1
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Nagpal A, Tyagi N, Neelakandan PP. BODIPY-fused uracil: synthesis, photophysical properties, and applications. Photochem Photobiol Sci 2024; 23:365-376. [PMID: 38227134 DOI: 10.1007/s43630-023-00524-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024]
Abstract
Fluorescent nucleobase and nucleic acid analogs are important tools in chemical and molecular biology as fluorescent labelling of nucleobases has applications in cellular imaging and anti-tumor activity. Boron-dipyrromethene (BODIPY) dyes exhibiting high brightness and good photostability are extensively used as fluorescent labelling agents and as type II photosensitizers for photodynamic therapy. Thus, the combination of nucleobases and BODIPY to obtain new compounds with both anti-tumor activity and fluorescent imaging functions is the focus of our research. We synthesized two new nucleobase analogs 1 and 2 by fusing the BODIPY core directly with uracil which resulted in favorable photophysical properties and high emission quantum efficiencies particularly in organic solvents. Further, we explored the newly synthesized derivatives, which possessed good singlet oxygen generation efficiencies and bio-compatibility, as potential PDT agents and our results show that they exhibit in vitro anti-tumor activities.
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Affiliation(s)
- Ayushi Nagpal
- Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, 140306, Punjab, India
| | - Nidhi Tyagi
- Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, 140306, Punjab, India
| | - Prakash P Neelakandan
- Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, 140306, Punjab, India.
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2
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Neitz H, Höbartner C. A tolane-modified 5-ethynyluridine as a universal and fluorogenic photochemical DNA crosslinker. Chem Commun (Camb) 2023; 59:12003-12006. [PMID: 37727895 DOI: 10.1039/d3cc03796g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
We report the fluorescent nucleoside ToldU and its application as a photoresponsive crosslinker in three different DNA architectures with enhanced fluorescence emission of the crosslinked products. The fluorogenic ToldU crosslinking reaction enables the assembly of DNA polymers in a hybridization chain reaction for the concentration-dependent detection of a specific DNA sequence.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
- Center for Nanosystems Chemistry (CNC), University of Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
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3
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Serrano JL. Water-Soluble Pd-Imidate Complexes as Versatile Catalysts for the Modification of Unprotected Halonucleosides. CHEM REC 2022; 22:e202200179. [PMID: 36094784 DOI: 10.1002/tcr.202200179] [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: 07/14/2022] [Revised: 08/24/2022] [Indexed: 12/15/2022]
Abstract
Modification of unprotected nucleosides has been attracting continuous interest, since these building blocks themselves and their phosphate-upgraded corresponding nucleotides have shown a plethora of uses in fields like biochemistry or pharmacy. Pd-catalyzed cross-coupling reactions, conducted in water or its mixtures with polar organic solvents, have frequently been the researchers' choice for the functionalization of the purine/pyrimidine base of the unprotected nucleosides. In this scenario, the availability of hydrophilic ligands and its water-soluble palladium complexes has markedly set the pace of the advances. The approach of our group to the synthesis of such complexes, Pd-imidates specifically, has faced critical stages, namely the jump to synthesize water soluble complexes from our experience working in conventional solvents, the preparation of phosphine free complexes and the overall goal of getting catalytic systems able to work close to room temperature. The continuous feedback with Kapdi's group, experienced in the chemistry of nucleosides, has produced over the last decade the interesting results in both fields presented here.
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Affiliation(s)
- José Luis Serrano
- Departamento de Ingeniería Química y Ambiental., Área de Química Inorgánica, Universidad Politécnica de Cartagena member of European University of Technology, 30203, Cartagena, Spain
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4
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Shaughnessy KH. Covalent Modification of Nucleobases using Water-Soluble Palladium Catalysts. CHEM REC 2022; 22:e202200190. [PMID: 36074958 DOI: 10.1002/tcr.202200190] [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: 07/29/2022] [Revised: 08/25/2022] [Indexed: 12/15/2022]
Abstract
Nucleosides represent one of the key building blocks of biochemistry. There is significant interest in the synthesis of nucleoside-derived materials for applications as probes, biochemical models, and pharmaceuticals. Palladium-catalyzed cross-coupling reactions are effective methods for making covalent modification of carbon and nitrogen sites on nucleobases under mild conditions. Water-soluble catalysts derived from palladium and hydrophilic ligands, such as tris(3-sulfonatophenyl)phosphine trisodium (TPPTS), are efficient catalysts for a range of coupling reactions of unprotected halonucleosides. Over the past two decades, these methods have been extended to direct functionalization of halonucleotides, as well as RNA and DNA oligonucleotides (ONs) containing halogenated bases. These methods can be run under biocompatible conditions, including examples of Suzuki coupling of modified DNA in whole cells and tissue samples. In this account, development of this methodology by our group and others is highlighted along with the extension of these catalyst systems to modification of nucleotides and ONs.
