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Schrödter M, Wagenknecht HA. Natural Epigenetic DNA Modifications Cause Remote DNA Photodamage. J Am Chem Soc 2024. [PMID: 39037865 DOI: 10.1021/jacs.4c03883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
5-Formyl-2'-deoxycytidine, an intermediate during the erasure of epigenetic marker 5-methyl-2'-deoxycytidine, and 5-formyl-2'-deoxyuridine, an oxidative lesion of thymidine, are naturally occurring DNA modifications. The carbonyl groups of these DNA modifications are the smallest possible photosensitizers and have the potential to generate cyclobutane pyrimidine dimers upon irradiation with UV light. To evidence this damaging potential, ternary DNA architectures were used, in which the photosensitizer and the damage site were located at well-defined positions in the sequences. The quantitative and time-dependent analysis revealed not only the high photodamaging potential of both natural DNA modifications but also the mechanisms for this new pathway to photodamage. 5-Formyl-2'-deoxycytidine is more efficiently generating cyclobutane pyrimidine dimers than 5-formyl-2'-deoxyuridine because the latter is also photochemically converted to 5-carboxy-2'-deoxyuridine. This demonstrates for the first time that epigenetic DNA modifications regulating gene expression interact with sunlight and can induce DNA photodamages.
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Affiliation(s)
- Maren Schrödter
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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2
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Burns D, Khatiwada B, Singh A, Purslow JA, Potoyan DA, Venditti V. An α-ketoglutarate conformational switch controls iron accessibility, activation, and substrate selection of the human FTO protein. Proc Natl Acad Sci U S A 2024; 121:e2404457121. [PMID: 38865275 PMCID: PMC11194561 DOI: 10.1073/pnas.2404457121] [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: 03/05/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024] Open
Abstract
The fat mass and obesity-associated fatso (FTO) protein is a member of the Alkb family of dioxygenases and catalyzes oxidative demethylation of N6-methyladenosine (m6A), N1-methyladenosine (m1A), 3-methylthymine (m3T), and 3-methyluracil (m3U) in single-stranded nucleic acids. It is well established that the catalytic activity of FTO proceeds via two coupled reactions. The first reaction involves decarboxylation of alpha-ketoglutarate (αKG) and formation of an oxyferryl species. In the second reaction, the oxyferryl intermediate oxidizes the methylated nucleic acid to reestablish Fe(II) and the canonical base. However, it remains unclear how binding of the nucleic acid activates the αKG decarboxylation reaction and why FTO demethylates different methyl modifications at different rates. Here, we investigate the interaction of FTO with 5-mer DNA oligos incorporating the m6A, m1A, or m3T modifications using solution NMR, molecular dynamics (MD) simulations, and enzymatic assays. We show that binding of the nucleic acid to FTO activates a two-state conformational equilibrium in the αKG cosubstrate that modulates the O2 accessibility of the Fe(II) catalyst. Notably, the substrates that provide better stabilization to the αKG conformation in which Fe(II) is exposed to O2 are demethylated more efficiently by FTO. These results indicate that i) binding of the methylated nucleic acid is required to expose the catalytic metal to O2 and activate the αKG decarboxylation reaction, and ii) the measured turnover of the demethylation reaction (which is an ensemble average over the entire sample) depends on the ability of the methylated base to favor the Fe(II) state accessible to O2.
