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Tsuruta H, Sonohara Y, Tohashi K, Aoki Shioi N, Iwai S, Kuraoka I. Effects of acetaldehyde-induced DNA lesions on DNA metabolism. Genes Environ 2020; 42:2. [PMID: 31921374 PMCID: PMC6945695 DOI: 10.1186/s41021-019-0142-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/26/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Acetaldehyde, produced upon exposure to alcohol, cigarette smoke, polluted air and sugar, is a highly reactive compound that is carcinogenic to humans and causes a variety of DNA lesions in living human cells. Previously, we reported that acetaldehyde reacts with adjacent deoxyguanosine residues on oligonucleotides, but not with single deoxyguanosine residues or other deoxyadenosine, deoxycytosine, or thymidine residues, and revealed that it forms reversible intrastrand crosslinks with the dGpdG sequence (GG dimer). RESULTS Here, we show that restriction enzymes that recognize a GG sequence digested acetaldehyde-treated plasmid DNA with low but significant efficiencies, whereas restriction enzymes that recognize other sequences were able to digest such DNA. This suggested that acetaldehyde produced GG dimers in plasmid DNA. Additionally, acetaldehyde-treated oligonucleotides were efficient in preventing digestion by the exonuclease function of T4 DNA polymerase compared to non-treated oligonucleotides, suggesting structural distortions of DNA caused by acetaldehyde-treatment. Neither in vitro DNA synthesis reactions of phi29 DNA polymerase nor in vitro RNA synthesis reactions of T7 RNA polymerase were observed when acetaldehyde-treated plasmid DNA was used, compared to when non-treated plasmid DNA was used, suggesting that acetaldehyde-induced DNA lesions inhibited replication and transcription in DNA metabolism. CONCLUSIONS Acetaldehyde-induced DNA lesions could affect the relative resistance to endo- and exo-nucleolytic activity and also inhibit in vitro replication and in vitro transcription. Thus, investigating the effects of acetaldehyde-induced DNA lesions may enable a better understanding of the toxicity and carcinogenicity of acetaldehyde.
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Affiliation(s)
- Haruka Tsuruta
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
| | - Yuina Sonohara
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 Japan
| | - Kosuke Tohashi
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 Japan
| | - Narumi Aoki Shioi
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 Japan
| | - Isao Kuraoka
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
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3
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Mishra B, Zhang S, Zhao H, Darzynkiewicz Z, Lee EY, Lee MY, Zhang Z. Discovery of a novel DNA polymerase inhibitor and characterization of its antiproliferative properties. Cancer Biol Ther 2018; 20:474-486. [PMID: 30427259 PMCID: PMC6422523 DOI: 10.1080/15384047.2018.1529126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 09/22/2018] [Indexed: 12/31/2022] Open
Abstract
Chromosomal duplication is targeted by various chemotherapeutic agents for the treatment of cancer. However, there is no specific inhibitor of DNA polymerases that is viable for cancer management. Through structure-based in silico screening of the ZINC database, we identified a specific inhibitor of DNA polymerase δ. The discovered inhibitor, Zelpolib, is projected to bind to the active site of Pol δ when it is actively engaged in DNA replication through interactions with DNA template and primer. Zelpolib shows robust inhibition of Pol δ activity in reconstituted DNA replication assays. Under cellular conditions, Zelpolib is taken up readily by cancer cells and inhibits DNA replication in assays to assess global DNA synthesis or single-molecule bases by DNA fiber fluorography. In addition, we show that Zelpolib displays superior antiproliferative properties to methotrexate, 5-flourouracil, and cisplatin in triple-negative breast cancer cell line, pancreatic cancer cell line and platinum-resistant pancreatic cancer cell line. Pol δ is not only involved in DNA replication, it is also a key component in many DNA repair pathways. Pol δ is the key enzyme responsible for D-loop extension during homologous recombination. Indeed, Zelpolib shows robust inhibition of homologous recombination repair of DNA double-strand breaks and induces "BRCAness" in HR-proficient cancer cells and enhances their sensitivity to PARP inhibitors.
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Affiliation(s)
- Bhanvi Mishra
- Department of Biochemistry and Molecular Biology, Valhalla, NY, USA
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, Valhalla, NY, USA
| | - Hong Zhao
- Department of Pathology, New York Medical College, Valhalla, NY, USA
| | | | - Ernest Y.C. Lee
- Department of Biochemistry and Molecular Biology, Valhalla, NY, USA
| | | | - Zhongtao Zhang
- Department of Biochemistry and Molecular Biology, Valhalla, NY, USA
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4
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Tom EF, Molineux IJ, Paff ML, Bull JJ. Experimental evolution of UV resistance in a phage. PeerJ 2018; 6:e5190. [PMID: 30013847 PMCID: PMC6042481 DOI: 10.7717/peerj.5190] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/13/2018] [Indexed: 11/20/2022] Open
Abstract
The dsDNA bacteriophage T7 was subjected to 30 cycles of lethal ultraviolet light (UV) exposure to select increased resistance to UV. The exposure effected a 0.9999 kill of the ancestral population, and survival of the ending population was nearly 50-fold improved. At the end point, a 2.1 kb deletion of early genes and three substitutions in structural-genes were the only changes observed at high frequency throughout the 40 kb genome; no changes were observed in genes affecting DNA metabolism. The deletion accounted for only a two-fold improvement in survival. One possible explanation of its benefit is that it represents an error catastrophe, whereby the genome experiences a reduced mutation rate. The mechanism of benefit provided by the three structural-gene mutations remains unknown. The results offer some hope of artificially evolving greater protection against sunlight damage in applications of phage therapy to plants, but the response of T7 is weak compared to that observed in bacteria selected to resist ionizing radiation. Because of the weak response, mathematical analysis of the selection process was performed to determine how the protocol might have been modified to achieve a greater response, but the greatest protection may well come from evolving phages to bind materials that block the UV.