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Affiliation(s)
- Kevin H Shaughnessy
- Department of Chemistry & Biochemistry, The University of Alabama, Box 870336, Tuscaloosa, AL 35487-0336, USA
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5
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Schreier VN, Loehr MO, Lattmann E, Luedtke NW. Active Uptake and Trafficking of Nucleoside Triphosphates In Vivo. ACS Chem Biol 2022; 17:1799-1810. [PMID: 35700414 DOI: 10.1021/acschembio.2c00153] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Modified nucleoside triphosphates (NTPs) are powerful probes and medicines, but their anionic character impedes membrane permeability. As such, invasive delivery techniques, transport carriers, or prodrug strategies are required for their in vivo use. Here, we present a fluorescent 2'-deoxyribonucleoside triphosphate "TAMRA-dATP" that exhibits surprisingly high bioavailability in vivo. TAMRA-dATP spontaneously forms nanoparticles in Mg+2-containing buffers that are taken into the vesicles of living cells and animals by energy-dependent processes. In cell cultures, photochemical activation with yellow laser light (561 nm) facilitated endosomal escape of TAMRA-dATP, resulting in its metabolic incorporation into DNA in vitro. In contrast, in vivo studies revealed that TAMRA-dATP is extensively trafficked by active pathways into cellular DNA of zebrafish (Danio rerio) and Caenorhabditis elegans where DNA labeling was observed in live animals, even without photochemical release. Metabolic labeling of DNA in whole, living animals can therefore be achieved by simply soaking animals in a buffer containing TAMRA-dATP or a structurally related compound, Cy3-dATP.
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Affiliation(s)
- Verena N Schreier
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland.,Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Morten O Loehr
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland.,Department of Chemistry, McGill University, Montréal, Quebec H3A 0B8, Canada
| | - Evelyn Lattmann
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Nathan W Luedtke
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland.,Department of Chemistry, McGill University, Montréal, Quebec H3A 0B8, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montréal, Quebec H3G 1Y6, Canada
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6
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Abstract
Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells. Out of the numerous labeling concepts that have been devised, covalent labeling provides the most stable linkage, an unrivaled choice of small and highly fluorescent labels and - thanks to recent advances in click chemistry - an incredible versatility. Depending on the approach, site-, sequence- and cell-specificity can be achieved. DNA and RNA labeling are rapidly developing fields that bring together multiple areas of research: on the one hand, synthetic and biophysical chemists develop new fluorescent labels and isomorphic nucleobases as well as faster and more selective bioorthogonal reactions. On the other hand, the number of enzymes that can be harnessed for post-synthetic and site-specific labeling of nucleic acids has increased significantly. Together with protein engineering and genetic manipulation of cells, intracellular and cell-specific labeling has become possible. In this review, we provide a structured overview of covalent labeling approaches for nucleic acids and highlight notable developments, in particular recent examples. The majority of this review will focus on fluorescent labeling; however, the principles can often be readily applied to other labels. We will start with entirely chemical approaches, followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic acids. Each section is subdivided into direct (or one-step) and two-step labeling approaches and will start with DNA before treating RNA.
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Affiliation(s)
- Nils Klöcker
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, D-48149 Münster, Germany.
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7
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Kuba M, Pohl R, Hocek M. Synthesis of 2′-deoxycytidine and its triphosphate bearing tryptophan-based imidazolinone fluorophore for environment sensitive fluorescent labelling of DNA. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.09.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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8
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Güixens-Gallardo P, Zawada Z, Matyašovský J, Dziuba D, Pohl R, Kraus T, Hocek M. Brightly Fluorescent 2′-Deoxyribonucleoside Triphosphates Bearing Methylated Bodipy Fluorophore for in Cellulo Incorporation to DNA, Imaging, and Flow Cytometry. Bioconjug Chem 2018; 29:3906-3912. [DOI: 10.1021/acs.bioconjchem.8b00721] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Pedro Güixens-Gallardo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 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
| | - Zbigniew Zawada
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 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
| | - Dmytro Dziuba
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 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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9
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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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10
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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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11
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Development of a fluorescent probe for detection of citrulline based on photo-induced electron transfer. Bioorg Med Chem Lett 2018; 28:969-973. [PMID: 29439901 DOI: 10.1016/j.bmcl.2018.01.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/13/2018] [Accepted: 01/16/2018] [Indexed: 01/11/2023]
Abstract
Peptidyl arginine deiminases (PADs) catalyze the post-translational deimination of peptidyl arginine residues to form citrulline residues. Aberrant citrullination of histones by one of the PAD isozymes, PAD4, is associated with various diseases, including rheumatoid arthritis, so high-throughput screening systems are needed to identify PAD4 inhibitors as chemical tools to investigate the role of PAD4, and as candidate therapeutic agents. Here, we utilized the addition-cyclization reaction between phenylglyoxal and citrulline under acidic conditions to design turn-on fluorescent probes for citrulline based on the donor-excited photoinduced electron transfer (d-PeT) mechanism. Among several derivatives of phenylglyoxal bearing a fluorescent moiety, we found that FGME enabled detection of citrulline without a neutralization process, and we used it to establish a simple methodology for turn-on fluorescence detection of citrulline.
