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Kladova OA, Iakovlev DA, Groisman R, Ishchenko AA, Saparbaev MK, Fedorova OS, Kuznetsov NA. An Assay for the Activity of Base Excision Repair Enzymes in Cellular Extracts Using Fluorescent DNA Probes. BIOCHEMISTRY (MOSCOW) 2021; 85:480-489. [PMID: 32569555 DOI: 10.1134/s0006297920040082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Damaged DNA bases are removed by the base excision repair (BER) mechanism. This enzymatic process begins with the action of one of DNA glycosylases, which recognize damaged DNA bases and remove them by hydrolyzing N-glycosidic bonds with the formation of apurinic/apyrimidinic (AP) sites. Apurinic/apyrimidinic endonuclease 1 (APE1) hydrolyzes the phosphodiester bond on the 5'-side of the AP site with generation of the single-strand DNA break. A decrease in the functional activity of BER enzymes is associated with the increased risk of cardiovascular, neurodegenerative, and oncological diseases. In this work, we developed a fluorescence method for measuring the activity of key human DNA glycosylases and AP endonuclease in cell extracts. The efficacy of fluorescent DNA probes was tested using purified enzymes; the most efficient probes were tested in the enzymatic activity assays in the extracts of A549, MCF7, HeLa, WT-7, HEK293T, and HKC8 cells. The activity of enzymes responsible for the repair of AP sites and removal of uracil and 5,6-dihydrouracil residues was higher in cancer cell lines as compared to the normal HKC8 human kidney cell line.
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Affiliation(s)
- O A Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - D A Iakovlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - R Groisman
- Groupe "Réparation de l'AND", Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Université Paris-Sud, Université Paris-Saclay, Villejuif, F-94805, France.,Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - A A Ishchenko
- Groupe "Réparation de l'AND", Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Université Paris-Sud, Université Paris-Saclay, Villejuif, F-94805, France.,Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - M K Saparbaev
- Groupe "Réparation de l'AND", Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Université Paris-Sud, Université Paris-Saclay, Villejuif, F-94805, France.,Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - O S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - N A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia
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Zakharenko AL, Lebedeva NA, Lavrik OI. DNA Repair Enzymes as Promising Targets in Oncotherapy. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162017060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ramdzan ZM, Pal R, Kaur S, Leduy L, Bérubé G, Davoudi S, Vadnais C, Nepveu A. The function of CUX1 in oxidative DNA damage repair is needed to prevent premature senescence of mouse embryo fibroblasts. Oncotarget 2016; 6:3613-26. [PMID: 25682875 PMCID: PMC4414141 DOI: 10.18632/oncotarget.2919] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/11/2014] [Indexed: 12/19/2022] Open
Abstract
Despite having long telomeres, mouse embryo fibroblasts (MEFs) senesce more rapidly than human diploid fibroblasts because of the accumulation of oxidative DNA damage. The CUX1 homeodomain protein was recently found to prevent senescence in RAS-driven cancer cells that produce elevated levels of reactive-oxygen species. Here we show that Cux1-/- MEFs are unable to proliferate in atmospheric (20%) oxygen although they can proliferate normally in physiological (3%) oxygen levels. CUX1 contains three domains called Cut repeats. Structure/function analysis established that a single Cut repeat domain can stimulate the DNA binding, Schiff-base formation, glycosylase and AP-lyase activities of 8-oxoguanine DNA glycosylase 1, OGG1. Strikingly and in contrast to previous reports, OGG1 exhibits efficient AP-lyase activity in the presence of a Cut repeat. Repair of oxidative DNA damage and proliferation in 20% oxygen were both rescued in Cux1-/- MEFs by ectopic expression of CUX1 or of a recombinant Cut repeat protein that stimulates OGG1 but is devoid of transcription activation potential. These findings reinforce the causal link between oxidative DNA damage and cellular senescence and suggest that the role of CUX1 as an accessory factor in DNA repair will be critical in physiological situations that generate higher levels of reactive oxygen species.
