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Recent advances in nucleotide analogue-based techniques for tracking dividing stem cells: An overview. J Biol Chem 2021; 297:101345. [PMID: 34717955 PMCID: PMC8592869 DOI: 10.1016/j.jbc.2021.101345] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 01/14/2023] Open
Abstract
Detection of thymidine analogues after their incorporation into replicating DNA represents a powerful tool for the study of cellular DNA synthesis, progression through the cell cycle, cell proliferation kinetics, chronology of cell division, and cell fate determination. Recent advances in the concurrent detection of multiple such analogues offer new avenues for the investigation of unknown features of these vital cellular processes. Combined with quantitative analysis, temporal discrimination of multiple labels enables elucidation of various aspects of stem cell life cycle in situ, such as division modes, differentiation, maintenance, and elimination. Data obtained from such experiments are critically important for creating descriptive models of tissue histogenesis and renewal in embryonic development and adult life. Despite the wide use of thymidine analogues in stem cell research, there are a number of caveats to consider for obtaining valid and reliable labeling results when marking replicating DNA with nucleotide analogues. Therefore, in this review, we describe critical points regarding dosage, delivery, and detection of nucleotide analogues in the context of single and multiple labeling, outline labeling schemes based on pulse-chase, cumulative and multilabel marking of replicating DNA for revealing stem cell proliferative behaviors, and determining cell cycle parameters, and discuss preconditions and pitfalls in conducting such experiments. The information presented in our review is important for rational design of experiments on tracking dividing stem cells by marking replicating DNA with thymidine analogues.
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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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Krell K, Harijan D, Ganz D, Doll L, Wagenknecht HA. Postsynthetic Modifications of DNA and RNA by Means of Copper-Free Cycloadditions as Bioorthogonal Reactions. Bioconjug Chem 2020; 31:990-1011. [DOI: 10.1021/acs.bioconjchem.0c00072] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katja Krell
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dennis Harijan
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dorothée Ganz
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Larissa Doll
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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Hilko DH, Bornaghi LF, Poulsen SA. Stereoselective Synthesis of Highly Functionalized Arabinosyl Nucleosides through Application of an N-Nitro Protecting Group. J Org Chem 2018; 83:11944-11955. [PMID: 30153729 DOI: 10.1021/acs.joc.8b01834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
2'-Deoxy-2',5-disubstituted arabinosyl uridine derivatives bearing a halogen (Cl, Br or I) at C2' and an ethynyl group at C5 have been synthesized in 6 steps from 2',3',5'-tri- O-acetyl-5-iodo-uridine in overall yields of 61% (compound 3, Cl), 47% (compound 4, Br), and 19% (compound 5, I). Stabilization of a 2'- O-triflyl leaving group intermediate to overcome spontaneous intramolecular 2,2'-anhydro uridine formation was pivotal to the synthesis. Specifically, to favor SN2 reaction with a halogen nucleophile over intramolecular cyclization, the nucleophilicity of O-2 oxygen was reduced by incorporation of an adjacent electron withdrawing nitro substituent at N-3. The introduction of the 3- N-nitro group proceeded rapidly (nitronium trifluoroacetate, 1 min) and in quantitative yield. A one-pot method to remove the 3- N-nitro group by reductive nitration (zinc metal in acetic acid, 5 min) and the silyl protecting groups of the alkyne and 3',5' hydroxyls (fluoride reagent, 16 h) was established as the final synthetic step. This application of the 3- N-nitro protecting group addresses the significant shortfalls of the conventional approach to synthesis of 2' modified nucleosides, wherein condensation of a 2' modified sugar fragment with a pyrimidine base provides poor stereocontrol of N-glycosylation, low yields and incompatibility with 2' iodo sugars.
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Affiliation(s)
- David H Hilko
- Griffith Institute for Drug Discovery , Griffith University , Don Young Road , Nathan, Brisbane , Queensland 4111 , Australia
| | - Laurent F Bornaghi
- Griffith Institute for Drug Discovery , Griffith University , Don Young Road , Nathan, Brisbane , Queensland 4111 , Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery , Griffith University , Don Young Road , Nathan, Brisbane , Queensland 4111 , Australia
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Rieder U, Luedtke NW. Alkene-tetrazine ligation for imaging cellular DNA. Angew Chem Int Ed Engl 2014; 53:9168-72. [PMID: 24981416 DOI: 10.1002/anie.201403580] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Indexed: 01/05/2023]
Abstract
5-Vinyl-2'-deoxyuridine (VdU) is the first reported metabolic probe for cellular DNA synthesis that can be visualized by using an inverse electron demand Diels-Alder reaction with a fluorescent tetrazine. VdU is incorporated by endogenous enzymes into the genomes of replicating cells, where it exhibits reduced genotoxicity compared to 5-ethynyl-2'-deoxyuridine (EdU). The VdU-tetrazine ligation reaction is rapid (k≈0.02 M(-1) s(-1)) and chemically orthogonal to the alkyne-azide "click" reaction of EdU-modified DNA. Alkene-tetrazine ligation reactions provide the first alternative to azide-alkyne click reactions for the bioorthogonal chemical labeling of nucleic acids in cells and facilitate time-resolved, multicolor labeling of DNA synthesis.