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12
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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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13
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Disubstituted cobalt bis(1,2-dicarbollide)(-I) terminal alkynes: Synthesis, reactivity in the Sonogashira reaction and application in the synthesis of cobalt bis(1,2-dicarbollide)(-I) nucleoside conjugates. J Organomet Chem 2017. [DOI: 10.1016/j.jorganchem.2017.02.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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14
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Giner EA, Gómez-Gallego M, Merinero AD, Casarrubios L, Ramírez de Arellano C, Sierra MA. Sequential Reactions of Alkynes on an Iridium(III) Single Site. Chemistry 2017; 23:8941-8948. [PMID: 28440592 DOI: 10.1002/chem.201701100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Indexed: 01/01/2023]
Abstract
Sequential insertion of terminal alkynes on IrIII cyclometalated complexes allow the formation of novel metallapolycycles in a controlled and efficient manner. ortho-Methylarylethynyl derivatives led to an unprecedented cascade combination of three fundamental processes (C-C bond formation, C(sp3 )-H activation, and reductive coupling) on a single IrIII center, in a process compatible with functionalized biomolecules and photoactive substrates. The reaction with tert-butylacetylene led to a [6,5,4]-polycycle that incorporates an iridacyclobutenylidene in its structure. The sequence is a multicomponent reaction in which the metal not only promotes the different steps but also determines their stereoselectivity. This is an elegant example of the synergy between a metal-promoting reaction and a symmetry-defined stereochemistry.
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Affiliation(s)
- Elena A Giner
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040, Madrid, Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA)., Universidad Complutense., 28040, Madrid, Spain
| | - Mar Gómez-Gallego
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040, Madrid, Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA)., Universidad Complutense., 28040, Madrid, Spain
| | - Alba D Merinero
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040, Madrid, Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA)., Universidad Complutense., 28040, Madrid, Spain
| | - Luis Casarrubios
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040, Madrid, Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA)., Universidad Complutense., 28040, Madrid, Spain
| | - Carmen Ramírez de Arellano
- Departamento de Química Orgánica, Facultad de Química, Universidad de Valencia, 46100, Valencia, Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA)., Universidad Complutense., 28040, Madrid, Spain
| | - Miguel A Sierra
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040, Madrid, Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA)., Universidad Complutense., 28040, Madrid, Spain
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15
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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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16
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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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17
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Olszewska A, Pohl R, Brázdová M, Fojta M, Hocek M. Chloroacetamide-Linked Nucleotides and DNA for Cross-Linking with Peptides and Proteins. Bioconjug Chem 2016; 27:2089-94. [PMID: 27479485 DOI: 10.1021/acs.bioconjchem.6b00342] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nucleotides, 2'-deoxyribonucleoside triphosphates (dNTPs), and DNA probes bearing reactive chloroacetamido group linked to nucleobase (cytosine or 7-deazadaenine) through a propargyl tether were prepared and tested in cross-linking with cysteine- or histidine-containing peptides and proteins. The chloroacetamide-modifed dNTPs proved to be good substrates for DNA polymerases in the enzymatic synthesis of modified DNA probes. Modified nucleotides and DNA reacted efficiently with cysteine and cysteine-containing peptides, whereas the reaction with histidine was sluggish and low yielding. The modified DNA efficiently cross-linked with p53 protein through alkylation of cysteine and showed potential for cross-linking with histidine (in C277H mutant of p53).
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Affiliation(s)
- Agata Olszewska
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Marie Brázdová
- Institute of Biophysics, Czech Academy of Sciences , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, Czech Academy of Sciences , Kralovopolska 135, 612 65 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University , Kamenice 753/5, CZ-625 00 Brno, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 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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18
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Wieczorek A, Buckup T, Wombacher R. Rigid tetrazine fluorophore conjugates with fluorogenic properties in the inverse electron demand Diels-Alder reaction. Org Biomol Chem 2016; 12:4177-85. [PMID: 24826902 DOI: 10.1039/c4ob00245h] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
1,2,4,5-Tetrazine fluorophore derivatives with structurally rigid molecular designs were synthesized using Sonogashira and Stille cross-coupling as well as copper-catalyzed azide-alkyne cycloaddition. The synthesized bichromophoric systems exhibit low fluorescence quantum yields due to quenching by the tetrazine. The extent of fluorescence quenching observed for those systems was shown to depend on the distance between the fluorophore and the tetrazine. The decreased fluorescence is "turned on" by conversion of the tetrazine in the inverse electron demand Diels-Alder cycloaddition. Time resolved spectroscopy indicated resonance energy transfer between BODIPY and the tetrazine as the underlying quenching mechanism. The synthesized conjugates were successfully applied in protein labeling experiments.
