1
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Krömer M, Poštová Slavětínská L, Hocek M. Glyco-DNA: Enzymatic Synthesis of Base-Modified and Hypermodified DNA Displaying up to Four Different Monosaccharide Units in the Major Groove. Chemistry 2024:e202402318. [PMID: 38896019 DOI: 10.1002/chem.202402318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 06/19/2024] [Accepted: 06/19/2024] [Indexed: 06/21/2024]
Abstract
A portfolio of six modified 2'-deoxyribonucleoside triphosphate (dNTP) derivatives derived from 5-substituted pyrimidine or 7-substituted 7-deazapurine bearing different carbohydrate units (d-glucose, d-galactose, d-mannose, l-fucose, sialic acid and N-Ac-d-galactosamine) tethered through propargyl-glycoside linker was designed and synthesized via the Sonogashira reactions of halogenated dNTPs with the corresponding propargyl-glycosides. The nucleotides were found to be good substrates for DNA polymerases in enzymatic primer extension and PCR synthesis of modified and hypermodified DNA displaying up to four different sugars. Proof of concept binding study of sugar-modified oligonucleotides with concanavalin A showed positive effect of avidity and sugar units count.
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Affiliation(s)
- Matouš Krömer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843, Prague 2, Czech Republic
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2
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Sett A, Gadewar M, Babu MA, Panja A, Sachdeva P, Almutary AG, Upadhye V, Jha SK, Jha NK. Orchestration and theranostic applications of synthetic genome with Hachimoji bases/building blocks. Chem Biol Drug Des 2024; 103:e14378. [PMID: 38230795 DOI: 10.1111/cbdd.14378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 01/18/2024]
Abstract
Synthetic genomics is a novel field of chemical biology where the chemically modified genetic alphabets have been considered in central dogma of life. Tweaking of chemical compositions of natural nucleotide bases could be developed as novel building blocks of DNA/RNA. The modified bases (dP, dZ, dS, and dB etc.) have been demonstrated to be adaptable for replication, transcription and follow Darwinism law of evolution. With advancement of chemical biology especially nucleotide chemistry, synthetic genetic codes have been discovered and Hachimoji nucleotides are the most important and significant one among them. These additional nucleotide bases can form orthogonal base-pairing, and also follow Darwinian evolution and other structural features. In the Hachimoji base pairing, synthetic building blocks are formed using eight modified nucleotide (DNA/RNA) letters (hence the name "Hachimoji"). Their structural conformations, like polyelectrolyte backbones and stereo-regular building blocks favor thermodynamic stability and confirm Schrodinger aperiodic crystal. From the structural genomics aspect, these synthetic bases could be incorporated into the central dogma of life. Researchers have shown Hachimoji building blocks were transcribed to its RNA counterpart as a functional fluorescent Hachimoji aptamer. Apart from several unnatural nucleotide base pairs maneuvered into its in vitro and in vivo applications, this review describes future perspective towards the development and therapeutic utilization of the genetic codes, a primary objective of synthetic and chemical biology.
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Affiliation(s)
- Arghya Sett
- ERIN Department, Luxembourg Institute of Science and Technology, 5 Av. des Hauts-Fourneaux, Belval, 4362, Esch, Luxembourg
| | - Manoj Gadewar
- Department of Pharmacology, School of Medical and Allied Sciences, K R Mangalam University, Gurgaon, India
| | - M Arockia Babu
- Institute of Pharmaceutical Research, GLA University, Mathura, India
| | | | | | - Abdulmajeed G Almutary
- Department of Biomedical Sciences, College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Vijay Upadhye
- Centre of Research for Development (CR4D) and Department of Microbiology, Parul University, Vadodara, Gujarat, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Niraj Kumar Jha
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
- Centre of Research Impact and Outreach, Chitkara University Institute of Engineering and Technology, Chitkara University, Punjab, India
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, 144411, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, 140413, India
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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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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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5
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Shanmugasundaram M, Senthilvelan A, Kore AR. C-5 Substituted Pyrimidine Nucleotides/Nucleosides: Recent Progress in Synthesis, Functionalization, and Applications. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190809124310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The chemistry of C5 substituted pyrimidine nucleotide serves as a versatile molecular
biology probe for the incorporation of DNA/RNA that has been involved in various
molecular biology applications such as gene expression, chromosome, and mRNA
fluorescence in situ hybridization (FISH) experiment, mutation detection on arrays and
microarrays, in situ RT-PCR, and PCR. In addition to C5 substituted pyrimidine nucleotide,
C5 substituted pyrimidine nucleoside displays a broad spectrum of biological applications
such as antibacterial, antiviral and anticancer activities. This review focusses on
the recent development in the synthesis of aminoallyl pyrimidine nucleotide, aminopropargyl
pyrimidine nucleotide, fluorescent probes containing C5 substituted pyrimidine nucleotide,
2′-deoxycytidine nucleoside containing vinylsulfonamide and acrylamide modification,
C5 alkenyl, C5 alkynyl, and C5 aryl pyrimidine nucleosides through palladium-catalyzed reaction,
pyrimidine nucleoside containing triazole moiety through Click reaction, 5-isoxazol-3-yl-pyrimidine nucleoside,
C5 azide modified pyrimidine nucleoside, 2′-deoxycytidine nucleotide containing photocleavable moiety,
and uridine nucleoside containing germane and their biological applications are outlined.