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Affiliation(s)
- Ulrike Rieder
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich (Switzerland) http://www.bioorganic-chemistry.com
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Dynamic metabolic labeling of DNA in vivo with arabinosyl nucleosides. Proc Natl Acad Sci U S A 2011; 108:20404-9. [PMID: 22143759 DOI: 10.1073/pnas.1101126108] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Commonly used metabolic labels for DNA, including 5-ethynyl-2'-deoxyuridine (EdU) and BrdU, are toxic antimetabolites that cause DNA instability, necrosis, and cell-cycle arrest. In addition to perturbing biological function, these properties can prevent metabolic labeling studies where subsequent tissue survival is needed. To bypass the metabolic pathways responsible for toxicity, while maintaining the ability to be metabolically incorporated into DNA, we synthesized and evaluated a small family of arabinofuranosyl-ethynyluracil derivatives. Among these, (2'S)-2'-deoxy-2'-fluoro-5-ethynyluridine (F-ara-EdU) exhibited selective DNA labeling, yet had a minimal impact on genome function in diverse tissue types. Metabolic incorporation of F-ara-EdU into DNA was readily detectable using copper(I)-catalyzed azide-alkyne "click" reactions with fluorescent azides. F-ara-EdU is less toxic than both BrdU and EdU, and it can be detected with greater sensitivity in experiments where long-term cell survival and/or deep-tissue imaging are desired. In contrast to previously reported 2'-arabino modified nucleosides and EdU, F-ara-EdU causes little or no cellular arrest or DNA synthesis inhibition. F-ara-EdU is therefore ideally suited for pulse-chase experiments aimed at "birth dating" DNA in vivo. As a demonstration, Zebrafish embryos were microinjected with F-ara-EdU at the one-cell stage and chased by BrdU at 10 h after fertilization. Following 3 d of development, complex patterns of quiescent/senescent cells containing only F-ara-EdU were observed in larvae along the dorsal side of the notochord and epithelia. Arabinosyl nucleoside derivatives therefore provide unique and effective means to introduce bioorthogonal functional groups into DNA for diverse applications in basic research, biotechnology, and drug discovery.
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Časar Z, Bevk D, Svete J, Stanovnik B. Reaction of methyl (2E)-3-dimethylamino-2-(1H-indol-3-yl)-propenoate with ureas: facile entry into the polycyclic meridianin analogues with uracil structural unit. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.05.075] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Majumdar KC, Das TK, Jana M. Regioselective Synthesis of Pyrimidine‐Annulated Spiro Heterocycles by Radical Cyclization. SYNTHETIC COMMUN 2005. [DOI: 10.1081/scc-200065003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Majumdar K, Basu P, Mukhopadhyay P, Sarkar S, Ghosh S, Biswas P. Regioselective synthesis of 1H,3H,6H[2]benzopyrano[4,3-d]pyrimidine-2,4-diones and 12H-benzopyrano[3,2-c][1]benzopyran-5-ones by radical cyclization. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00182-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Regioselective synthesis of pyrimidine annelated heterocycles from 6-(cyclohex-2-enyl)-1,3-dimethyl-5-hydroxyuracil. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00656-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Majumdar KC, Jana NK. Synthesis of Pyrimidine-Annelated Heterocycles: Regioselective Synthesis of 1,3,6-Trialkyl Thieno[3,2-d]-Pyrimidine-2,4-Diones. SYNTHETIC COMMUN 2000. [DOI: 10.1080/00397910008087036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kalman TI, Nie Z, Kamat A. Mechanism-based inactivation of thymidylate synthase by 5-(3-fluoropropyn-1-yl)-2'-deoxyuridine 5'-phosphate. Bioorg Med Chem Lett 2000; 10:391-4. [PMID: 10714507 DOI: 10.1016/s0960-894x(00)00012-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
5-Fluoropropynyl-2'-deoxyuridine 5'-phosphate (3) was designed as a mechanism-based inactivator of thymidylate synthase (TS). The inhibitor was synthesized from 5-iodo-2'-deoxyuridine and propargyl alcohol by palladium-catalyzed coupling, followed by fluorination and selective phosphorylation. Incubation of TS with 3, in the presence or absence of the CH2H4folate cofactor, caused rapid, irreversible inactivation of the enzyme.
