retain cells under flow conditions. The simple preparation of the DNA material and its wide scope of applications open new perspectives for various cell study challenges and medical applications.
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Affiliation(s)
- Alexander Finke
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversity of Konstanz Universitätsstraße 10 78464 Konstanz Germany
| | - Ann‐Kathrin Schneider
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1) Hermann‐von‐Helmholtz‐Platz D‐76344 Eggenstein‐Leopoldshafen Germany
| | - Anna‐Sophie Spreng
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversity of Konstanz Universitätsstraße 10 78464 Konstanz Germany
| | - Marcel Leist
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversity of Konstanz Universitätsstraße 10 78464 Konstanz Germany
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1) Hermann‐von‐Helmholtz‐Platz D‐76344 Eggenstein‐Leopoldshafen Germany
| | - Andreas Marx
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversity of Konstanz Universitätsstraße 10 78464 Konstanz Germany
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13
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Engineering Polymerases for New Functions. Trends Biotechnol 2019; 37:1091-1103. [PMID: 31003719 DOI: 10.1016/j.tibtech.2019.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/08/2019] [Accepted: 03/19/2019] [Indexed: 01/04/2023]
Abstract
DNA polymerases are critical tools in biotechnology, enabling efficient and accurate amplification of DNA templates, yet many desired functions are not readily available in natural DNA polymerases. New or improved functions can be engineered in DNA polymerases by mutagenesis or through the creation of protein chimeras. Engineering often necessitates the development of new techniques, such as selections in water-in-oil emulsions that connect genotype to phenotype and allow more flexibility in engineering than phage display. Engineering efforts have led to DNA polymerases that can withstand extreme conditions or the presence of inhibitors, as well as polymerases with the ability to copy modified DNA templates. In this review we discuss polymerases for biotechnology that have been reported along with tools to enable further development.
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14
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Welter M, Marx A. Preparation and Application of Enzyme-Nucleotide Conjugates. ACTA ACUST UNITED AC 2019; 10:49-71. [PMID: 30040238 DOI: 10.1002/cpch.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this unit the preparation and application of enzyme-nucleotide conjugates is depicted. First, a modified nucleoside triphosphate is synthesized bearing a long and flexible linker equipped with a thiol group. The nucleotide is then reacted with maleimide-activated horseradish peroxidase to yield an enzyme-nucleotide conjugate, which due to the long linker, can be used as a substrate by DNA polymerases in primer extension reactions. Finally, an assay based on these findings is described that provides a fast and easy nucleic acid detection and genotyping platform. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Moritz Welter
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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15
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Matyašovský J, Pohl R, Hocek M. 2-Allyl- and Propargylamino-dATPs for Site-Specific Enzymatic Introduction of a Single Modification in the Minor Groove of DNA. Chemistry 2018; 24:14938-14941. [PMID: 30074286 PMCID: PMC6221035 DOI: 10.1002/chem.201803973] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Indexed: 12/15/2022]
Abstract
A series of 2-alkylamino-2'-deoxyadenosine triphosphates (dATP) was prepared and found to be substrates for the Therminator DNA polymerase, which incorporated only one modified nucleotide into the primer. Using a template encoding for two consecutive adenines, conditions were found for incorporation of either one or two modified nucleotides. In all cases, addition of a mixture of natural dNTPs led to primer extension resulting in site-specific single modification of DNA in the minor groove. The allylamino-substituted DNA was used for the thiol-ene addition, whereas the propargylamino-DNA for the CuAAC click reaction was used to label the DNA with a fluorescent dye in the minor groove. The approach was used to construct FRET probes for detection of oligonucleotides.
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Affiliation(s)
- Ján Matyašovský
- 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
| | - 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
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16
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Balintová J, Welter M, Marx A. Antibody-nucleotide conjugate as a substrate for DNA polymerases. Chem Sci 2018; 9:7122-7125. [PMID: 30310633 PMCID: PMC6137436 DOI: 10.1039/c8sc01839a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023] Open
Abstract
Here we report on the development of an antibody-modified nucleotide and its sequence-selective incorporation into nascent DNA catalysed by DNA polymerases. Although the modification of the nucleotide is several orders of magnitude larger than the natural dNTP substrate and even exceeds the size of the DNA polymerase, it is well accepted by the enzyme. Moreover, the recognition of the antibody is not abolished by the conjugation but can be recognized by a secondary antibody that is conjugated to a signal-generating enzyme (i.e., horse radish peroxidase). This product can thus be exploited for a colorimetric read-out of nucleotide incorporation by the naked eye that allows detection of DNA as low as 10 amol. In future, assays like the one described herein might allow nucleic acid diagnostics at single nucleotide resolution without any laboratory equipment.