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Affiliation(s)
- Achim Wieczorek
- Institut für Pharmazie und Molekulare Biotechnologie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
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19
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Hottin A, Marx A. Structural Insights into the Processing of Nucleobase-Modified Nucleotides by DNA Polymerases. Acc Chem Res 2016; 49:418-27. [PMID: 26947566 DOI: 10.1021/acs.accounts.5b00544] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The DNA polymerase-catalyzed incorporation of modified nucleotides is employed in many biological technologies of prime importance, such as next-generation sequencing, nucleic acid-based diagnostics, transcription analysis, and aptamer selection by systematic enrichment of ligands by exponential amplification (SELEX). Recent studies have shown that 2'-deoxynucleoside triphosphates (dNTPs) that are functionalized with modifications at the nucleobase such as dyes, affinity tags, spin and redox labels, or even oligonucleotides are substrates for DNA polymerases, even if modifications of high steric demand are used. The position at which the modification is introduced in the nucleotide has been identified as crucial for retaining substrate activity for DNA polymerases. Modifications are usually attached at the C5 position of pyrimidines and the C7 position of 7-deazapurines. Furthermore, it has been shown that the nature of the modification may impact the efficiency of incorporation of a modified nucleotide into the nascent DNA strand by a DNA polymerase. This Account places functional data obtained in studies of the incorporation of modified nucleotides by DNA polymerases in the context of recently obtained structural data. Crystal structure analysis of a Thermus aquaticus (Taq) DNA polymerase variant (namely, KlenTaq DNA polymerase) in ternary complex with primer-template DNA and several modified nucleotides provided the first structural insights into how nucleobase-modified triphosphates are tolerated. We found that bulky modifications are processed by KlenTaq DNA polymerase as a result of cavities in the protein that enable the modification to extend outside the active site. In addition, we found that the enzyme is able to adapt to different modifications in a flexible manner and adopts different amino acid side-chain conformations at the active site depending on the nature of the nucleotide modification. Different "strategies" (i.e., hydrogen bonding, cation-π interactions) enable the protein to stabilize the respective protein-substrate complex without significantly changing the overall structure of the complex. Interestingly, it was also discovered that a modified nucleotide may be more efficiently processed by KlenTaq DNA polymerase when the 3'-primer terminus is also a modified nucleotide instead of a nonmodified natural one. Indeed, the modifications of two modified nucleotides at adjacent positions can interact with each other (i.e., by π-π interactions) and thereby stabilize the enzyme-substrate complex, resulting in more efficient transformation. Several studies have indicated that archeal DNA polymerases belonging to sequence family B are better suited for the incorporation of nucleobase-modified nucleotides than enzymes from family A. However, significantly less structural data are available for family B DNA polymerases. In order to gain insights into the preference for modified substrates by members of family B, we succeeded in obtaining binary structures of 9°N and KOD DNA polymerases bound to primer-template DNA. We found that the major groove of the archeal family B DNA polymerases is better accessible than in family A DNA polymerases. This might explain the observed superiority of family B DNA polymerases in polymerizing nucleotides that bear bulky modifications located in the major groove, such as modification at C5 of pyrimidines and C7 of 7-deazapurines. Overall, this Account summarizes our recent findings providing structural insight into the mechanism by which modified nucleotides are processed by DNA polymerases. It provides guidelines for the design of modified nucleotides, thus supporting future efforts based on the acceptance of modified nucleotides by DNA polymerases.
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Affiliation(s)
- Audrey Hottin
- Department
of Chemistry and
Konstanz Research School Chemical Biology University of Konstanz Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department
of Chemistry and
Konstanz Research School Chemical Biology University of Konstanz Universitätsstrasse 10, 78457 Konstanz, Germany
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20
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Kuznetsova VE, Spitsyn MA, Shershov VE, Guseinov TO, Fesenko EE, Lapa SA, Ikonnikova AY, Avdonina MA, Nasedkina TV, Zasedatelev AS, Chudinov AV. Novel fluorescently labeled nucleotides: synthesis, spectral properties and application in polymerase chain reaction. MENDELEEV COMMUNICATIONS 2016. [DOI: 10.1016/j.mencom.2016.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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21
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Dadová J, Cahová H, Hocek M. Polymerase Synthesis of Base-Modified DNA. MODIFIED NUCLEIC ACIDS 2016. [DOI: 10.1007/978-3-319-27111-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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22
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Shaughnessy KH. Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides. Molecules 2015; 20:9419-54. [PMID: 26007192 PMCID: PMC6272472 DOI: 10.3390/molecules20059419] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/15/2015] [Accepted: 05/19/2015] [Indexed: 11/30/2022] Open
Abstract
Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.