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Affiliation(s)
- Eric F Tom
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Ian J Molineux
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Matthew L Paff
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - James J Bull
- Department of Integrative Biology, University of Texas, Austin, TX, USA
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5
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Lodato MA, Rodin RE, Bohrson CL, Coulter ME, Barton AR, Kwon M, Sherman MA, Vitzthum CM, Luquette LJ, Yandava CN, Yang P, Chittenden TW, Hatem NE, Ryu SC, Woodworth MB, Park PJ, Walsh CA. Aging and neurodegeneration are associated with increased mutations in single human neurons. Science 2018; 359:555-559. [PMID: 29217584 PMCID: PMC5831169 DOI: 10.1126/science.aao4426] [Citation(s) in RCA: 367] [Impact Index Per Article: 61.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/22/2017] [Indexed: 12/27/2022]
Abstract
It has long been hypothesized that aging and neurodegeneration are associated with somatic mutation in neurons; however, methodological hurdles have prevented testing this hypothesis directly. We used single-cell whole-genome sequencing to perform genome-wide somatic single-nucleotide variant (sSNV) identification on DNA from 161 single neurons from the prefrontal cortex and hippocampus of 15 normal individuals (aged 4 months to 82 years), as well as 9 individuals affected by early-onset neurodegeneration due to genetic disorders of DNA repair (Cockayne syndrome and xeroderma pigmentosum). sSNVs increased approximately linearly with age in both areas (with a higher rate in hippocampus) and were more abundant in neurodegenerative disease. The accumulation of somatic mutations with age-which we term genosenium-shows age-related, region-related, and disease-related molecular signatures and may be important in other human age-associated conditions.
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Affiliation(s)
- Michael A Lodato
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rachel E Rodin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Neuroscience and Harvard/MIT MD-PHD Program, Harvard Medical School, Boston, MA, USA
| | - Craig L Bohrson
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Michael E Coulter
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Neuroscience and Harvard/MIT MD-PHD Program, Harvard Medical School, Boston, MA, USA
| | - Alison R Barton
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Minseok Kwon
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Maxwell A Sherman
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Carl M Vitzthum
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chandri N Yandava
- Computational Statistics and Bioinformatics Group, Advanced Artificial Intelligence Research Laboratory, WuXi NextCODE, Cambridge, MA, USA
| | - Pengwei Yang
- Computational Statistics and Bioinformatics Group, Advanced Artificial Intelligence Research Laboratory, WuXi NextCODE, Cambridge, MA, USA
| | - Thomas W Chittenden
- Computational Statistics and Bioinformatics Group, Advanced Artificial Intelligence Research Laboratory, WuXi NextCODE, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicole E Hatem
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven C Ryu
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mollie B Woodworth
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Borkotoky S, Meena CK, Murali A. Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives - An In Silico Approach. Bioinform Biol Insights 2016; 10:155-66. [PMID: 27594785 PMCID: PMC5004996 DOI: 10.4137/bbi.s40427] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/31/2016] [Accepted: 08/07/2016] [Indexed: 12/26/2022] Open
Abstract
The single subunit T7 RNA polymerase (T7RNAP) is a model enzyme for studying the transcription process and for various biochemical and biophysical studies. Heparin is a commonly used inhibitor against T7RNAP and other RNA polymerases. However, exact interaction between heparin and T7RNAP is still not completely understood. In this work, we analyzed the binding pattern of heparin by docking heparin and few of its low molecular weight derivatives to T7RNAP, which helps in better understanding of T7RNAP inhibition mechanism. The efficiency of the compounds was calculated by docking the selected compounds and post-docking molecular mechanics/generalized Born surface area analysis. Evaluation of the simulation trajectories and binding free energies of the complexes after simulation showed enoxaparin to be the best among low molecular weight heparins. Binding free energy analysis revealed that van der Waals interactions and polar solvation energy provided the substantial driving force for the binding process. Furthermore, per-residue free energy decomposition analysis revealed that the residues Asp 471, Asp 506, Asp 537, Tyr 571, Met 635, Asp 653, Pro 780, and Asp 812 are important for heparin interaction. Apart from these residues, most favorable contribution in all the three complexes came from Asp 506, Tyr 571, Met 635, Glu 652, and Asp 653, which can be essential for binding of heparin-like structures with T7RNAP. The results obtained from this study will be valuable for the future rational design of novel and potent inhibitors against T7RNAP and related proteins.
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Affiliation(s)
- Subhomoi Borkotoky
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Chetan Kumar Meena
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ayaluru Murali
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
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