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Popov AA, Shamanin VA, Petruseva IO, Evdokimov AN, Lavrik OI. Use of qPCR to Evaluate Efficiency of the Bulky DNA Damage Removal in Extracts of Mammalian Cells with Different Maximum Lifespan. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:1183-1191. [PMID: 39218017 DOI: 10.1134/s0006297924070022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 09/04/2024]
Abstract
Proteins of nucleotide excision repair system (NER) are responsible for detecting and removing a wide range of bulky DNA damages, thereby contributing significantly to the genome stability maintenance within mammalian cells. Evaluation of NER functional status in the cells is important for identifying pathological changes in the body and assessing effectiveness of chemotherapy. The following method, described herein, has been developed for better assessment of bulky DNA damages removal in vitro, based on qPCR. Using the developed method, NER activity was compared for the extracts of the cells from two mammals with different lifespans: a long-lived naked mole-rat (Heterocephalus glaber) and a short-lived mouse (Mus musculus). Proteins of the H. glaber cell extract have been shown to be 1.5 times more effective at removing bulky damage from the model DNA substrate than the proteins of the M. musculus cell extract. These results are consistent with the experimental data previously obtained. The presented method could be applied not only in fundamental studies of DNA repair in mammalian cells, but also in clinical practice.
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Affiliation(s)
- Aleksei A Popov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | | | - Irina O Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Aleksei N Evdokimov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk National Research State University, Novosibirsk, 630090, Russia
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Popov AA, Petruseva IO, Naumenko NV, Lavrik OI. Methods for Assessment of Nucleotide Excision Repair Efficiency. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1844-1856. [PMID: 38105203 DOI: 10.1134/s0006297923110147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 12/19/2023]
Abstract
Nucleotide excision repair (NER) is responsible for removing a wide variety of bulky adducts from DNA, thus contributing to the maintenance of genome stability. The efficiency with which proteins of the NER system recognize and remove bulky adducts depends on many factors and is of great clinical and diagnostic significance. The review examines current concepts of the NER system molecular basis in eukaryotic cells and analyzes methods for the assessment of the NER-mediated DNA repair efficiency both in vitro and ex vivo.
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Affiliation(s)
- Aleksei A Popov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Irina O Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Natalya V Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk National Research State University, Novosibirsk, 630090, Russia
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Popov AA, Orishchenko KE, Naumenko KN, Evdokimov AN, Petruseva IO, Lavrik OI. A Method for Assessing the Efficiency of the Nucleotide Excision Repair System Ex Vivo. Acta Naturae 2021; 13:122-125. [PMID: 34707905 PMCID: PMC8526188 DOI: 10.32607/actanaturae.11430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/23/2021] [Indexed: 11/20/2022] Open
Abstract
The nucleotide excision repair (NER) is one of the main repair systems present in the cells of living organisms. It is responsible for the removal of a wide range of bulky DNA lesions. We succeeded in developing a method for assessing the efficiency of NER in the cell (ex vivo), which is a method based on the recovery of TagRFP fluorescent protein production through repair of the damage that blocks the expression of the appropriate gene. Our constructed plasmids containing bulky nFlu or nAnt lesions near the tagrfp gene promoter were shown to undergo repair in eukaryotic cells (HEK 293T) and that they can be used to analyze the efficiency of NER ex vivo. A comparative analysis of the time dependence of fluorescent cells accumulation after transfection with nFlu- and nAnt-DNA revealed that there are differences in how efficient their repair by the NER system of HEK 293T cells can be. The method can be used to assess the cell repair status and the repair efficiency of different structural damages.