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Affiliation(s)
- Muthian Shanmugasundaram
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, United States
| | - Annamalai Senthilvelan
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, United States
| | - Anilkumar R. Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, United States
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6
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Flamme M, McKenzie LK, Sarac I, Hollenstein M. Chemical methods for the modification of RNA. Methods 2019; 161:64-82. [PMID: 30905751 DOI: 10.1016/j.ymeth.2019.03.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
RNA is often considered as being the vector for the transmission of genetic information from DNA to the protein synthesis machinery. However, besides translation RNA participates in a broad variety of fundamental biological roles such as gene expression and regulation, protein synthesis, and even catalysis of chemical reactions. This variety of function combined with intricate three-dimensional structures and the discovery of over 100 chemical modifications in natural RNAs require chemical methods for the modification of RNAs in order to investigate their mechanism, location, and exact biological roles. In addition, numerous RNA-based tools such as ribozymes, aptamers, or therapeutic oligonucleotides require the presence of additional chemical functionalities to strengthen the nucleosidic backbone against degradation or enhance the desired catalytic or binding properties. Herein, the two main methods for the chemical modification of RNA are presented: solid-phase synthesis using phosphoramidite precursors and the enzymatic polymerization of nucleoside triphosphates. The different synthetic and biochemical steps required for each method are carefully described and recent examples of practical applications based on these two methods are discussed.
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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; Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Luke K McKenzie
- 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
| | - 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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7
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Shanmugasundaram M, Senthilvelan A, Kore AR. An Efficient Synthesis of 5-Aminopropargyl-Pyrimidine-5'-O-Triphosphates Through Palladium-Catalyzed Sonogashira Coupling. ACTA ACUST UNITED AC 2019; 77:e81. [PMID: 30883045 DOI: 10.1002/cpnc.81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The utilization of 5-aminopropargyl nucleotide serves as a versatile molecular biology tool for the introduction of functional groups into a nucleic acid target of interest by using in-vitro enzymatic incorporation method. This article describes a simple, reliable, general, and efficient two-step chemical method for the synthesis of 5-(3-aminopropargyl)-2'-deoxycytidine-5'-O-triphosphate, 5-(3-aminopropargyl)-cytidine-5'-O-triphosphate, 5-(3-aminopropargyl)-2'-deoxyuridine-5'-O-triphosphate, and 5-(3-aminopropargyl)-uridine-5'-O-triphosphate, starting from the corresponding pyrimidine triphosphate. The first step involves regioselective C-5 iodination of pyrimidine triphosphate using N-iodosuccinimide and sodium azide. In the second step, propargylamine is coupled to the iodo-pyrimidine using the palladium-catalyzed Sonogashira reaction, producing good yields of highly pure (>99.5% HPLC) 5-aminopropargyl-pyrimidine-5'-O-triphosphate. In this approach, the palladium-catalyzed Sonogashira coupling reaction is highly chemoselective and does not involve protection and deprotection. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas
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8
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Bruno JG. Potential Inherent Stimulation of the Innate Immune System by Nucleic Acid Aptamers and Possible Corrective Approaches. Pharmaceuticals (Basel) 2018; 11:ph11030062. [PMID: 29937498 PMCID: PMC6161019 DOI: 10.3390/ph11030062] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 01/25/2023] Open
Abstract
It is well known that unmethylated 2′-deoxycytidine-phosphate-2′-guanine (CpG) sequences alone or in longer DNA and RNA oligonucleotides can act like pathogen-associated molecular patterns (PAMPs) and trigger the innate immune response leading to deleterious cytokine production via Toll-like receptors (TLRs). Clearly, such CpG or CpG-containing sequences in aptamers intended for therapy could present very damaging side effects to patients. Previous antisense oligonucleotide developers were faced with the same basic CpG dilemma and devised not only avoidance, but other effective strategies from which current aptamer developers can learn to ameliorate or eliminate damaging CpG effects. These strategies include obvious methylation of cytosines in the aptamer structure, as long as it does not affect aptamer binding in vivo, truncation of the aptamer to its essential binding site, backbone modifications, co-administration of antagonistic or suppressive oligonucleotides, or other novel drugs under development to lessen the toxic CpG effect on innate immunity.
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Affiliation(s)
- John G Bruno
- Operational Technologies Corporation, 4100 NW Loop 410, Suite 100, San Antonio, TX 78229, USA.
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9
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Krömer M, Bártová K, Raindlová V, Hocek M. Synthesis of Dihydroxyalkynyl and Dihydroxyalkyl Nucleotides as Building Blocks or Precursors for Introduction of Diol or Aldehyde Groups to DNA for Bioconjugations. Chemistry 2018; 24:11890-11894. [PMID: 29790604 DOI: 10.1002/chem.201802282] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Indexed: 01/18/2023]
Abstract
(3,4-Dihydroxybut-1-ynyl)uracil, -cytosine and -7-deazaadenine 2'-deoxyribonucleoside triphosphates (dNTPs) were prepared by direct aqueous Sonogashira cross-coupling of halogenated dNTPs with dihydroxybut-1-yne and converted to 3,4-dihydroxybutyl dNTPs through catalytic hydrogenation. Sodium periodate oxidative cleavage of dihydroxybutyl-dUTP gave the desired aliphatic aldehyde-linked dUTP, whereas the oxidative cleavage of the corresponding deazaadenine dNTP gave a cyclic aminal. All dihydroxyalkyl or -alkynyl dNTPs and the formylethyl-dUTP were good substrates for DNA polymerases and were used for synthesis of diol- or aldehyde-linked DNA. The aldehyde linked DNA was used for the labelling or bioconjugations through hydrazone formation or reductive aminations.
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Affiliation(s)
- Matouš Krömer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Veronika Raindlová
- 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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10
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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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11
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Crystal structures of ternary complexes of archaeal B-family DNA polymerases. PLoS One 2017; 12:e0188005. [PMID: 29211756 PMCID: PMC5718519 DOI: 10.1371/journal.pone.0188005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/30/2017] [Indexed: 01/04/2023] Open
Abstract
Archaeal B-family polymerases drive biotechnology by accepting a wide substrate range of chemically modified nucleotides. By now no structural data for archaeal B-family DNA polymerases in a closed, ternary complex are available, which would be the basis for developing next generation nucleotides. We present the ternary crystal structures of KOD and 9°N DNA polymerases complexed with DNA and the incoming dATP. The structures reveal a third metal ion in the active site, which was so far only observed for the eukaryotic B-family DNA polymerase δ and no other B-family DNA polymerase. The structures reveal a wide inner channel and numerous interactions with the template strand that provide space for modifications within the enzyme and may account for the high processivity, respectively. The crystal structures provide insights into the superiority over other DNA polymerases concerning the acceptance of modified nucleotides.