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Affiliation(s)
- Zubaidah M Ramdzan
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Ranjana Pal
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Biological Sciences, Presidency University, Kolkata 700073, India
| | - Simran Kaur
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Ginette Bérubé
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Sayeh Davoudi
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Charles Vadnais
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Alain Nepveu
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Oncology, McGill University, Montreal, Quebec H3A 1A3, Canada
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Lebedeva NA, Anarbaev RO, Kupryushkin MS, Rechkunova NI, Pyshnyi DV, Stetsenko DA, Lavrik OI. Design of a New Fluorescent Oligonucleotide-Based Assay for a Highly Specific Real-Time Detection of Apurinic/Apyrimidinic Site Cleavage by Tyrosyl-DNA Phosphodiesterase 1. Bioconjug Chem 2015; 26:2046-53. [PMID: 26335988 DOI: 10.1021/acs.bioconjchem.5b00451] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) promotes catalytic scission of a phosphodiester bond between the 3'-end of DNA and the hydroxyl group of a tyrosine residue, as well as cleaving off a variety of other 3'-terminal phosphate-linked DNA substituents. We have shown recently that Tdp1 can initiate an apurinic/apyrimidinic (AP) site repair pathway that is independent from the one mediated by AP endonuclease 1 (APE1). Until recently, there was no method available of tracking the AP-site cleaving activity of Tdp1 by real-time fluorescence assay. In the present study we demonstrate a highly specific real-time detection of the AP-site cleaving activity of Tdp1 which allows one to distinguish it from the activity of APE1 by using a short hairpin oligonucleotide with a 1,12-dodecanediol loop, a 5'-fluorophore, and a 3'-quencher. Specific phosphodiesterase activity of Tdp1, which is usually able to remove quencher from the 3'-end of DNA, was suppressed in our approach by introducing a noncleavable phosphate group mimic between the 3'-end and the quencher. As a nondigestible 3'-phosphate analogue, we have used a new uncharged tetramethyl phosphoryl guanidine (Tmg) group, which is resistant to 3'-phosphodiesterase cleavage.
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Affiliation(s)
- Natalia A Lebedeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University , 2 Pirogov Street, Novosibirsk 630090, Russia
| | - Rashid O Anarbaev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University , 2 Pirogov Street, Novosibirsk 630090, Russia
| | - Maxim S Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Nadejda I Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University , 2 Pirogov Street, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University , 2 Pirogov Street, Novosibirsk 630090, Russia
| | - Dmitry A Stetsenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University , 2 Pirogov Street, Novosibirsk 630090, Russia
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Fluorogenic DNA ligase and base excision repair enzyme assays using substrates labeled with single fluorophores. Anal Biochem 2015; 477:69-77. [PMID: 25728944 DOI: 10.1016/j.ab.2015.02.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/19/2015] [Indexed: 01/27/2023]
Abstract
Continuing our work on fluorogenic substrates labeled with single fluorophores for nucleic acid modifying enzymes, here we describe the development of such substrates for DNA ligases and some base excision repair enzymes. These substrates are hairpin-type synthetic DNA molecules with a single fluorophore located on a base close to the 3' ends, an arrangement that results in strong fluorescence quenching. When such substrates are subjected to an enzymatic reaction, the position of the dyes relative to that end of the molecules is altered, resulting in significant fluorescence intensity changes. The ligase substrates described here were 5' phosphorylated and either blunt-ended or carrying short, self-complementary single-stranded 5' extensions. The ligation reactions resulted in the covalent joining of the ends of the molecules, decreasing the quenching effect of the terminal bases on the dyes. To generate fluorogenic substrates for the base excision repair enzymes formamido-pyrimidine-DNA glycosylase (FPG), human 8-oxo-G DNA glycosylase/AP lyase (hOGG1), endonuclease IV (EndoIV), and apurinic/apyrimidinic endonuclease (APE1), we introduced abasic sites or a modified nucleotide, 8-oxo-dG, at such positions that their enzymatic excision would result in the release of a short fluorescent fragment. This was also accompanied by strong fluorescence increases. Overall fluorescence changes ranged from approximately 4-fold (ligase reactions) to more than 20-fold (base excision repair reactions).