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Affiliation(s)
- J Balintová
- Department of Chemistry , University of Konstanz , Universitätsstrasse 10 , 78457 Konstanz , Germany .
| | - M Welter
- Department of Chemistry , University of Konstanz , Universitätsstrasse 10 , 78457 Konstanz , Germany .
| | - A Marx
- Department of Chemistry , University of Konstanz , Universitätsstrasse 10 , 78457 Konstanz , Germany .
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17
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Snapshots of a modified nucleotide moving through the confines of a DNA polymerase. Proc Natl Acad Sci U S A 2018; 115:9992-9997. [PMID: 30224478 PMCID: PMC6176618 DOI: 10.1073/pnas.1811518115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Despite being evolved to process the four canonical nucleotides, DNA polymerases are known to incorporate and extend from modified nucleotides, which is the key to numerous core biotechnology applications. The structural basis for postincorporation elongation remained elusive. We successfully crystallized KlenTaq DNA polymerase in six complexes, providing high-resolution snapshots of the modification “moving” from the 3′ terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme’s activity. This highlights the unexpected plasticity of the system as origin of the broad substrate properties of the DNA polymerase and guide for the design of improved systems. DNA polymerases have evolved to process the four canonical nucleotides accurately. Nevertheless, these enzymes are also known to process modified nucleotides, which is the key to numerous core biotechnology applications. Processing of modified nucleotides includes incorporation of the modified nucleotide and postincorporation elongation to proceed with the synthesis of the nascent DNA strand. The structural basis for postincorporation elongation is currently unknown. We addressed this issue and successfully crystallized KlenTaq DNA polymerase in six closed ternary complexes containing the enzyme, the modified DNA substrate, and the incoming nucleotide. Each structure shows a high-resolution snapshot of the elongation of a modified primer, where the modification “moves” from the 3′-primer terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme’s activity significantly. The study highlights the plasticity of the system as origin of the broad substrate properties of DNA polymerases and facilitates the design of improved systems.
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18
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Röthlisberger P, Hollenstein M. Aptamer chemistry. Adv Drug Deliv Rev 2018; 134:3-21. [PMID: 29626546 DOI: 10.1016/j.addr.2018.04.007] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules capable of tightly binding to specific targets. These functional nucleic acids are obtained by an in vitro Darwinian evolution method coined SELEX (Systematic Evolution of Ligands by EXponential enrichment). Compared to their proteinaceous counterparts, aptamers offer a number of advantages including a low immunogenicity, a relative ease of large-scale synthesis at affordable costs with little or no batch-to-batch variation, physical stability, and facile chemical modification. These alluring properties have propelled aptamers into the forefront of numerous practical applications such as the development of therapeutic and diagnostic agents as well as the construction of biosensing platforms. However, commercial success of aptamers still proceeds at a weak pace. The main factors responsible for this delay are the susceptibility of aptamers to degradation by nucleases, their rapid renal filtration, suboptimal thermal stability, and the lack of functional group diversity. Here, we describe the different chemical methods available to mitigate these shortcomings. Particularly, we describe the chemical post-SELEX processing of aptamers to include functional groups as well as the inclusion of modified nucleoside triphosphates into the SELEX protocol. These methods will be illustrated with successful examples of chemically modified aptamers used as drug delivery systems, in therapeutic applications, and as biosensing devices.
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19
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Olszewska A, Pohl R, Hocek M. Trifluoroacetophenone-Linked Nucleotides and DNA for Studying of DNA-Protein Interactions by 19F NMR Spectroscopy. J Org Chem 2018; 82:11431-11439. [PMID: 28991457 DOI: 10.1021/acs.joc.7b01920] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A series of 7-[4-(trifluoroacetyl)phenyl]-7-deazaadenine and -7-deazaguanine as well as 5-substituted uracil and cytosine 2'-deoxyribonucleosides and mono- and triphosphates were synthesized through aqueous Suzuki-Miyaura crosscoupling of halogenated nucleosides or nucleotides with 4-(trifluoroacetyl)phenylboronic acid. The modified nucleoside triphosphates were good substrates for DNA polymerases applicable in primer extension or PCR synthesis of modified oligonucleotides or DNA. Attempted cross-linking with a serine-containing protein did not proceed, however the trifluoroacetophenone group was a sensitive probe for the study of DNA-protein interactions by 19F NMR.