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Affiliation(s)
- Daniel Burns
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA50011
| | | | - Aayushi Singh
- Department of Chemistry, Iowa State University, Ames, IA50011
| | | | - Davit A. Potoyan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA50011
- Department of Chemistry, Iowa State University, Ames, IA50011
| | - Vincenzo Venditti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA50011
- Department of Chemistry, Iowa State University, Ames, IA50011
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3
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Li Y, Tian X, Luo J, Bao T, Wang S, Wu X. Molecular mechanisms of aging and anti-aging strategies. Cell Commun Signal 2024; 22:285. [PMID: 38790068 PMCID: PMC11118732 DOI: 10.1186/s12964-024-01663-1] [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: 02/03/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Aging is a complex and multifaceted process involving a variety of interrelated molecular mechanisms and cellular systems. Phenotypically, the biological aging process is accompanied by a gradual loss of cellular function and the systemic deterioration of multiple tissues, resulting in susceptibility to aging-related diseases. Emerging evidence suggests that aging is closely associated with telomere attrition, DNA damage, mitochondrial dysfunction, loss of nicotinamide adenine dinucleotide levels, impaired macro-autophagy, stem cell exhaustion, inflammation, loss of protein balance, deregulated nutrient sensing, altered intercellular communication, and dysbiosis. These age-related changes may be alleviated by intervention strategies, such as calorie restriction, improved sleep quality, enhanced physical activity, and targeted longevity genes. In this review, we summarise the key historical progress in the exploration of important causes of aging and anti-aging strategies in recent decades, which provides a basis for further understanding of the reversibility of aging phenotypes, the application prospect of synthetic biotechnology in anti-aging therapy is also prospected.
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Affiliation(s)
- Yumeng Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Xutong Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Juyue Luo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Tongtong Bao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Shujin Wang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Xin Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
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Liu MH, Zhao NN, Yu WT, Qiu JG, Jiang BH, Zhang Y, Zhang CY. Construction of a label-free fluorescent biosensor for homogeneous detection of m 6A eraser FTO in breast cancer tissues. Talanta 2024; 272:125784. [PMID: 38364555 DOI: 10.1016/j.talanta.2024.125784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/24/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
Fat mass and obesity-associated protein (FTO) is a crucial eraser of RNA N6- methyladenosine (m6A) modification, and abnormal FTO expression level is implicated in pathogenesis of numerous cancers. Herein, we demonstrate the construction of a label-free fluorescent biosensor for homogeneous detection of m6A eraser FTO in breast cancer tissues. When FTO is present, it specifically erases the methyl group in m6A, inducing the cleavage of demethylated DNA by endonuclease DpnII and the generation of a single-stranded DNA (ssDNA) with a 3'-hydroxyl group. Subsequently, terminal deoxynucleotidyl transferase (TdT) promotes the incorporation of dTTPs into the ssDNA to obtain a long polythymidine (T) DNA sequence. The resultant long poly (T) DNA sequence can act as a template to trigger hyperbranched strand displacement amplification (HSDA), yielding numerous DNA fragments that may be stained by SYBR Gold to produce an enhanced fluorescence signal. This biosensor processes ultrahigh sensitivity with a detection limit of 1.65 × 10-10 mg/mL (2.6 fM), and it can detect the FTO activity in a single MCF-7 cell. Moreover, this biosensor can screen the FTO inhibitors, evaluate enzyme kinetic parameters, and discriminate the FTO expression levels in the tissues of breast cancer patients and healthy persons.
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Affiliation(s)
- Ming-Hao Liu
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China; College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China; College of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, 250200, China
| | - Ning-Ning Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Wan-Tong Yu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Jian-Ge Qiu
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Bing-Hua Jiang
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Yan Zhang
- College of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, 250200, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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5
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Han Y, Li DL, Han Q, Ma F, Zhang CY. Integration of Demethylation-Activated DNAzyme with a Single Quantum Dot Nanosensor for Sensitive Detection of O 6-Methylguanine DNA Methyltransferase in Breast Tissues. Anal Chem 2024; 96:4487-4494. [PMID: 38451469 DOI: 10.1021/acs.analchem.3c05090] [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: 03/08/2024]
Abstract
O6-Methylguanine-DNA-methyltransferase (MGMT) is a demethylation protein that dynamically regulates the O6-methylguanine modification (O6 MeG), and dysregulated MGMT is implicated in various malignant tumors. Herein, we integrate demethylation-activated DNAzyme with a single quantum dot nanosensor to sensitively detect MGMT in breast tissues. The presence of MGMT induces the demethylation of the O6 MeG-caged DNAzyme and the restoration of catalytic activity. The activated DNAzyme then specifically cleaves the ribonucleic acid site of hairpin DNA to expose toehold sequences. The liberated toehold sequence may act as a primer to trigger a cyclic exponential amplification reaction for the generation of enormous signal strands that bind with the Cy5/biotin-labeled probes to form sandwich hybrids. The assembly of sandwich hybrids onto 605QD obtains 605QD-dsDNA-Cy5 nanostructures, inducing efficient FRET between the 605QD donor and Cy5 acceptor. Notably, the introduction of a mismatched base in hairpin DNA can greatly minimize the background and improve the signal-to-noise ratio. This nanosensor achieves a dynamic range of 1.0 × 10-8 to 0.1 ng/μL and a detection limit of 155.78 aM, and it can screen MGMT inhibitors and monitor cellular MGMT activity with single-cell sensitivity. Moreover, it can distinguish the MGMT level in tissues of breast cancer patients and healthy persons, holding great potential in clinical diagnostics and epigenetic research studies.