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Walker S, Meisenberg C, Bibby RA, Askwith T, Williams G, Rininsland FH, Pearl LH, Oliver AW, El-Khamisy S, Ward S, Atack JR. Development of an oligonucleotide-based fluorescence assay for the identification of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors. Anal Biochem 2014; 454:17-22. [PMID: 24637157 PMCID: PMC4007590 DOI: 10.1016/j.ab.2014.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 02/03/2014] [Accepted: 03/06/2014] [Indexed: 01/17/2023]
Abstract
Topoisomerase 1 (TOP1) generates transient nicks in the DNA to relieve torsional stress encountered during the cellular processes of transcription, replication, and recombination. At the site of the nick there is a covalent linkage of TOP1 with DNA via a tyrosine residue. This reversible TOP1-cleavage complex intermediate can become trapped on DNA by TOP1 poisons such as camptothecin, or by collision with replication or transcription machinery, thereby causing protein-linked DNA single- or double-strand breaks and resulting in cell death. Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a key enzyme involved in the repair of TOP1-associated DNA breaks via hydrolysis of 3'-phosphotyrosine bonds. Inhibition of TDP1 is therefore an attractive strategy for targeting cancer cells in conjunction with TOP1 poisons. Existing methods for monitoring the phosphodiesterase activity of TDP1 are generally gel based or of high cost. Here we report a novel, oligonucleotide-based fluorescence assay that is robust, sensitive, and suitable for high-throughput screening of both fragment and small compound libraries for the detection of TDP1 inhibitors. We further validated the assay using whole cell extracts, extending its potential application to determine of TDP1 activity in clinical samples from patients undergoing chemotherapy.
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Affiliation(s)
- Sarah Walker
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Cornelia Meisenberg
- Wellcome Trust DNA Repair Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Rachel A Bibby
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Science Park Road, Brighton BN1 9RQ, UK
| | - Trevor Askwith
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Gareth Williams
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | | | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Science Park Road, Brighton BN1 9RQ, UK
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Science Park Road, Brighton BN1 9RQ, UK
| | - Sherif El-Khamisy
- Wellcome Trust DNA Repair Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK; Mammalian Genome Stability Group, Kreb's Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
| | - Simon Ward
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK.
| | - John R Atack
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK.
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Raoof A, Depledge P, Hamilton NM, Hamilton NS, Hitchin JR, Hopkins GV, Jordan AM, Maguire LA, McGonagle AE, Mould DP, Rushbrooke M, Small HF, Smith KM, Thomson GJ, Turlais F, Waddell ID, Waszkowycz B, Watson AJ, Ogilvie DJ. Toxoflavins and deazaflavins as the first reported selective small molecule inhibitors of tyrosyl-DNA phosphodiesterase II. J Med Chem 2013; 56:6352-70. [PMID: 23859074 DOI: 10.1021/jm400568p] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently discovered enzyme tyrosyl-DNA phosphodiesterase 2 (TDP2) has been implicated in the topoisomerase-mediated repair of DNA damage. In the clinical setting, it has been hypothesized that TDP2 may mediate drug resistance to topoisomerase II (topo II) inhibition by etoposide. Therefore, selective pharmacological inhibition of TDP2 is proposed as a novel approach to overcome intrinsic or acquired resistance to topo II-targeted drug therapy. Following a high-throughput screening (HTS) campaign, toxoflavins and deazaflavins were identified as the first reported sub-micromolar and selective inhibitors of this enzyme. Toxoflavin derivatives appeared to exhibit a clear structure-activity relationship (SAR) for TDP2 enzymatic inhibition. However, we observed a key redox liability of this series, and this, alongside early in vitro drug metabolism and pharmacokinetics (DMPK) issues, precluded further exploration. The deazaflavins were developed from a singleton HTS hit. This series showed distinct SAR and did not display redox activity; however low cell permeability proved to be a challenge.
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Affiliation(s)
- Ali Raoof
- Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Manchester M20 4BX, U.K.
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