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Affiliation(s)
- Kevin H Shaughnessy
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, AL 35487-0336, USA.
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23
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Hervé G, Len C. Heck and Sonogashira couplings in aqueous media – application to unprotected nucleosides and nucleotides. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40508-015-0029-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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24
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Valencia M, Martín-Ortiz M, Gómez-Gallego M, Ramírez de Arellano C, Sierra MA. On the use of metal purine derivatives (M=Ir, Rh) for the selective labeling of nucleosides and nucleotides. Chemistry 2015; 20:3831-8. [PMID: 24677547 DOI: 10.1002/chem.201304091] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/11/2013] [Indexed: 12/30/2022]
Abstract
The reactions of neutral or cationic IrIII and RhIII derivatives of phenyl purine nucleobases with unsymmetrical alkynes produce new metallacycles in a predictable manner, which allows for the incorporation of either photoactive (anthracene or pyrene) or electroactive (ferrocene) labels in the nucleotide or nucleoside moiety. The reported methodology (metalation of the purine derivative and subsequent marker insertion) could be used for the postfunctionalization and unambiguous labeling of oligonucleotides.
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25
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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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26
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Dziuba D, Pohl R, Hocek M. Bodipy-labeled nucleoside triphosphates for polymerase synthesis of fluorescent DNA. Bioconjug Chem 2014; 25:1984-95. [PMID: 25290695 DOI: 10.1021/bc5003554] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
New fluorescent nucleosides and nucleoside triphosphate (dNTPs) analogs bearing the F-Bodipy fluorophore linked through a short, flexible nonconjugate tether were synthesized. The Bodipy-labeled dNTPs were substrates for several DNA polymerases which incorporated them into DNA in primer extension, nicking enzyme amplification reaction, and polymerase chain reaction. The fluorescence of F-Bodipy is not quenched upon incorporation in DNA and can be detected both in solutions and on gels.
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Affiliation(s)
- Dmytro Dziuba
- 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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Hocek M. Synthesis of base-modified 2'-deoxyribonucleoside triphosphates and their use in enzymatic synthesis of modified DNA for applications in bioanalysis and chemical biology. J Org Chem 2014; 79:9914-21. [PMID: 25321948 DOI: 10.1021/jo5020799] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The synthesis of 2'-deoxyribonucleoside triphosphates (dNTPs) either by classical triphosphorylation of nucleosides or by aqueous cross-coupling reactions of halogenated dNTPs is discussed. Different enzymatic methods for synthesis of modified oligonucleotides and DNA by polymerase incorporation of modified nucleotides are summarized, and the applications in redox or fluorescent labeling, as well as in bioconjugations and modulation of interactions of DNA with proteins, are outlined.
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Affiliation(s)
- Michal Hocek
- 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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28
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Krause A, Hertl A, Muttach F, Jäschke A. Phosphine-free Stille-Migita chemistry for the mild and orthogonal modification of DNA and RNA. Chemistry 2014; 20:16613-9. [PMID: 25322724 DOI: 10.1002/chem.201404843] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Indexed: 12/31/2022]
Abstract
An optimized catalyst system of [Pd2 (dba)3 ] and AsPh3 efficiently catalyzes the Stille reaction between a diverse set of functionalized stannanes and halogenated mono-, di- and oligonucleotides. The methodology allows for the facile conjugation of short and long nucleic acid molecules with moieties that are not compatible with conventional chemical or enzymatic synthesis, among them acid-, base-, or fluoride-labile protecting groups, fluorogenic and synthetically challenging moieties with good to near-quantitative yields. Notably, even azides can be directly introduced into oligonucleotides and (deoxy)nucleoside triphosphates, thereby giving direct access to "clickable" nucleic acids.