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Affiliation(s)
- Agata Olszewska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo namesti 2, 160 00 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo namesti 2, 160 00 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo namesti 2, 160 00 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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20
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Röthlisberger P, Levi-Acobas F, Sarac I, Marlière P, Herdewijn P, Hollenstein M. On the enzymatic incorporation of an imidazole nucleotide into DNA. Org Biomol Chem 2018; 15:4449-4455. [PMID: 28485736 DOI: 10.1039/c7ob00858a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of the genetic alphabet with an additional, artificial base pair is of high relevance for numerous applications in synthetic biology. The enzymatic construction of metal base pairs is an alluring strategy that would ensure orthogonality to canonical nucleic acids. So far, very little is known on the enzymatic fabrication of metal base pairs. Here, we report on the synthesis and the enzymatic incorporation of an imidazole nucleotide into DNA. The imidazole nucleotide dIm is known to form highly stable dIm-Ag+-dIm artificial base pairs that cause minimal structural perturbation of DNA duplexes and was considered to be an ideal candidate for the enzymatic construction of metal base pairs. We demonstrate that dImTP is incorporated with high efficiency and selectivity opposite a templating dIm nucleotide by the Kf exo-. The presence of Mn2+, and to a smaller extent Ag+, enhances the efficiency of this polymerization reaction, however, without being strictly required. In addition, multiple incorporation events could be observed, albeit with modest efficiency. We demonstrate that the dIm-Mn+-dIm cannot be constructed by DNA polymerases and suggest that parameters other than stability of a metal base pair and its impact on the structure of DNA duplexes govern the enzymatic formation of artificial metal base pairs.
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Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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21
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Yang Q, Hao Q, Lei J, Ju H. Portable Photoelectrochemical Device Integrated with Self-Powered Electrochromic Tablet for Visual Analysis. Anal Chem 2018; 90:3703-3707. [DOI: 10.1021/acs.analchem.7b05232] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Qianhui Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Qing Hao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
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22
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Botha F, Slavíčková M, Pohl R, Hocek M. Copper-mediated arylsulfanylations and arylselanylations of pyrimidine or 7-deazapurine nucleosides and nucleotides. Org Biomol Chem 2018; 14:10018-10022. [PMID: 27722411 DOI: 10.1039/c6ob01917j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The syntheses of 5-arylsulfanyl- or 5-arylselanylpyrimidine and 7-arylsulfanyl- or 7-arylselanyl-7-deazapurine nucleosides and nucleotides were developed by the Cu-mediated sulfanylations or selanylations of the corresponding 5-iodopyrimidine or 7-iodo-7-deazapurine nucleosides or nucleotides with diaryldisulfides or -diselenides. The reactions were also applicable for direct modifications of 2'-deoxycytidine triphosphate and the resulting 5-arylsulfanyl or 5-arylselanyl-dCTP served as substrates for the polymerase synthesis of modified DNA bearing arylsulfanyl or arylselanyl groups in the major groove.
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Affiliation(s)
- Filip Botha
- Institute of Organic Chemistry and Biochemistry, Academy of Science Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
| | - Michaela Slavíčková
- Institute of Organic Chemistry and Biochemistry, Academy of Science Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Science 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 Science Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6, Czech Republic. and Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843 Prague 2, Czech Republic
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23
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Balintová J, Simonova A, Białek-Pietras M, Olejniczak A, Lesnikowski ZJ, Hocek M. Carborane-linked 2'-deoxyuridine 5'-O-triphosphate as building block for polymerase synthesis of carborane-modified DNA. Bioorg Med Chem Lett 2017; 27:4786-4788. [PMID: 29017785 DOI: 10.1016/j.bmcl.2017.09.064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/13/2017] [Accepted: 09/30/2017] [Indexed: 11/16/2022]
Abstract
5-[(p-Carborane-2-yl)ethynyl]-2'-deoxyuridine 5'-O-triphosphate was synthesized and used as a good substrate in enzymatic construction of carborane-modified DNA or oligonucleotides containing up to 21 carborane moieties in primer extension reactions by DNA polymerases.