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Affiliation(s)
- Yun Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Dong-Ling Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Qian Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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Gade M, Gardner JM, Jain P, Laurino P. Nucleoside-Driven Specificity of DNA Methyltransferase. Chembiochem 2023; 24:e202300094. [PMID: 37548117 DOI: 10.1002/cbic.202300094] [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: 02/05/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/08/2023]
Abstract
We have studied the adenosine binding specificities of two bacterial DNA methyltransferases, Taq methyltransferase (M.TaqI), and HhaI methyltransferase (M.HhaI). While they have similar cofactor binding pocket interactions, experimental data showed different specificity for novel S-nucleobase-l-methionine cofactors (SNMs; N=guanosyl, cytidyl, uridyl). Protein dynamics corroborate the experimental data on the cofactor specificities. For M.TaqI the specificity for S-adenosyl-l-methionine (SAM) is governed by the tight binding on the nucleoside part of the cofactor, while for M.HhaI the degree of freedom of the nucleoside chain allows the acceptance of other bases. The experimental data prove catalytically productive methylation by the M.HhaI binding pocket for all the SNMs. Our results suggest a new route for successful design of unnatural SNM analogues for methyltransferases as a tool for cofactor engineering.
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Affiliation(s)
- Madhuri Gade
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Jasmine M Gardner
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Prashant Jain
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
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Zhang LS, Ju CW, Jiang B, He C. Base-resolution quantitative DAMM-seq for mapping RNA methylations in tRNA and mitochondrial polycistronic RNA. Methods Enzymol 2023; 692:39-54. [PMID: 37925186 PMCID: PMC10882886 DOI: 10.1016/bs.mie.2023.08.001] [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] [Indexed: 11/06/2023]
Abstract
The human AlkB family proteins, such as FTO and ALKBH5, are known to mediate RNA m6A demethylation. However, although ALKBH7 localizes in mitochondria and affects metabolism, the detailed biological function and mechanism have remained unknown for years. We developed Demethylation-Assisted Multiple Methylation sequencing (DAMM-seq) to simultaneously detect N1-methyladenosine (m1A), N3-methylcytidine (m3C), N1-methylguanosine (m1G) and N2,N2-dimethylguanosine (m22G) methylations in both steady-state RNA and nascent RNA, and discovered that human ALKBH7 demethylates m22G and m1A within mt-Ile and mt-Leu1 pre-tRNA regions, respectively, in mitochondrial polycistronic RNA. DAMM-seq quantitatively and sensitively monitors the methylation stoichiometry change at pre-tRNA junctions within nascent mt-RNA, revealing the target region where ALKBH7 regulates RNA processing and local structural switch of polycistronic mt-RNAs. A new RNA demethylase in human cells was characterized through the base-resolution quantification of multiple RNA methylations in nascent mt-RNA, resolving the long-standing question about the functional substrate of ALKBH7.