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Affiliation(s)
- André Krause
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg
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29
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Ilinova A, Semioshkin A, Lobanova I, Bregadze VI, Mironov AF, Paradowska E, Studzińska M, Jabłońska A, Białek-Pietras M, Leśnikowski ZJ. Synthesis, cytotoxicity and antiviral activity studies of the conjugates of cobalt bis(1,2-dicarbollide)(-I) with 5-ethynyl-2′-deoxyuridine and its cyclic derivatives. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.06.072] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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30
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Preparation of ferrocene-functionalized gold nanoparticles by primer extension reaction on the particle surface. Bioorg Med Chem Lett 2014; 24:2661-3. [DOI: 10.1016/j.bmcl.2014.04.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/09/2014] [Accepted: 04/16/2014] [Indexed: 11/20/2022]
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31
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Zhang Y, Yue X, Kim B, Yao S, Belfield KD. Deoxyribonucleoside-Modified Squaraines as Near-IR Viscosity Sensors. Chemistry 2014; 20:7249-53. [DOI: 10.1002/chem.201403003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Indexed: 12/18/2022]
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32
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Pesnot T, Tedaldi LM, Jambrina PG, Rosta E, Wagner GK. Exploring the role of the 5-substituent for the intrinsic fluorescence of 5-aryl and 5-heteroaryl uracil nucleotides: a systematic study. Org Biomol Chem 2014; 11:6357-71. [PMID: 23945704 DOI: 10.1039/c3ob40485d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Derivatives of UMP (uridine monophosphate) with a fluorogenic substituent in position 5 represent a small but unique class of fluorophores, which has found important applications in chemical biology and biomolecular chemistry. In this study, we have synthesised a series of derivatives of the uracil nucleotides UMP, UDP and UTP with different aromatic and heteroaromatic substituents in position 5, in order to systematically investigate the influence of the 5-substituent on fluorescence emission. We have determined relevant photophysical parameters for all derivatives in this series, including quantum yields for the best fluorophores. The strongest fluorescence emission was observed with a 5-formylthien-2-yl substituent in position 5 of the uracil base, while the corresponding 3-formylthien-2-yl-substituted regioisomer was significantly less fluorescent. The 5-(5-formylthien-2-yl) uracil fluorophore was studied further in solvents of different polarity and proticity. In conjunction with results from a conformational analysis based on NMR data and computational experiments, these findings provide insights into the steric and electronic factors that govern fluorescence emission in this class of fluorophores. In particular, they highlight the interplay between fluorescence emission and conformation in this series. Finally, we carried out ligand-binding experiments with the 5-(5-formylthien-2-yl) uracil fluorophore and a UDP-sugar-dependent glycosyltransferase, demonstrating its utility for biological applications. The results from our photophysical and biological studies suggest, for the first time, a structural explanation for the fluorescence quenching effect that is observed upon binding of these fluorophores to a target protein.
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Affiliation(s)
- Thomas Pesnot
- School of Pharmacy, University of East Anglia, Norwich, UK
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33
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Kim DR, Kim TS, Kim E, Min SJ, Shin D, Ahn DR. Synthesis of 3'-O-fluorescently mono-modified reversible terminators and their uses in sequencing-by-synthesis. Bioorg Med Chem Lett 2013; 24:209-13. [PMID: 24332495 DOI: 10.1016/j.bmcl.2013.11.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/13/2013] [Accepted: 11/15/2013] [Indexed: 11/18/2022]
Abstract
Next-generation sequencing (NGS) technologies recently developed are now used for study of genomes from various organisms. Sequencing-by-synthesis (SBS) is a key strategy in the NGS. The SBS uses nucleotides so-called dual-modified reversible terminators (DRTs) in which bases are labeled with fluorophores and 3'-OH is protected with a reversibly cleavable chemical group, respectively. In this study, we examined the possibility of performing SBS with mono-modified reversible terminators (MRTs), in which the reversible blocking group on the 3'-OH plays a dual role as a fluorescent signal report as well as a chemical protection. We studied cyclic reversible termination by using two MRTs (dA and dT), wherein the modifications were two different fluorophores and cleavable to regenerate a free 3'-OH. We here demonstrated that SBS could be achieved with incorporation of MRTs by a DNA polymerase and correct base-calls based on the two different colors from the fluorophores.
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Affiliation(s)
- Da-Rae Kim
- Center for Theragnosis, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Taek-Soo Kim
- College of Pharmacy, Gachon University, 191 Hambakmoero, Yoensu-Gu, Incheon, Republic of Korea
| | - Eunsun Kim
- Center for Neuro-medicine, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Sun-Joon Min
- Center for Neuro-medicine, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, University of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Dongyun Shin
- College of Pharmacy, Gachon University, 191 Hambakmoero, Yoensu-Gu, Incheon, Republic of Korea.
| | - Dae-Ro Ahn
- Center for Theragnosis, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, University of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea.
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34
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Obeid S, Bußkamp H, Welte W, Diederichs K, Marx A. Snapshot of a DNA polymerase while incorporating two consecutive C5-modified nucleotides. J Am Chem Soc 2013; 135:15667-9. [PMID: 24090271 DOI: 10.1021/ja405346s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Functional nucleotides are important in many cutting-edge biomolecular techniques. Often several modified nucleotides have to be incorporated consecutively. This structural study of KlenTaq DNA polymerase, a truncated form of Thermus aquaticus DNA polymerase, gives first insights how multiple modifications are processed by a DNA polymerase and, therefore, contribute to the understanding of these enzymes in their interplay with artificial substrates.