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12
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Lauder K, Toscani A, Scalacci N, Castagnolo D. Synthesis and Reactivity of Propargylamines in Organic Chemistry. Chem Rev 2017; 117:14091-14200. [PMID: 29166000 DOI: 10.1021/acs.chemrev.7b00343] [Citation(s) in RCA: 290] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Propargylamines are a versatile class of compounds which find broad application in many fields of chemistry. This review aims to describe the different strategies developed so far for the synthesis of propargylamines and their derivatives as well as to highlight their reactivity and use as building blocks in the synthesis of chemically relevant organic compounds. In the first part of the review, the different synthetic approaches to synthesize propargylamines, such as A3 couplings and C-H functionalization of alkynes, have been described and organized on the basis of the catalysts employed in the syntheses. Both racemic and enantioselective approaches have been reported. In the second part, an overview of the transformations of propargylamines into heterocyclic compounds such as pyrroles, pyridines, thiazoles, and oxazoles, as well as other relevant organic derivatives, is presented.
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Affiliation(s)
- Kate Lauder
- School of Cancer and Pharmaceutical Sciences, King's College London , Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Anita Toscani
- School of Cancer and Pharmaceutical Sciences, King's College London , Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Nicolò Scalacci
- School of Cancer and Pharmaceutical Sciences, King's College London , Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Daniele Castagnolo
- School of Cancer and Pharmaceutical Sciences, King's College London , Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
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13
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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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14
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Guo X, Ingale SA, Yang H, He Y, Seela F. MercuryII-mediated base pairs in DNA: unexpected behavior in metal ion binding and duplex stability induced by 2′-deoxyuridine 5-substituents. Org Biomol Chem 2017; 15:870-883. [PMID: 28045181 DOI: 10.1039/c6ob02560a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA accepts small substituents at the 5-position of 2′-deoxyuridine residues within mercury ion mediated dU–HgII–dU base pairs, while triple bonds interact with mercury ions and those with space demanding aromatic side chains block metal ion mediated base pair formation.
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Affiliation(s)
- Xiurong Guo
- Precision Medicine Research Laboratory
- West China Hospital
- West China School of Medicine
- Sichuan University
- 610041 Chengdu
| | - Sachin A. Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
| | - Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
| | - Yang He
- Precision Medicine Research Laboratory
- West China Hospital
- West China School of Medicine
- Sichuan University
- 610041 Chengdu
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
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15
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Ren X, El-Sagheer AH, Brown T. Efficient enzymatic synthesis and dual-colour fluorescent labelling of DNA probes using long chain azido-dUTP and BCN dyes. Nucleic Acids Res 2016; 44:e79. [PMID: 26819406 PMCID: PMC4856977 DOI: 10.1093/nar/gkw028] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/11/2016] [Indexed: 12/12/2022] Open
Abstract
A sterically undemanding azide analogue of dTTP (AHP dUTP) with an alkyl chain and ethynyl attachment to the nucleobase was designed and incorporated into DNA by primer extension, reverse transcription and polymerase chain reaction (PCR). An azide-modified 523 bp PCR amplicon with all 335 thymidines replaced by AHP dU was shown to be a perfect copy of the template from which it was amplified. Replacement of thymidine with AHP dU increases duplex stability, accounting in part for the high incorporation efficiency of the azide-modified triphosphate. Single-stranded azide-labelled DNA was conveniently prepared from PCR products by λ-exonuclease digestion and streptavidin magnetic bead isolation. Efficient fluorescent labelling of single and double-stranded DNA was carried out using dyes functionalized with bicyclo[6.1.0]non-4-yne (BCN) via the strain-promoted alkyne-azide cycloaddition (SPAAC) reaction. This revealed that the degree of labelling must be carefully controlled to achieve optimum fluorescence and avoid fluorescence quenching. Dual-coloured probes were obtained in a single tube fluorescent labelling reaction; and varying the ratios of the two dyes provides a simple method to prepare DNA probes with unique fluorescent signatures. AHP dUTP is a versatile clickable nucleotide with potentially wide applications in biology and nanotechnology including single molecule studies and synthesis of modified aptamer libraries via SELEX.
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Affiliation(s)
- Xiaomei Ren
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
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16
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Kore AR, Senthilvelan A, Shanmugasundaram M. Highly regioselective C-5 iodination of pyrimidine nucleotides and subsequent chemoselective Sonogashira coupling with propargylamine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:92-102. [PMID: 25621703 DOI: 10.1080/15257770.2014.964411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
An efficient C-5 iodination of pyrimidine-5'-triphosphates and subsequent palladium-catalyzed Sonogashira coupling reaction with propargylamine is described. The iodination reaction is highly regioselective and the coupling reaction is highly chemoselective that furnishes exclusive 5-(3-aminopropargyl)-pyrimidine-5'-triphosphate in good yield with high purity (>99%).