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Affiliation(s)
- T I Kalman
- Department of Medicinal Chemistry, State University of New York at Buffalo, 14260, USA
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Majumdar KC, Das U. Studies in Pyrimidine-Annelated Heterocycles1 by Tandem Cyclization: Regioselective Synthesis of [6,6]Pyranopyran by Intramolecular [1,6] Michael Addition. J Org Chem 1998. [DOI: 10.1021/jo972058a] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K. C. Majumdar
- Department of Chemistry, University of Kalyani, Kalyani- 741 235, W. B., India
| | - U. Das
- Department of Chemistry, University of Kalyani, Kalyani- 741 235, W. B., India
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Kundu NG, Dasgupta SK, Chaudhuri LN, Mahanty JS, Spears CP, Shahinian AH. Synthesis and biological activities of [E]-5-(2-acylvinyl)uracils. Eur J Med Chem 1993. [DOI: 10.1016/0223-5234(93)90015-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kundu NG, Dasgupta SK. Synthesis of 5-(acylethynyl)uracils and their corresponding 2′-deoxyribonucleosides through palladium-catalysed reactions. ACTA ACUST UNITED AC 1993. [DOI: 10.1039/p19930002657] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Sani BP, Vaid A, Cory JG, Brockman RW, Elliott RD, Montgomery JA. 5'-Haloacetamido-5'-deoxythymidines: novel inhibitors of thymidylate synthase. BIOCHIMICA ET BIOPHYSICA ACTA 1986; 881:175-84. [PMID: 3955073 DOI: 10.1016/0304-4165(86)90003-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
5'-Bromoacetamido-5'-deoxythymidine (BAT), 5'-iodoacetamido-5'-deoxythymidine (IAT), 5'-chloroacetamido-5'-deoxythymidine (CAT) and [14C]BAT were synthesized and their interactions with thymidylate synthase purified from L1210 cells were investigated. The inhibitory effects of these compounds on thymidylate synthase were in the order BAT greater than IAT greater than CAT, which is in agreement with their cytotoxic effects in L1210 cells. In the presence of substrate during preincubation, the concentration required for 50% inhibition of the enzyme activity by these inhibitors was 4-8-fold higher than it was in the absence of dUMP. The I50 values for BAT were 1 X 10(-5) M and 1.2 X 10(-6) M in the presence and absence, respectively, of dUMP during preincubation. These results were in agreement with the observed inhibition of thymidylate synthase by BAT in intact L1210 cells. A Lineweaver-Burk plot revealed that BAT behaved as a competitive inhibitor. The Km for the enzyme was 9.2 microM, and the Ki determined for competitive inhibition by BAT was 5.4 microM. Formation of a tight, irreversible complex is inferred from the finding that BAT-inactivation of thymidylate synthase was not reversible on prolonged dialysis and that the enzyme-BAT complex was nondissociable by gel filtration through a Sephadex G-25 column or by TSK-125 column chromatography. Incubation of thymidylate synthase with BAT resulted in time-dependent, irreversible loss of enzyme activity by first-order kinetics. The rate constant for inactivation was 0.4 min-1, and the steady-state constant of inactivation, Ki, was estimated to be 6.6 microM. The 5'-haloacetamido-5'-deoxythymidines provide specific inhibitors of thymidylate synthase that may also serve as reagents for studying the enzyme mechanism.
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Abstract
The modified base 5-methylcytidine has been found in the DNA of a number of different eukaryotic cells where it occurs principally in the dinucleotide sequence -CmpG- which is present as a palindrome in double-strand nucleic acid molecules. There is considerable evidence to indicate and suggest that 5-methylcytosine serves as a regulatory signal in eukaryotic gene expression. Replication of DNA containing -CmpG- gives rise to daughter DNA molecules containing new -CpG- dinucleotide sequences in which the cytidine residues are not methylated. Methylation of these residues is carried out by a methylase enzyme using S-adenosyl-L-methionine as a specific methyl group donor. The model discussed in the present communication tries to explain in chemical and biological terms the mechanism of the methylation reaction. The first reactions of the scheme are well known through the work of other investigators. However, we introduce a new concept into our reaction mechanism by postulating the direct involvement of S-adenosyl-L-methionine in the reaction through its covalent attachment to the cytosine ring followed by a specific ring closure and methylation involving transfer of a hydride ion. The model also gives a possible explanation of mechanism of interaction of dimethyl sulphoxide with the enzyme systems of certain eukaryotic cells, which are altered or changed in the regulation of gene expression by this chemical reagent.
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Silverman RB, Hoffman SJ. The organic chemistry of mechanism-based enzyme inhibition: a chemical approach to drug design. Med Res Rev 1984; 4:415-47. [PMID: 6087044 DOI: 10.1002/med.2610040305] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Barr PJ, Robins MJ, Santi DV. Reaction of 5-ethynyl-2'-deoxyuridylate with thiols and thymidylate synthetase. Biochemistry 1983; 22:1696-703. [PMID: 6405782 DOI: 10.1021/bi00276a027] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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