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Affiliation(s)
- Jana Balintová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
| | - Anna Simonova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
| | - Magdalena Białek-Pietras
- Institute of Medical Biology, Polish Academy of Sciences, Laboratory of Molecular Virology and Biological Chemistry, 106 Lodowa St., Lodz 93-232, Poland
| | - Agnieszka Olejniczak
- Institute of Medical Biology, Polish Academy of Sciences, Laboratory of Molecular Virology and Biological Chemistry, 106 Lodowa St., Lodz 93-232, Poland
| | - Zbigniew J Lesnikowski
- Institute of Medical Biology, Polish Academy of Sciences, Laboratory of Molecular Virology and Biological Chemistry, 106 Lodowa St., Lodz 93-232, Poland.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic.
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24
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DNA polymerases and biotechnological applications. Curr Opin Biotechnol 2017; 48:187-195. [PMID: 28618333 DOI: 10.1016/j.copbio.2017.04.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 04/17/2017] [Indexed: 01/04/2023]
Abstract
A multitude of biotechnological techniques used in basic research as well as in clinical diagnostics on an everyday basis depend on DNA polymerases and their intrinsic capability to replicate DNA strands with astoundingly high fidelity. Applications with fundamental importance to modern molecular biology, including the polymerase chain reaction and DNA sequencing, would not be feasible without the advances made in characterizing these enzymes over the course of the last 60 years. Nonetheless, the still growing application scope of DNA polymerases necessitates the identification of novel enzymes with tailor-made properties. In the recent past, DNA polymerases optimized for diverse PCR and sequencing applications as well as enzymes that accept a variety of unnatural substrates for the synthesis and reverse transcription of modified nucleic acids have been developed.
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25
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Fozooni T, Ravan H, Sasan H. Signal Amplification Technologies for the Detection of Nucleic Acids: from Cell-Free Analysis to Live-Cell Imaging. Appl Biochem Biotechnol 2017; 183:1224-1253. [DOI: 10.1007/s12010-017-2494-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/24/2017] [Indexed: 12/15/2022]
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26
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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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27
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Houlihan G, Arangundy-Franklin S, Holliger P. Exploring the Chemistry of Genetic Information Storage and Propagation through Polymerase Engineering. Acc Chem Res 2017; 50:1079-1087. [PMID: 28383245 PMCID: PMC5406124 DOI: 10.1021/acs.accounts.7b00056] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Nucleic
acids are a distinct form of sequence-defined biopolymer.
What sets them apart from other biopolymers such as polypeptides or
polysaccharides is their unique capacity to encode, store, and propagate
genetic information (molecular heredity). In nature, just two closely
related nucleic acids, DNA and RNA, function as repositories and carriers
of genetic information. They therefore are the molecular embodiment
of biological information. This naturally leads to questions regarding
the degree of variation from this seemingly ideal “Goldilocks”
chemistry that would still be compatible with the fundamental property
of molecular heredity. To address this question, chemists have
created a panoply of synthetic
nucleic acids comprising unnatural sugar ring congeners, backbone
linkages, and nucleobases in order to establish the molecular parameters
for encoding genetic information and its emergence at the origin of
life. A deeper analysis of the potential of these synthetic genetic
polymers for molecular heredity requires a means of replication and
a determination of the fidelity of information transfer. While non-enzymatic
synthesis is an increasingly powerful method, it currently remains
restricted to short polymers. Here we discuss efforts toward establishing
enzymatic synthesis, replication, and evolution of synthetic genetic
polymers through the engineering of polymerase enzymes found in nature. To endow natural polymerases with the ability to efficiently utilize
non-cognate nucleotide substrates, novel strategies for the screening
and directed evolution of polymerase function have been realized.
High throughput plate-based screens, phage display, and water-in-oil
emulsion technology based methods have yielded a number of engineered
polymerases, some of which can synthesize and reverse transcribe synthetic
genetic polymers with good efficiency and fidelity. The inception
of such polymerases demonstrates that, at a basic
level at least, molecular heredity is not restricted to the natural
nucleic acids DNA and RNA, but may be found in a large (if finite)
number of synthetic genetic polymers. And it has opened up these novel
sequence spaces for investigation. Although largely unexplored, first
tentative forays have yielded ligands (aptamers) against a range of
targets and several catalysts elaborated in a range of different chemistries.
Finally, taking the lead from established DNA designs, simple polyhedron
nanostructures have been described. We anticipate that further
progress in this area will expand the
range of synthetic genetic polymers that can be synthesized, replicated,
and evolved providing access to a rich sequence, structure, and phenotypic
space. “Synthetic genetics”, that is, the exploration
of these spaces, will illuminate the chemical parameter range for
en- and decoding information, 3D folding, and catalysis and yield
novel ligands, catalysts, and nanostructures and devices for applications
in biotechnology and medicine.