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Affiliation(s)
- Anilkumar R Kore
- a Thermo Fisher Scientific , Bioorganic Chemistry Division , Austin , TX , USA
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17
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Wang X, Chen X, Liu Y, Zhu J. Primer Extension Reaction Assays for Incorporation of Deoxynucleotide Analogue into DNA. CHINESE J CHEM 2015. [DOI: 10.1002/cjoc.201400731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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18
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Huynh N, Dickson C, Zencak D, Hilko DH, Mackay-Sim A, Poulsen SA. Labeling of Cellular DNA with aCyclosal Phosphotriester Pronucleotide Analog of 5-ethynyl-2′-deoxyuridine. Chem Biol Drug Des 2015; 86:400-9. [DOI: 10.1111/cbdd.12506] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/24/2014] [Accepted: 09/30/2014] [Indexed: 01/02/2023]
Affiliation(s)
- Ngoc Huynh
- Eskitis Institute for Drug Discovery; Griffith University; Don Young Road Nathan Qld 4111 Australia
| | - Charlotte Dickson
- Eskitis Institute for Drug Discovery; Griffith University; Don Young Road Nathan Qld 4111 Australia
| | - Dusan Zencak
- Eskitis Institute for Drug Discovery; Griffith University; Don Young Road Nathan Qld 4111 Australia
| | - David H. Hilko
- Eskitis Institute for Drug Discovery; Griffith University; Don Young Road Nathan Qld 4111 Australia
| | - Alan Mackay-Sim
- Eskitis Institute for Drug Discovery; Griffith University; Don Young Road Nathan Qld 4111 Australia
| | - Sally-Ann Poulsen
- Eskitis Institute for Drug Discovery; Griffith University; Don Young Road Nathan Qld 4111 Australia
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19
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Deng H, Gao Z. Bioanalytical applications of isothermal nucleic acid amplification techniques. Anal Chim Acta 2015; 853:30-45. [DOI: 10.1016/j.aca.2014.09.037] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/16/2014] [Accepted: 09/21/2014] [Indexed: 12/31/2022]
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20
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Ren X, Gerowska M, El-Sagheer AH, Brown T. Enzymatic incorporation and fluorescent labelling of cyclooctyne-modified deoxyuridine triphosphates in DNA. Bioorg Med Chem 2014; 22:4384-90. [PMID: 24953951 DOI: 10.1016/j.bmc.2014.05.050] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 05/16/2014] [Accepted: 05/22/2014] [Indexed: 11/25/2022]
Abstract
The amino group of 5-aminopropargyl-2'-deoxyuridine-5'-triphosphate was labelled with dibenzocyclooctyne (DIBO) and two derivatives of bicyclo [6.1.0] non-4-yne (BCN) with short and long linkers to produce three different cycloalkyne-modified deoxyuridine triphosphates. BCN was successfully incorporated into DNA at multiple sites by enzyme-mediated primer extension and the polymerase chain reaction (PCR). Efficient fluorescent labelling of the BCN-DNA and DIBO-DNA with Cy3-azide was demonstrated.
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Affiliation(s)
- Xiaomei Ren
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK
| | - Marta Gerowska
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK; Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK.
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21
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Takei F, Nakatani K. The Chemistry of Polymerase Chain Reaction^|^mdash;Development of the PCR Method Using New Modified Primers^|^mdash;. J SYN ORG CHEM JPN 2014. [DOI: 10.5059/yukigoseikyokaishi.72.370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Wu J, Wang J, Tang X. Synthesis of photolabile dUTP analogues and their enzymatic incorporation for DNA labeling. Sci China Chem 2013. [DOI: 10.1007/s11426-013-5034-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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23
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Ingale SA, Mei H, Leonard P, Seela F. Ethynyl side chain hydration during synthesis and workup of "clickable" oligonucleotides: bypassing acetyl group formation by triisopropylsilyl protection. J Org Chem 2013; 78:11271-82. [PMID: 24138578 DOI: 10.1021/jo401780u] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Clickable oligonucleotides with ethynyl residues in the 5-position of pyrimidines ((eth)dC and (eth)dU) or the 7-position of 7-deazaguanine ((eth)c(7)G(d)) are hydrated during solid-phase oligonucleotide synthesis and workup conditions. The side products were identified as acetyl derivatives by MALDI-TOF mass spectra of oligonucleotides and by detection of modified nucleosides after enzymatic phosphodiester hydrolysis. Ethynyl → acetyl group conversion was also studied on ethynylated nucleosides under acidic and basic conditions. It could be shown that side chain conversion depends on the nucleobase structure. Triisopropylsilyl residues were introduced to protect ethynyl residues from hydration. Pure, acetyl group free oligonucleotides were isolated after desilylation in all cases.
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Affiliation(s)
- Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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24
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Dadová J, Vidláková P, Pohl R, Havran L, Fojta M, Hocek M. Aqueous Heck cross-coupling preparation of acrylate-modified nucleotides and nucleoside triphosphates for polymerase synthesis of acrylate-labeled DNA. J Org Chem 2013; 78:9627-37. [PMID: 23992435 DOI: 10.1021/jo4011574] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aqueous-phase Heck coupling methodology was developed for direct attachment of butyl acrylate to 5-iodoracil, 5-iodocytosine, 7-iodo-7-deazaadenine, and 7-iodo-7-deazaguanine 2'-deoxyribonucleoside 5'-O-monophosphates (dNMPs) and 5'-O-triphosphates (dNTPs) and compared with the classical approach of phosphorylation of the corresponding modified nucleosides. The 7-substituted 7-deazapurine nucleotides (dA(BA)MP, dA(BA)TP, dG(BA)MP, and dG(BA)TP) were prepared by the direct Heck coupling of nucleotides in good yields (35-55%), whereas the pyrimidine nucleotides reacted poorly and the corresponding BA-modified dNTPs were prepared by triphosphorylation of the modified nucleosides. The acrylate-modified dN(BA)TPs (N = A, C, and U) were good substrates for DNA polymerases and were used for enzymatic synthesis of acrylate-modified DNA by primer extension, whereas dG(BA)TP was an inhibitor of polymerases. The butyl acrylate group was found to be a useful redox label giving a strong reduction peak at -1.3 to -1.4 V in cyclic voltammetry.