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Affiliation(s)
- Li-Sheng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Hong Kong SAR, P.R. China; Department of Chemistry, The Hong Kong University of Science and Technology (HKUST), Hong Kong SAR, P.R. China; Department of Chemistry, The University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States.
| | - Cheng-Wei Ju
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, United States
| | - Bochen Jiang
- Department of Chemistry, The University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States
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Zhang Q, Zhao S, Su C, Han Q, Han Y, Tian X, Li Y, Zhang CY. Construction of a Quantum-Dot-Based FRET Nanosensor through Direct Encoding of Streptavidin-Binding RNA Aptamers for N6-Methyladenosine Demethylase Detection. Anal Chem 2023; 95:13201-13210. [PMID: 37603851 DOI: 10.1021/acs.analchem.3c02149] [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: 08/23/2023]
Abstract
N6-Methyladenosine (m6A) demethylases can catalyze the removal of the methyl modification on m6A, and it is closely associated with the occurrence, proliferation, differentiation, and metastasis of malignancies. The m6A demethylases (e.g., fat mass and obesity-associated protein (FTO)) may act as a cancer biomarker and are crucial for anticancer drug screening and early clinical diagnosis. Herein, we demonstrate the construction of a quantum-dot-based Förster resonance energy-transfer (FRET) nanosensor through direct encoding of streptavidin-binding RNA aptamers (SA aptamers) for m6A demethylase detection. This nanosensor employs multiple Cy5-molecule-labeled SA aptamers as the building materials to construct the 605QD-RNA-Cy5 nanoassembly, and it exploits the hinder effect of m6A upon elongation and ligation reactions to distinguish m6A-containing RNA probes from demethylated RNA probes. When m6A demethylase is present, the m6A-containing RNA probes are demethylated to generate the demethylated RNA probes, initiating strand extension and ligation reactions to yield a complete transcription template for SA aptamers. Subsequently, a T7-assisted cascade transcription amplification reaction is activated to transcribe abundant SA aptamers with the incorporation of multiple Cy5 fluorophores. The Cy5-incorporated SA aptamers can self-assembly onto the streptavidin-coated 605QD surface to obtain the 605QD-SA aptamer-Cy5 nanoassemblies, resulting in the generation of distinct FRET signals. This nanosensor exhibits ultrahigh sensitivity and excellent specificity, and it can detect endogenous FTO at the single-cell level. Furthermore, this nanosensor can precisely measure enzyme kinetic parameters, screen m6A demethylase inhibitors, and differentiate the FTO expression between breast cancer patients and healthy individual tissues, offering a versatile platform for clinical diagnostic and drug discovery.
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Affiliation(s)
- Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Shuangnan Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Cong Su
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Qian Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yun Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Xiaorui Tian
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Yueying Li
- Henan Institute of Medical and Pharmaceutical Sciences & BGI College, Zhengzhou University, Zhengzhou 450052, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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Lirussi L, Nilsen HL. DNA Glycosylases Define the Outcome of Endogenous Base Modifications. Int J Mol Sci 2023; 24:10307. [PMID: 37373453 DOI: 10.3390/ijms241210307] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Chemically modified nucleic acid bases are sources of genomic instability and mutations but may also regulate gene expression as epigenetic or epitranscriptomic modifications. Depending on the cellular context, they can have vastly diverse impacts on cells, from mutagenesis or cytotoxicity to changing cell fate by regulating chromatin organisation and gene expression. Identical chemical modifications exerting different functions pose a challenge for the cell's DNA repair machinery, as it needs to accurately distinguish between epigenetic marks and DNA damage to ensure proper repair and maintenance of (epi)genomic integrity. The specificity and selectivity of the recognition of these modified bases relies on DNA glycosylases, which acts as DNA damage, or more correctly, as modified bases sensors for the base excision repair (BER) pathway. Here, we will illustrate this duality by summarizing the role of uracil-DNA glycosylases, with particular attention to SMUG1, in the regulation of the epigenetic landscape as active regulators of gene expression and chromatin remodelling. We will also describe how epigenetic marks, with a special focus on 5-hydroxymethyluracil, can affect the damage susceptibility of nucleic acids and conversely how DNA damage can induce changes in the epigenetic landscape by altering the pattern of DNA methylation and chromatin structure.