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Affiliation(s)
- Gillian Houlihan
- MRC Laboratory of Molecular Biology, Francis Crick
Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick
Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
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28
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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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29
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Röthlisberger P, Levi-Acobas F, Hollenstein M. New synthetic route to ethynyl-dUTP: A means to avoid formation of acetyl and chloro vinyl base-modified triphosphates that could poison SELEX experiments. Bioorg Med Chem Lett 2017; 27:897-900. [PMID: 28089700 DOI: 10.1016/j.bmcl.2017.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 01/10/2023]
Abstract
5-Ethynyl-2'-deoxyuridine is a common base-modified nucleoside analogue that has served in various applications including selection experiments for potent aptamers and in biosensing. The synthesis of the corresponding triphosphates involves a mild acidic deprotection step. Herein, we show that this deprotection leads to the formation of other nucleoside analogs which are easily converted to triphosphates. The modified nucleoside triphosphates are excellent substrates for numerous DNA polymerases under both primer extension and PCR conditions and could thus poison selection experiments by blocking sites that need to be further modified. The formation of these nucleoside analogs can be circumvented by application of a new synthetic route that is described herein.
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Affiliation(s)
- Pascal Röthlisberger
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; CNRS UMR3523 Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; CNRS UMR3523 Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; CNRS UMR3523 Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
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30
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Guo C, Hili R. Fidelity of the DNA Ligase-Catalyzed Scaffolding of Peptide Fragments on Nucleic Acid Polymers. Bioconjug Chem 2016; 28:314-318. [DOI: 10.1021/acs.bioconjchem.6b00647] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Chun Guo
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602-2556, United States
| | - Ryan Hili
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602-2556, United States
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31
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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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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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Cahová H, Panattoni A, Kielkowski P, Fanfrlík J, Hocek M. 5-Substituted Pyrimidine and 7-Substituted 7-Deazapurine dNTPs as Substrates for DNA Polymerases in Competitive Primer Extension in the Presence of Natural dNTPs. ACS Chem Biol 2016; 11:3165-3171. [PMID: 27668519 DOI: 10.1021/acschembio.6b00714] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A complete series of 5-substituted uracil or cytosine, as well as 7-substituted 7-deazaadenine and 7-deazaguanine 2'-deoxyribonucleoside triphosphates (dNTPs) bearing substituents of increasing bulkiness (H, Me, vinyl, ethynyl, and phenyl) were systematically studied in competitive primer extension in the presence of their natural counterparts (nonmodified dNTPs), and their kinetic data were determined. The results show that modified dNTPs bearing π-electron-containing substituents (vinyl, ethynyl, Ph) are typically excellent substrates for DNA polymerases comparable to or better than natural dNTPs. The kinetic studies revealed that these modified dNTPs have higher affinity to the active site of the enzyme-primer-template complex, and the calculations (semiempirical quantum mechanical scoring function) suggest that it is due to the cation-π interaction of the modified dNTP with Arg629 in the active site of Bst DNA polymerase.
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Affiliation(s)
- Hana Cahová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Alessandro Panattoni
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Pavel Kielkowski
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2 12843, Czech Republic
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Slavíčková M, Pohl R, Hocek M. Additions of Thiols to 7-Vinyl-7-deazaadenine Nucleosides and Nucleotides. Synthesis of Hydrophobic Derivatives of 2'-Deoxyadenosine, dATP and DNA. J Org Chem 2016; 81:11115-11125. [PMID: 27709938 DOI: 10.1021/acs.joc.6b02098] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Additions of alkyl- or arylthiols to 7-vinyl-7-deaza-2'-deoxyadenosine gave a series of 7-[2-(alkyl- or arylsulfanyl)ethyl]-7-deaza-2'-deoxyadenosines in 45-85% yields. The nucleosides were converted to 5'-O-mono-(dASRMP) or triphosphates (dASRTP) by phosphorylation. The modified triphosphates were also prepared by thiol addition to 7-vinyl-7-deaza-dATP. The triphosphates dASRTP were good substrates for DNA polymerases useful in the enzymatic synthesis of base-modified oligonucleotides (ONs) or DNA containing flexibly linked hydrophobic substituents in the major groove. Primer extension was used for the synthesis of ONs with one or several modifications, PCR was used for the synthesis of heavily modified DNA, whereas terminal deoxynucleotidyl transferase was used for a single-nucleotide labeling of the 3'-end.
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Affiliation(s)
- Michaela Slavíčková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague , Hlavova 8, Prague-2 12843, Czech Republic
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