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Affiliation(s)
- Jitka Dadová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center , Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
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25
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26
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Ménová P, Raindlová V, Hocek M. Scope and limitations of the nicking enzyme amplification reaction for the synthesis of base-modified oligonucleotides and primers for PCR. Bioconjug Chem 2013; 24:1081-93. [PMID: 23682869 DOI: 10.1021/bc400149q] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Enzymatic synthesis of short (10-22 nt) base-modified oligonucleotides (ONs) was developed by nicking enzyme amplification reaction (NEAR) using Vent(exo-) polymerase, Nt.BstNBI nicking endonuclease, and a modified deoxyribonucleoside triphosphate (dNTP) derivative. The scope and limitations of the methodology in terms of different nucleobases, length, sequences, and modifications has been thoroughly studied. The methodology including isolation of the modified ONs was scaled up to nanomolar amounts and the modified ONs were successfully used as primers in primer extension and PCR. Two simple and efficient methods for fluorescent labeling of the PCR products were developed, based either on direct fluorescent labeling of primers or on NEAR synthesis of ethynylated primers, PCR, and final click labeling with fluorescent azides.
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Affiliation(s)
- Petra Ménová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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27
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Synthesis and enzymatic incorporation of photolabile dUTP analogues into DNA and their applications for DNA labeling. Bioorg Med Chem 2013; 21:6205-11. [PMID: 23719284 DOI: 10.1016/j.bmc.2013.04.081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 04/26/2013] [Accepted: 04/30/2013] [Indexed: 11/22/2022]
Abstract
Two novel photolabile nucleotide triphosphate (NTP) analogues were synthesized through Sonogashira coupling and their enzymatic incorporation into DNA was evaluated with three different DNA polymerases (Taq, Vent exo- and T4) by polymerase chain reaction. Both nucleotide triphosphate analogues were recognized by these DNA polymerases as substrates for primer extension. Light irradiation of PCR products removed the photolabile group and released the amino and carboxyl moieties. Further site-specific dual-labeling for oligodeoxynucleotides (ODNs) and random labeling for a long DNA construct with fluorophores were successfully achieved with incorporation of the photolabile amine modified deoxyuridine triphosphate (dUnTP).
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28
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Ménová P, Cahová H, Plucnara M, Havran L, Fojta M, Hocek M. Polymerase synthesis of oligonucleotides containing a single chemically modified nucleobase for site-specific redox labelling. Chem Commun (Camb) 2013; 49:4652-4. [PMID: 23579777 DOI: 10.1039/c3cc41438h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzymatic construction of single-nucleobase redox-labelled oligonucleotides was developed either based on polymerase incorporation of a single modified nucleoside triphosphate (dNTP) followed by primer extension (PEX) with natural dNTPs or based on PEX with a biotinylated one-nucleotide overhang template, magnetoseparation and the second PEX with a full-length template.
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Affiliation(s)
- Petra Ménová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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29
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Hollenstein M. Nucleoside triphosphates--building blocks for the modification of nucleic acids. Molecules 2012; 17:13569-91. [PMID: 23154273 PMCID: PMC6268876 DOI: 10.3390/molecules171113569] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/07/2012] [Accepted: 11/09/2012] [Indexed: 11/16/2022] Open
Abstract
Nucleoside triphosphates are moldable entities that can easily be functionalized at various locations. The enzymatic polymerization of these modified triphosphate analogues represents a versatile platform for the facile and mild generation of (highly) functionalized nucleic acids. Numerous modified triphosphates have been utilized in a broad palette of applications spanning from DNA-tagging and -labeling to the generation of catalytic nucleic acids. This review will focus on the recent progress made in the synthesis of modified nucleoside triphosphates as well as on the understanding of the mechanisms underlying their polymerase acceptance. In addition, the usefulness of chemically altered dNTPs in SELEX and related methods of in vitro selection will be highlighted, with a particular emphasis on the generation of modified DNA enzymes (DNAzymes) and DNA-based aptamers.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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30
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Kasahara Y, Kuwahara M. Artificial specific binders directly recovered from chemically modified nucleic acid libraries. J Nucleic Acids 2012; 2012:156482. [PMID: 23094139 PMCID: PMC3472525 DOI: 10.1155/2012/156482] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 08/19/2012] [Indexed: 11/18/2022] Open
Abstract
Specific binders comprised of nucleic acids, that is, RNA/DNA aptamers, are attractive functional biopolymers owing to their potential broad application in medicine, food hygiene, environmental analysis, and biological research. Despite the large number of reports on selection of natural DNA/RNA aptamers, there are not many examples of direct screening of chemically modified nucleic acid aptamers. This is because of (i) the inferior efficiency and accuracy of polymerase reactions involving transcription/reverse-transcription of modified nucleotides compared with those of natural nucleotides, (ii) technical difficulties and additional time and effort required when using modified nucleic acid libraries, and (iii) ambiguous efficacies of chemical modifications in binding properties until recently; in contrast, the effects of chemical modifications on biostability are well studied using various nucleotide analogs. Although reports on the direct screening of a modified nucleic acid library remain in the minority, chemical modifications would be essential when further functional expansion of nucleic acid aptamers, in particular for medical and biological uses, is considered. This paper focuses on enzymatic production of chemically modified nucleic acids and their application to random screenings. In addition, recent advances and possible future research are also described.
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Affiliation(s)
- Yuuya Kasahara
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu 376-8515, Japan
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31
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Riedl J, Ménová P, Pohl R, Orság P, Fojta M, Hocek M. GFP-like fluorophores as DNA labels for studying DNA-protein interactions. J Org Chem 2012; 77:8287-93. [PMID: 22935023 DOI: 10.1021/jo301684b] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
GFP-like 3,5-difluoro-4-hydroxybenzylideneimidazolinone (FBI) and 3,5-bis(methoxy)-4-hydroxy-benzylideneimidazolinone (MBI) labels were attached to dCTP through a propargyl linker, and the resulting labeled nucleotides (dC(MBI)TP and dC(FBI)TP) were used for a facile enzymatic synthesis of oligonucleotide or DNA probes by polymerase-catalyzed primer extension. The MBI/FBI-labeled DNA probes exerted low fluorescence that was increased 2-3.2 times upon binding of a protein. The concept was demonstrated on sequence-specific binding of p53 to dsDNA and on nonspecific binding of single strand binding protein to an oligonucleotide. The FBI label was also used for a time-resolved experiment monitoring a single-nucleotide incorporation followed by primer extension by Vent(exo-) polymerase.