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Affiliation(s)
- Lisa Lirussi
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Section of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Hilde Loge Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
- Unit for Precision Medicine, Akershus University Hospital, 1478 Lørenskog, Norway
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Ji TT, Xie NB, Ding JH, Wang M, Guo X, Chen YY, Yu SY, Feng YQ, Yuan BF. Enzymatic Cleavage-Mediated Extension Stalling Enables Accurate Recognition and Quantification of Locus-Specific Uracil Modification in DNA. Anal Chem 2023; 95:8384-8392. [PMID: 37192336 DOI: 10.1021/acs.analchem.3c01410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Chemical modifications in DNA have profound influences on the structures and functions of DNA. Uracil, a naturally occurring DNA modification, can originate from the deamination of cytosine or arise from misincorporation of dUTP into DNA during DNA replication. Uracil in DNA will imperil genomic stability due to their potential in producing detrimental mutations. An in-depth understanding of the functions of uracil modification requires the accurate determination of its site as well as content in genomes. Herein, we characterized that a new member of the uracil-DNA glycosylase (UDG) family enzyme (UdgX-H109S) could selectively cleave both uracil-containing single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). Based on this unique property of UdgX-H109S, we developed an enzymatic cleavage-mediated extension stalling (ECES) method for the locus-specific detection and quantification of uracil in genomic DNA. In the ECES method, UdgX-H109S specifically recognizes and cleaves the N-glycosidic bond of uracil from dsDNA and generates an apurinic/apyrimidinic (AP) site, which could be broken by APE1 to form a one-nucleotide gap. The specific cleavage by UdgX-H109S is then evaluated and quantified by qPCR. With the developed ECES approach, we demonstrated that the level of uracil at position Chr4:50566961 in genomic DNA of breast cancer tissues was significantly decreased. Collectively, the ECES method has been proved to be accurate and reproducible in the locus-specific quantification of uracil in genomic DNA from biological and clinical samples.
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Affiliation(s)
- Tong-Tong Ji
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Neng-Bin Xie
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- School of Public Health, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430060, China
| | - Jiang-Hui Ding
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Min Wang
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Xia Guo
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Ying-Ying Chen
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Si-Yu Yu
- School of Public Health, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430060, China
| | - Yu-Qi Feng
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- School of Public Health, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430060, China
| | - Bi-Feng Yuan
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- School of Public Health, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430060, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Wuhan Research Center for Infectious Diseases and Cancer, Zhongnan Hospital of Wuhan University, Chinese Academy of Medical Sciences, Wuhan, Hubei 430071, China
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Yoshikawa N, Nakamura K, Kajiyama H. Current understanding of Plasma-activated solutions for potential cancer therapy. Free Radic Res 2023:1-12. [PMID: 36944223 DOI: 10.1080/10715762.2023.2193308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Cancer therapy consists of multidisciplinary treatment combining surgery, chemotherapy, radiotherapy, and immunotherapy. Despite the elucidation of cancer mechanisms by comprehensive genomic and epigenomic analyses and the development of molecular therapy, drug resistance and severe side effects have presented challenges to the long-awaited development of new therapies. With the rapid technological advances in the last decade, there are now reports concerning potential applications of non-equilibrium atmospheric pressure plasma (NEAPP) in cancer therapy. Two approaches have been tried: direct irradiation with NEAPP (direct plasma) and the administration of a liquid (e.g., culture medium, saline, Ringer's lactate) activated by NEAPP (plasma-activated solutions: PAS). Direct plasma is a unique treatment method in which various active species, charged ions, and photons are delivered to the affected area, but the direct plasma approach has physical limitations related to the device used, such as a limited depth of reach and limited irradiation area. PAS is a liquid that contains reactive oxygen species generated by PAS, and it has been confirmed to have antitumor activity that functions in the same manner as direct plasma. This review introduces recent studies of PAS and informs researchers about the potential of PAS for cancer therapy.Key Policy HighlightsPotential applications of plasma-activated solutions (PAS) in cancer therapy are described.Plasma-activated species generated in PAS, its effect on tumor cells, contribution to non-malignant immune cells, selectivity and safety are presented.The proposed anti-tumor mechanisms of PAS to date are described.Efficacy and safety evaluations of PAS have been studied in experimental animal models, but no human studies have been conducted.