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Affiliation(s)
- A. A. Popov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090 Russia
| | - K. E. Orishchenko
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090 Russia
- Novosibirsk National Research State University, Novosibirsk, 630090 Russia
| | - K. N. Naumenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090 Russia
| | - A. N. Evdokimov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090 Russia
| | - I. O. Petruseva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090 Russia
| | - O. I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090 Russia
- Novosibirsk National Research State University, Novosibirsk, 630090 Russia
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Petruseva I, Naumenko N, Kuper J, Anarbaev R, Kappenberger J, Kisker C, Lavrik O. The Interaction Efficiency of XPD-p44 With Bulky DNA Damages Depends on the Structure of the Damage. Front Cell Dev Biol 2021; 9:617160. [PMID: 33777931 PMCID: PMC7991749 DOI: 10.3389/fcell.2021.617160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/22/2021] [Indexed: 11/28/2022] Open
Abstract
The successful elimination of bulky DNA damages via the nucleotide excision repair (NER) system is largely determined by the damage recognition step. This step consists of primary recognition and verification of the damage. The TFIIH helicase XPD plays a key role in the verification step during NER. To date, the mechanism of damage verification is not sufficiently understood and requires further detailed research. This study is a systematic investigation of the interaction of ctXPD (Chaetomium thermophilum) as well as ctXPD-ctp44 with model DNAs, which contain structurally different bulky lesions with previously estimated NER repair efficiencies. We have used ATPase and DNA binding studies to assess the interaction of ctXPD with damaged DNA. The result of the analysis of ctXPD-ctp44 binding to DNA containing fluorescent and photoactivatable lesions demonstrates the relationship between the affinity of XPD for DNAs containing bulky damages and the ability of the NER system to eliminate the damage. Photo-cross-linking of ctXPD with DNA probes containing repairable and unrepairable photoactivatable damages reveals differences in the DNA interaction efficiency in the presence and absence of ctp44. In general, the results obtained indicate the ability of ctXPD-ctp44 to interact with a damage and suggest a significant role for ctp44 subunit in the verification process.
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Affiliation(s)
- Irina Petruseva
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Natalia Naumenko
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Jochen Kuper
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg, Germany
| | - Rashid Anarbaev
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Jeannette Kappenberger
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg, Germany
| | - Olga Lavrik
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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Abrosimova LA, Migur AY, Kubareva EA, Zatsepin TS, Gavshina AV, Yunusova AK, Perevyazova TA, Pingoud A, Oretskaya TS. A study on endonuclease BspD6I and its stimulus-responsive switching by modified oligonucleotides. PLoS One 2018; 13:e0207302. [PMID: 30475809 PMCID: PMC6261011 DOI: 10.1371/journal.pone.0207302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/28/2018] [Indexed: 11/18/2022] Open
Abstract
Nicking endonucleases (NEases) selectively cleave single DNA strands in double-stranded DNAs at a specific site. They are widely used in bioanalytical applications and in genome editing; however, the peculiarities of DNA-protein interactions for most of them are still poorly studied. Previously, it has been shown that the large subunit of heterodimeric restriction endonuclease BspD6I (Nt.BstD6I) acts as a NEase. Here we present a study of interaction of restriction endonuclease BspD6I with modified DNA containing single non-nucleotide insertion with an azobenzene moiety in the enzyme cleavage sites or in positions of sugar-phosphate backbone nearby. According to these data, we designed a number of effective stimulus-responsive oligonucleotide inhibitors bearing azobenzene or triethylene glycol residues. These modified oligonucleotides modulated the functional activity of Nt.BspD6I after cooling or heating. We were able to block the cleavage of T7 phage DNA by this enzyme in the presence of such inhibitors at 20-25°C, whereas the Nt.BspD6I ability to hydrolyze DNA was completely restored after heating to 45°C. The observed effects can serve as a basis for the development of a platform for regulation of NEase activity in vitro or in vivo by external signals.
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Affiliation(s)
- Liudmila A. Abrosimova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Anzhela Yu. Migur
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Elena A. Kubareva
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Timofei S. Zatsepin
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia
| | - Aleksandra V. Gavshina
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alfiya K. Yunusova
- Institute of Theoretical and Experimental Biophysics of Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Tatiana A. Perevyazova
- Institute of Theoretical and Experimental Biophysics of Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig University, Giessen, Germany
| | - Tatiana S. Oretskaya
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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Lukyanchikova NV, Petruseva IO, Evdokimov AN, Koroleva LS, Lavrik OI. DNA Bearing Bulky Fluorescent and Photoreactive Damage in Both Strands as Substrates of the Nucleotide Excision Repair System. Mol Biol 2018. [DOI: 10.1134/s0026893318020061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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