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Affiliation(s)
- Jan Riedl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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32
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Kore AR, Senthilvelan A, Shanmugasundaram M. Highly chemoselective palladium-catalyzed Sonogashira coupling of 5-iodouridine-5′-triphosphates with propargylamine: a new efficient method for the synthesis of 5-aminopropargyl-uridine-5′-triphosphates. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.04.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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33
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Ménová P, Hocek M. Preparation of short cytosine-modified oligonucleotides by nicking enzyme amplification reaction. Chem Commun (Camb) 2012; 48:6921-3. [PMID: 22644213 DOI: 10.1039/c2cc32930a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A method for enzymatic production of short (10-20 nt) cytosine-modified oligonucleotides was developed by nicking enzyme amplification reaction using Vent(exo-) polymerase, Nt.BstNBI nicking endonuclease and 5-substituted dCTP derivatives. The methodology including isolation was scaled up to nanomolar amounts and was proved to be suitable for production of diverse base-modified short single-stranded oligonucleotides (inaccessible by other enzymatic methods) that are of potential interest as labelled primers or functionalized aptamers.
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Affiliation(s)
- Petra Ménová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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34
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Raindlová V, Pohl R, Klepetářová B, Havran L, Šimková E, Horáková P, Pivoňková H, Fojta M, Hocek M. Synthesis of Hydrazone-Modified Nucleotides and Their Polymerase Incorporation onto DNA for Redox Labeling. Chempluschem 2012. [DOI: 10.1002/cplu.201200056] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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35
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Bergen K, Steck AL, Strütt S, Baccaro A, Welte W, Diederichs K, Marx A. Structures of KlenTaq DNA polymerase caught while incorporating C5-modified pyrimidine and C7-modified 7-deazapurine nucleoside triphosphates. J Am Chem Soc 2012; 134:11840-3. [PMID: 22475415 DOI: 10.1021/ja3017889] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The capability of DNA polymerases to accept chemically modified nucleotides is of paramount importance for many biotechnological applications. Although these analogues are widely used, the structural basis for the acceptance of the unnatural nucleotide surrogates has been only sparsely explored. Here we present in total six crystal structures of modified 2'-deoxynucleoside-5'-O-triphosphates (dNTPs) carrying modifications at the C5 positions of pyrimidines or C7 positions of 7-deazapurines in complex with a DNA polymerase and a primer/template complex. The modified dNTPs are in positions poised for catalysis leading to incorporation. These structural data provide insight into the mechanism of incorporation and acceptance of modified dNTPs. Our results open the door for rational design of modified nucleotides, which should offer great opportunities for future applications.
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Affiliation(s)
- Konrad Bergen
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
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36
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Raindlová V, Pohl R, Hocek M. Synthesis of aldehyde-linked nucleotides and DNA and their bioconjugations with lysine and peptides through reductive amination. Chemistry 2012; 18:4080-7. [PMID: 22337599 DOI: 10.1002/chem.201103270] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Indexed: 11/06/2022]
Abstract
5-(5-Formylthienyl)-, 5-(4-formylphenyl)- and 5-(2-fluoro-5-formylphenyl)cytosine 2'-deoxyribonucleoside mono- (dC(R)MP) and triphosphates (dC(R)TP) were prepared by aqueous Suzuki-Miyaura cross-coupling of 5-iodocytosine nucleotides with the corresponding formylarylboronic acids. The dC(R)TPs were excellent substrates for DNA polymerases and were incorporated into DNA by primer extension or PCR. Reductive aminations of the model dC(R)MPs with lysine or lysine-containing tripeptide were studied and optimized. In aqueous phosphate buffer (pH 6.7) the yields of the reductive aminations with tripeptide III were up to 25 %. Bioconjugation of an aldehyde-containing DNA with a lysine-containing tripeptide was achieved through reductive amination in yields of up to 90 % in aqueous phosphate buffer.
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Affiliation(s)
- Veronika Raindlová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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37
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Santner T, Siegmund V, Marx A, Micura R. The synthesis of 2'-methylseleno adenosine and guanosine 5'-triphosphates. Bioorg Med Chem 2012; 20:2416-8. [PMID: 22364745 PMCID: PMC3334826 DOI: 10.1016/j.bmc.2012.01.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Accepted: 01/26/2012] [Indexed: 11/18/2022]
Abstract
Modified nucleoside triphosphates (NTPs) represent powerful building blocks to generate nucleic acids with novel properties by enzymatic synthesis. We have recently demonstrated the access to 2′-SeCH3-uridine and 2′-SeCH3-cytidine derivatized RNAs for applications in RNA crystallography, using the corresponding nucleoside triphosphates and distinct mutants of T7 RNA polymerase. In the present note, we introduce the chemical synthesis of the novel 2′-methylseleno-2′-deoxyadenosine and -guanosine 5′-triphosphates (2′-SeCH3-ATP and 2′-SeCH3-GTP) that represent further candidates for the enzymatic RNA synthesis with engineered RNA polymerases.
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Affiliation(s)
- Tobias Santner
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, University of Innsbruck, 6020 Innsbruck, Austria
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38
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Riedl J, Pohl R, Ernsting NP, Orság P, Fojta M, Hocek M. Labelling of nucleosides and oligonucleotides by solvatochromic 4-aminophthalimide fluorophore for studying DNA–protein interactions. Chem Sci 2012. [DOI: 10.1039/c2sc20404e] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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39
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Yang S, Herdewijn P. Polymerase-dependent DNA synthesis from phosphoramidate-activated nucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:597-608. [PMID: 21888550 DOI: 10.1080/15257770.2011.598491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Nucleoside triphosphate mimetics, which are substrates for polymerases, can be used in the enzymatic synthesis of nucleic acids. Alternatively, they might also become reversible or irreversible enzyme inhibitors. In order to analyze the effects of 5'-phosphoramidate modification of deoxynucleotide in DNA synthesis, 3-phosphono-L-Ala-dNMP (N = A, T, or G) were evaluated as substrates of HIV-1 RT, Vent (exo(-)), and Therminator polymerase, respectively. The DNA-dependent DNA polymerase activity is significantly higher for Vent exo(-) polymerase than for HIV-1 RT, which is reflected by the capacity of Vent exo(-) polymerase to efficiently synthesize DNA without stalling effects. In addition, Vent (exo(-)) polymerase proved to be more accurate than Therminator polymerase, based on Watson-Crick base-pairing. The optimal yield (88%-97%) of full-length elongation can be obtained in 60 minutes by Vent (exo(-)) polymerase at 0.025 U/μL, with the phosphoramidate analogues as substrates. These data led us to conclude that the optimal pyrophosphate mimetic for the enzyme-catalyzed synthesis of DNA is polymerase dependent.