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Affiliation(s)
- Nobuhisa Yoshikawa
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine
| | - Kae Nakamura
- Center for Low-Temperature Plasma Sciences, Nagoya University, Nagoya, Nagoya
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine
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12
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Bessler L, Vogt LM, Lander M, Dal Magro C, Keller P, Kühlborn J, Kampf CJ, Opatz T, Helm M. A New Bacterial Adenosine-Derived Nucleoside as an Example of RNA Modification Damage. Angew Chem Int Ed Engl 2023; 62:e202217128. [PMID: 36629490 DOI: 10.1002/anie.202217128] [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: 11/21/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/12/2023]
Abstract
The fields of RNA modification and RNA damage both exhibit a plethora of non-canonical nucleoside structures. While RNA modifications have evolved to improve RNA function, the term RNA damage implies detrimental effects. Based on stable isotope labelling and mass spectrometry, we report the identification and characterisation of 2-methylthio-1,N6-ethenoadenosine (ms2 ϵA), which is related to 1,N6-ethenoadenine, a lesion resulting from exposure of nucleic acids to alkylating chemicals in vivo. In contrast, a sophisticated isoprene labelling scheme revealed that ms2 ϵA biogenesis involves cleavage of a prenyl moiety in the known transfer RNA (tRNA) modification 2-methylthio-N6-isopentenyladenosine (ms2 i6 A). The relative abundance of ms2 ϵA in tRNAs from translating ribosomes suggests reduced function in comparison to its parent RNA modification, establishing the nature of the new structure in a newly perceived overlap of the two previously separate fields, namely an RNA modification damage.
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Affiliation(s)
- Larissa Bessler
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Lea-Marie Vogt
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Marc Lander
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Christina Dal Magro
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Patrick Keller
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Jonas Kühlborn
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Christopher J Kampf
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
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13
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Profiling demethylase activity using epigenetically inactivated DNAzyme. Biosens Bioelectron 2022; 207:114186. [DOI: 10.1016/j.bios.2022.114186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/28/2022] [Accepted: 03/11/2022] [Indexed: 11/02/2022]
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14
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Waheed SO, Varghese A, Chaturvedi SS, Karabencheva-Christova TG, Christov CZ. How Human TET2 Enzyme Catalyzes the Oxidation of Unnatural Cytosine Modifications in Double-Stranded DNA. ACS Catal 2022; 12:5327-5344. [PMID: 36339349 PMCID: PMC9629818 DOI: 10.1021/acscatal.2c00024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methylation of cytosine bases is strongly linked to gene expression, imprinting, aging, and carcinogenesis. The Ten-eleven translocation (TET) family of enzymes, which are Fe(II)/2-oxoglutarate (2OG)-dependent enzymes, employ Fe(IV)=O species to dealkylate the lesioned bases to an unmodified cytosine. Recently, it has been shown that the TET2 enzyme can catalyze promiscuously DNA substrates containing unnatural alkylated cytosine. Such unnatural substrates of TET can be used as direct probes for measuring the TET activity or capturing TET from cellular samples. Herein, we studied the catalytic mechanisms during the oxidation of the unnatural C5-position modifications (5-ethylcytosine (5eC), 5-vinylcytosine (5vC) and 5-ethynylcytosine (5eyC)) and the demethylation of N4-methylated lesions (4-methylcytosine (4mC) and 4,4-dimethylcytosine(4dmC)) of the cytosine base by the TET2 enzyme using molecular dynamics (MD) and combined quantum mechanics and molecular mechanics (QM/MM) computational approaches. The results reveal that the chemical nature of the alkylation of the double-stranded (ds) DNA substrates induces distinct changes in the interactions in the binding site, the second coordination sphere, and long-range correlated motions of the ES complexes. The rate-determining hydrogen atom transfer (HAT) is faster in N4-methyl substituent substrates than in the C5-alkylations. Importantly, the calculations show the preference of hydroxylation over desaturation in both 5eC and 5vC substrates. The studies elucidate the post-hydroxylation rearrangements of the hydroxylated intermediates of 5eyC and 5vC to ketene and 5-formylmethylcytosine (5fmC), respectively, and hydrolysis of hemiaminal intermediate of 4mC to formaldehyde and unmodified cytosine proceed exclusively in aqueous solution outside of the enzyme environment. Overall, the studies show that the chemical nature of the unnatural alkylated cytosine substrates exercises distinct effects on the binding interactions, reaction mechanism, and dynamics of TET2.