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Affiliation(s)
- Samra Obeid
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz , Universitätsstrasse 10, 78457 Konstanz, Germany
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35
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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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36
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Semioshkin A, Ilinova A, Lobanova I, Bregadze V, Paradowska E, Studzińska M, Jabłońska A, Lesnikowski ZJ. Synthesis of the first conjugates of 5-ethynyl-2′-deoxyuridine with closo-dodecaborate and cobalt-bis-dicarbollide boron clusters. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.06.100] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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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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38
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Bailey CM, Sullivan TJ, Iyidogan P, Tirado-Rives J, Chung R, Ruiz-Caro J, Mohamed E, Jorgensen WL, Jorgensen W, Hunter R, Anderson KS. Bifunctional inhibition of human immunodeficiency virus type 1 reverse transcriptase: mechanism and proof-of-concept as a novel therapeutic design strategy. J Med Chem 2013; 56:3959-68. [PMID: 23659183 DOI: 10.1021/jm400160s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is a major target for currently approved anti-HIV drugs. These drugs are divided into two classes: nucleoside and non-nucleoside reverse transcriptase inhibitors (NRTIs and NNRTIs). This study illustrates the synthesis and biochemical evaluation of a novel bifunctional RT inhibitor utilizing d4T (NRTI) and a TMC-derivative (a diarylpyrimidine NNRTI) linked via a poly(ethylene glycol) (PEG) linker. HIV-1 RT successfully incorporates the triphosphate of d4T-4PEG-TMC bifunctional inhibitor in a base-specific manner. Moreover, this inhibitor demonstrates low nanomolar potency that has 4.3-fold and 4300-fold enhancement of polymerization inhibition in vitro relative to the parent TMC-derivative and d4T, respectively. This study serves as a proof-of-concept for the development and optimization of bifunctional RT inhibitors as potent inhibitors of HIV-1 viral replication.
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Affiliation(s)
- Christopher M Bailey
- Department of Pharmacology, School of Medicine, Yale University, New Haven, Connecticut 06520, USA
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39
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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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40
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Fresneau N, Hiebel MA, Agrofoglio LA, Berteina-Raboin S. Efficient synthesis of unprotected C-5-aryl/heteroaryl-2'-deoxyuridine via a Suzuki-Miyaura reaction in aqueous media. Molecules 2012; 17:14409-17. [PMID: 23519242 PMCID: PMC6268622 DOI: 10.3390/molecules171214409] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/20/2012] [Accepted: 11/23/2012] [Indexed: 12/22/2022] Open
Abstract
Following our previous results on an environmentally benign one-pot Sonogashira-cyclization protocol to obtain substituted furopyrimidine nucleosides under aqueous conditions, we investigate herein the Suzuki-Miyaura cross-coupling reactions of aryl and heteroaryl derivatives at the C5 position of unprotected 2'-deoxyuridine in the same media with a common catalyst system avoiding exotic ligands, since palladium acetate and triphenylphosphine afforded the expected products in moderate to good yields.
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Affiliation(s)
| | | | | | - Sabine Berteina-Raboin
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-2-3849-4856; Fax: +33-2-3841-7281
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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: 129] [Impact Index Per Article: 10.8] [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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42
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Hollenstein M. Synthesis of deoxynucleoside triphosphates that include proline, urea, or sulfonamide groups and their polymerase incorporation into DNA. Chemistry 2012; 18:13320-30. [PMID: 22996052 DOI: 10.1002/chem.201201662] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/21/2012] [Indexed: 01/02/2023]
Abstract
To expand the chemical array available for DNA sequences in the context of in vitro selection, I present herein the synthesis of five nucleoside triphosphate analogues containing side chains capable of organocatalysis. The synthesis involved the coupling of L-proline-containing residues (dU(tP)TP and dU(cP)TP), a dipeptide (dU(FP)TP), a urea derivative (dU(Bpu)TP), and a sulfamide residue (dU(Bs)TP) to a suitably protected common intermediate, followed by triphosphorylation. These modified dNTPs were shown to be excellent substrates for the Vent (exo(-)) and Pwo DNA polymerases, as well as the Klenow fragment of E. coli DNA polymerase I, although they were only acceptable substrates for the 9°N(m) polymerase. All of the modified dNTPs, with the exception of dU(Bpu)TP, were readily incorporated into DNA by the polymerase chain reaction (PCR). Modified oligonucleotides efficiently served as templates for PCR for the regeneration of unmodified DNA. Thermal denaturation experiments showed that these modifications are tolerated in the major groove. Overall, these heavily modified dNTPs are excellent candidates for SELEX.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry & Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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43
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Obeid S, Busskamp H, Welte W, Diederichs K, Marx A. Interactions of non-polar and "Click-able" nucleotides in the confines of a DNA polymerase active site. Chem Commun (Camb) 2012; 48:8320-2. [PMID: 22766607 DOI: 10.1039/c2cc34181f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modified nucleotides play a paramount role in many cutting-edge biomolecular techniques. The present structural study highlights the plasticity and flexibility of the active site of a DNA polymerase while incorporating non-polar "Click-able" nucleotide analogs and emphasizes new insights into rational design guidelines for modified nucleotides.