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Affiliation(s)
- Shiqiong Yang
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
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Balintová J, Pohl R, Horáková P, Vidláková P, Havran L, Fojta M, Hocek M. Anthraquinone as a redox label for DNA: synthesis, enzymatic incorporation, and electrochemistry of anthraquinone-modified nucleosides, nucleotides, and DNA. Chemistry 2011; 17:14063-73. [PMID: 22095665 DOI: 10.1002/chem.201101883] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Indexed: 11/11/2022]
Abstract
Modified 2'-deoxynucleosides and deoxynucleoside triphosphates (dNTPs) bearing anthraquinone (AQ) attached through an acetylene or propargylcarbamoyl linker at the 5-position of pyrimidine (C) or at the 7-position of 7-deazaadenine were prepared by Sonogashira cross-coupling of halogenated dNTPs with 2-ethynylanthraquinone or 2-(2-propynylcarbamoyl)anthraquinone. Polymerase incorporations of the AQ-labeled dNTPs into DNA by primer extension with KOD XL polymerase have been successfully developed. The electrochemical properties of the AQ-labeled nucleosides, nucleotides, and DNA were studied by cyclic and square-wave voltammetry, which show a distinct reversible couple of peaks around -0.4 V that make the AQ a suitable redox label for DNA.
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Affiliation(s)
- Jana Balintová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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41
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Kalachova L, Pohl R, Hocek M. Synthesis of nucleoside mono- and triphosphates bearing oligopyridine ligands, their incorporation into DNA and complexation with transition metals. Org Biomol Chem 2011; 10:49-55. [PMID: 22071986 DOI: 10.1039/c1ob06359f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Modified nucleoside mono- (dA(R)MPs and dC(R)MPs) and triphosphates (dA(R)TPs and dC(R)TPs) bearing bipyridine or terpyridine ligands attached via acetylene linker were prepared by single-step aqueous-phase Sonogashira cross-coupling of 7-iodo-7-deaza-dAMP or -dATP, and 5-iodo-dCMP or -dCTP with the corresponding bipyridine- or terpyridine-linked acetylenes. The modified dN(R)TPs were successfully incorporated into the oligonucleotides by primer extension experiment (PEX) using different DNA polymerases and the PEX products were used for post-synthetic complexation with Fe(2+).
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Affiliation(s)
- Lubica Kalachova
- Institute of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic
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Michalska B, Sobolewski I, Polska K, Zielonka J, Zylicz-Stachula A, Skowron P, Rak J. PCR synthesis of double stranded DNA labeled with 5-bromouridine. A step towards finding a bromonucleoside for clinical trials. J Pharm Biomed Anal 2011; 56:671-7. [PMID: 21840661 DOI: 10.1016/j.jpba.2011.07.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 07/08/2011] [Accepted: 07/22/2011] [Indexed: 11/24/2022]
Abstract
Incorporation of 5-bromouridine (5BrdU) into DNA makes it sensitive to UV and ionizing radiation, which opens up a prospective route for the clinical usage of 5-bromouridine and other halonucleosides. In the present work the polymerase chain reaction (PCR) protocol, which enables a long DNA fragment (resembling DNA synthesized in the cell in the presence of halonucleosides) to be completely substituted with 5BrdU, was optimized. Using HPLC coupled to enzymatic digestion, it was demonstrated that the actual amounts of native nucleosides and 5BrdU correspond very well to those calculated from the sequence of PCR products. The synthesized DNA is photosensitive to photons of 300nm. HPLC analysis demonstrated that the photolysis of labeled PCR products leads to a significant decrease in the 5BrdU signal and the simultaneous occurrence of a uridine peak. Agarose and polyacrylamide gel electrophoresis suggest that single strand breaks and cross-links are formed as a result of UV irradiation. The PCR protocol described in the current paper may be employed for labeling DNA not only with BrdU but also with other halonucleosides.
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Affiliation(s)
- Barbara Michalska
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
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Kielkowski P, Macíčková-Cahová H, Pohl R, Hocek M. Transient and Switchable (Triethylsilyl)ethynyl Protection of DNA against Cleavage by Restriction Endonucleases. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102898] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Kielkowski P, Macíčková-Cahová H, Pohl R, Hocek M. Transient and Switchable (Triethylsilyl)ethynyl Protection of DNA against Cleavage by Restriction Endonucleases. Angew Chem Int Ed Engl 2011; 50:8727-30. [DOI: 10.1002/anie.201102898] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 06/30/2011] [Indexed: 12/13/2022]
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45
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Lam CH, Hipolito CJ, Hollenstein M, Perrin DM. A divalent metal-dependent self-cleaving DNAzyme with a tyrosine side chain. Org Biomol Chem 2011; 9:6949-54. [PMID: 21670811 DOI: 10.1039/c1ob05359k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The enzymatic incorporation of a phenol-modified 2'-deoxyuridine triphosphate gave rise to a modified DNA library that was subsequently used in an in vitro selection for ribophosphodiester-cleaving DNAzymes in the presence of divalent zinc and magnesium cations. After 11 rounds of selection, cloning and sequencing resulted in 14 distinct sequences, the most active of which was Dz11-17PheO. Dz11-17PheO self-cleaved an embedded ribocytidine with an observed rate constant of 0.20 ± 0.02 min(-1) in the presence of 10 mM Mg(2+) and 1 mM Zn(2+) at room temperature. The activity was inhibited at low concentrations of Hg(2+) cations and somewhat higher concentrations of Eu(3+) cations.