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Affiliation(s)
- Sodiq O. Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Shobhit S. Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | | | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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15
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Solution structure ensemble of human obesity-associated protein FTO reveals druggable surface pockets at the interface between the N- and C-terminal domain. J Biol Chem 2022; 298:101907. [PMID: 35398093 PMCID: PMC9065727 DOI: 10.1016/j.jbc.2022.101907] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 12/17/2022] Open
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16
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Berger MB, Walker AR, Vázquez-Montelongo EA, Cisneros GA. Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families. Phys Chem Chem Phys 2021; 23:22227-22240. [PMID: 34586107 PMCID: PMC8516722 DOI: 10.1039/d1cp03800a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA alkylation is used as the key epigenetic mark in eukaryotes, however, most alkylation in DNA can result in deleterious effects. Therefore, this process needs to be tightly regulated. The enzymes of the AlkB and Ten-Eleven Translocation (TET) families are members of the Fe and alpha-ketoglutarate-dependent superfamily of enzymes that are tasked with dealkylating DNA and RNA in cells. Members of these families span all species and are an integral part of transcriptional regulation. While both families catalyze oxidative dealkylation of various bases, each has specific preference for alkylated base type as well as distinct catalytic mechanisms. This perspective aims to provide an overview of computational work carried out to investigate several members of these enzyme families including AlkB, ALKB Homolog 2, ALKB Homolog 3 and Ten-Eleven Translocate 2. Insights into structural details, mutagenesis studies, reaction path analysis, electronic structure features in the active site, and substrate preferences are presented and discussed.
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Affiliation(s)
- Madison B Berger
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
| | - Alice R Walker
- Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
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17
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DNA Demethylation in the Processes of Repair and Epigenetic Regulation Performed by 2-Ketoglutarate-Dependent DNA Dioxygenases. Int J Mol Sci 2021; 22:ijms221910540. [PMID: 34638881 PMCID: PMC8508711 DOI: 10.3390/ijms221910540] [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: 09/02/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/05/2022] Open
Abstract
Site-specific DNA methylation plays an important role in epigenetic regulation of gene expression. Chemical methylation of DNA, including the formation of various methylated nitrogenous bases, leads to the formation of genotoxic modifications that impair DNA functions. Despite the fact that different pathways give rise to methyl groups in DNA, the main pathway for their removal is oxidative demethylation, which is catalyzed by nonheme Fe(II)/α-ketoglutarate–dependent DNA dioxygenases. DNA dioxygenases share a common catalytic mechanism of the oxidation of the alkyl groups on nitrogenous bases in nucleic acids. This review presents generalized data on the catalytic mechanism of action of DNA dioxygenases and on the participation of typical representatives of this superfamily, such as prokaryotic enzyme AlkB and eukaryotic enzymes ALKBH1–8 and TET1–3, in both processes of direct repair of alkylated DNA adducts and in the removal of an epigenetic mark (5-methylcytosine).