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Affiliation(s)
- Samra Obeid
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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44
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Cho JH, Shaughnessy KH. Aqueous‐Phase Sonogashira Alkynylation to Synthesize 5‐Substituted Pyrimidine and 8‐Substituted Purine Nucleosides. ACTA ACUST UNITED AC 2012; Chapter 1:Unit1.27. [DOI: 10.1002/0471142700.nc0127s49] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Joon Hyung Cho
- Department of Chemistry, The University of Alabama Tuscaloosa Alabama
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45
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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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46
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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47
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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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48
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Riedl J, Pohl R, Rulíšek L, Hocek M. Synthesis and photophysical properties of biaryl-substituted nucleos(t)ides. Polymerase synthesis of DNA probes bearing solvatochromic and pH-sensitive dual fluorescent and 19F NMR labels. J Org Chem 2011; 77:1026-44. [PMID: 22148188 DOI: 10.1021/jo202321g] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The design of four new fluorinated biaryl fluorescent labels and their attachment to nucleosides and nucleoside triphosphates (dNTPs) by the aqueous cross-coupling reactions of biarylboronates is reported. The modified dNTPs were good substrates for KOD XL polymerase and were enzymatically incorporated into DNA probes. The photophysical properties of the biaryl-modified nucleosides, dNTPs, and DNA were studied systematically. The different substitution pattern of the biaryls was used for tuning of emission maxima in the broad range of 366-565 nm. Using methods of computational chemistry the emission maxima were reproduced with a satisfactory degree of accuracy, and it was shown that the large solvatochromic shifts observed for the studied probes are proportional to the differences in dipole moments of the ground (S(0)) and excited (S(1)) states that add on top of smaller shifts predicted already for these systems in vacuo. Thus, we present a set of compounds that may serve as multipurpose base-discriminating fluorophores for sensing of hairpins, deletions, and mismatches by the change of emission maxima and intensities of fluorescence and that can be also conviently studied by (19)F NMR spectroscopy. In addition, aminobenzoxazolyl-fluorophenyl-labeled nucleotides and DNA also exert dual pH-sensitive and solvatochromic fluorescence, which may imply diverse applications.
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Affiliation(s)
- Jan Riedl
- 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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49
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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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50
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Tanpure AA, Srivatsan SG. A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site. Chemistry 2011; 17:12820-7. [PMID: 21956450 DOI: 10.1002/chem.201101194] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/18/2011] [Indexed: 11/10/2022]
Abstract
Base-modified fluorescent ribonucleoside-analogue probes are valuable tools in monitoring RNA structure and function because they closely resemble the structure of natural nucleobases. Especially, 2-aminopurine, a highly environment-sensitive adenosine analogue, is the most extensively utilized fluorescent nucleoside analogue. However, only a few isosteric pyrimidine ribonucleoside analogues that are suitable for probing the structure and recognition properties of RNA molecules are available. Herein, we describe the synthesis and photophysical characterization of a small series of base-modified pyrimidine ribonucleoside analogues derived from tagging indole, N-methylindole, and benzofuran onto the 5-position of uracil. One of the analogues, based on a 5-(benzofuran-2-yl)pyrimidine core, shows emission in the visible region with a reasonable quantum yield and, importantly, displays excellent solvatochromism. The corresponding triphosphate substrate is effectively incorporated into oligoribonucleotides by T7 RNA polymerase to produce fluorescent oligoribonucleotide constructs. Steady-state and time-resolved spectroscopic studies with fluorescent oligoribonucleotide constructs demonstrate that the fluorescent ribonucleoside photophysically responds to subtle changes in its environment brought about by the interaction of the chromophore with neighboring bases. In particular, the emissive ribonucleoside, if incorporated into an oligoribonucleotide, positively reports the presence of a DNA abasic site with an appreciable enhancement in fluorescence intensity. The straightforward synthesis, amicability to enzymatic incorporation, and sensitivity to changes in the microenvironment highlight the potential of the benzofuran-conjugated pyrimidine ribonucleoside as an efficient fluorescent probe to investigate nucleic acid structure, dynamics, and recognition events.
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Affiliation(s)
- Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pashan, Pune, India
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