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Affiliation(s)
- Curtis H Lam
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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46
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Hocek M, Fojta M. Nucleobase modification as redox DNA labelling for electrochemical detection. Chem Soc Rev 2011; 40:5802-14. [PMID: 21625726 DOI: 10.1039/c1cs15049a] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Basic aspects of DNA electrochemistry with a strong focus on the use of modified nucleobases as redox probes for electrochemical bioanalysis are reviewed. Intrinsic electrochemical properties of nucleobases in combination with artificial redox-active nucleobase modifications are frequently applied in this field. Synthetic approaches (both chemical and enzymatic) to base-modified nucleic acids are briefly summarized and their applications in redox labelling are discussed. Finally, analytical applications including DNA hybridization, primer extension, PCR, SNP typing, DNA damage and DNA-protein interaction analysis are presented (critical review, 91 references).
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Prague, Czech Republic.
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Macíčková-Cahová H, Pohl R, Horáková P, Havran L, Špaček J, Fojta M, Hocek M. Alkylsulfanylphenyl derivatives of cytosine and 7-deazaadenine nucleosides, nucleotides and nucleoside triphosphates: synthesis, polymerase incorporation to DNA and electrochemical study. Chemistry 2011; 17:5833-41. [PMID: 21472803 DOI: 10.1002/chem.201003496] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Indexed: 01/19/2023]
Abstract
Aqueous Suzuki-Miyaura cross-coupling reactions of halogenated nucleosides, nucleotides and nucleoside triphosphates derived from 5-iodocytosine and 7-iodo-7-deazaadenine with methyl-, benzyl- and tritylsufanylphenylboronic acids gave the corresponding alkylsulfanylphenyl derivatives of nucleosides and nucleotides. The modified nucleoside triphosphates were incorporated into DNA by primer extension by using Vent(exo-) polymerase. The electrochemical behaviour of the alkylsulfanylphenyl nucleosides indicated formation of compact layers on the electrode. Modified nucleotides and DNA with incorporated benzyl- or tritylsulfanylphenyl moieties produced signals in [Co(NH(3))(6)](3+) ammonium buffer, attributed to the Brdička catalytic response, depending on the negative potential applied. Repeated constant current chronopotentiometric scans in this medium showed increased Brdička catalytic response, which suggests the deprotection of the alkylsulfanyl derivatives to free thiols under the conditions.
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Affiliation(s)
- Hana Macíčková-Cahová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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Ding P, Wunnicke D, Steinhoff HJ, Seela F. Site-directed spin-labeling of DNA by the azide-alkyne 'click' reaction: nanometer distance measurements on 7-deaza-2'-deoxyadenosine and 2'-deoxyuridine nitroxide conjugates spatially separated or linked to a 'dA-dT' base pair. Chemistry 2011; 16:14385-96. [PMID: 21117098 DOI: 10.1002/chem.201001572] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nucleobase-directed spin-labeling by the azide-alkyne 'click' (CuAAC) reaction has been performed for the first time with oligonucleotides. 7-Deaza-7-ethynyl-2'-deoxyadenosine (1) and 5-ethynyl-2'-deoxyuridine (2) were chosen to incorporate terminal triple bonds into DNA. Oligonucleotides containing 1 or 2 were synthesized on a solid phase and spin labeling with 4-azido-2,2,6,6-tetramethylpiperidine 1-oxyl (4-azido-TEMPO, 3) was performed by post-modification in solution. Two spin labels (3) were incorporated with high efficiency into the DNA duplex at spatially separated positions or into a 'dA-dT' base pair. Modification at the 5-position of the pyrimidine base or at the 7-position of the 7-deazapurine residue gave steric freedom to the spin label in the major groove of duplex DNA. By applying cw and pulse EPR spectroscopy, very accurate distances between spin labels, within the range of 1-2 nm, were measured. The spin-spin distance was 1.8±0.2 nm for DNA duplex 17(dA*(7,10))⋅11 containing two spin labels that are separated by two nucleotides within one individual strand. A distance of 1.4±0.2 nm was found for the spin-labeled 'dA-dT' base pair 15(dA*(7))⋅16(dT*(6)). The 'click' approach has the potential to be applied to all four constituents of DNA, which indicates the universal applicability of the method. New insights into the structural changes of canonical or modified DNA are expected to provide additional information on novel DNA structures, protein interaction, DNA architecture, and synthetic biology.
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Affiliation(s)
- Ping Ding
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
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Kielkowski P, Pohl R, Hocek M. Synthesis of acetylene linked double-nucleobase nucleos(t)ide building blocks and polymerase construction of DNA containing cytosines in the major groove. J Org Chem 2011; 76:3457-62. [PMID: 21425799 DOI: 10.1021/jo200436j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(Cytosin-5-yl)ethynyl derivatives of pyrimidine and 7-deazaadenine 2-deoxyribonucleosides and nucleoside triphosphates (dNTPs) were prepared in one step by the aqueous Sonogashira coupling of unprotected halogenated nucleos(t)ides with 5-ethynylcytosine. The modified dNTPs were good substrates for DNA polymerases suitable for primer extension or PCR construction of DNA bearing acetylene-linked cytosine(s) in the major groove mimicking the flipped-out nucleotide.
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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 nam.2, CZ-16610 Prague 6, Czech Republic
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50
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Macíčková-Cahová H, Pohl R, Hocek M. Cleavage of Functionalized DNA Containing 5-Modified Pyrimidines by Type II Restriction Endonucleases. Chembiochem 2011; 12:431-8. [DOI: 10.1002/cbic.201000644] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Indexed: 12/18/2022]
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