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18
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Wagenknecht HA. Remote Photodamaging of DNA by Photoinduced Energy Transport. Chembiochem 2021; 23:e202100265. [PMID: 34569126 PMCID: PMC9292490 DOI: 10.1002/cbic.202100265] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/14/2021] [Indexed: 12/11/2022]
Abstract
Local DNA photodamaging by light is well-studied and leads to a number of structurally identified direct damage, in particular cyclobutane pyrimidine dimers, and indirect oxidatively generated damage, such as 8-oxo-7,8-hydroxyguanine. Similar damages have now been found at remote sites, at least more than 105 Å (30 base pairs) away from the site of photoexcitation. In contrast to the established mechanisms of local DNA photodamaging, the processes of remote photodamage are only partially understood. Known pathways include those to remote oxidatively generated DNA photodamages, which were elucidated by studying electron hole transport through the DNA about 20 years ago. Recent studies with DNA photosensitizers and mechanistic proposals on photoinduced DNA-mediated energy transport are summarized in this minireview. These new mechanisms to a new type of remote DNA photodamaging provide an important extension to our general understanding to light-induced DNA damage and their mutations.
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Affiliation(s)
- Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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19
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Purslow JA, Nguyen TT, Khatiwada B, Singh A, Venditti V. N 6-methyladenosine binding induces a metal-centered rearrangement that activates the human RNA demethylase Alkbh5. SCIENCE ADVANCES 2021; 7:7/34/eabi8215. [PMID: 34407931 PMCID: PMC8373141 DOI: 10.1126/sciadv.abi8215] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/29/2021] [Indexed: 05/13/2023]
Abstract
Alkbh5 catalyzes demethylation of the N 6-methyladenosine (m6A), an epigenetic mark that controls several physiological processes including carcinogenesis and stem cell differentiation. The activity of Alkbh5 comprises two coupled reactions. The first reaction involves decarboxylation of α-ketoglutarate (αKG) and formation of a Fe4+═O species. This oxyferryl intermediate oxidizes the m6A to reestablish the canonical base. Despite coupling between the two reactions being required for the correct Alkbh5 functioning, the mechanisms linking dioxygen activation to m6A binding are not fully understood. Here, we use solution NMR to investigate the structure and dynamics of apo and holo Alkbh5. We show that binding of m6A to Alkbh5 induces a metal-centered rearrangement of αKG that increases the exposed area of the metal, making it available for binding O2 Our study reveals the molecular mechanisms underlying activation of Alkbh5, therefore opening new perspectives for the design of novel strategies to control gene expression and cancer progression.
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Affiliation(s)
| | - Trang T Nguyen
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | | | - Aayushi Singh
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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20
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Wang X, Yi X, Huang Z, He J, Wu Z, Chu X, Jiang J. “Repaired and Activated” DNAzyme Enables the Monitoring of DNA Alkylation Repair in Live Cells. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiangnan Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Xin Yi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Zhimei Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Jianjun He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Zhenkun Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Jian‐Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
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21
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Wang X, Yi X, Huang Z, He J, Wu Z, Chu X, Jiang JH. "Repaired and Activated" DNAzyme Enables the Monitoring of DNA Alkylation Repair in Live Cells. Angew Chem Int Ed Engl 2021; 60:19889-19896. [PMID: 34165234 DOI: 10.1002/anie.202106557] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/16/2021] [Indexed: 12/31/2022]
Abstract
Direct measurement of DNA repair is critical for the annotation of their clinical relevance and the discovery of drugs for cancer therapy. Here we reported a "repaired and activated" DNAzyme (RADzyme) by incorporating a single methyl lesion (O6 MeG, 3MeC, or 1MeA) at designated positions through systematic screening. We found that the catalytic activity of the RADzyme was remarkably suppressed and could be restored via enzyme-mediated DNA repair. Benefit from these findings, a fluorogenic RADzyme sensor was developed for the monitoring of MGMT-mediated repair of O6 MeG lesion. Importantly, the sensor allowed the evaluation of MGMT repair activity in different cells and under drugs treatment. Furthermore, another RADzyme sensor was engineered for the monitoring of ALKBH2-mediated repair of 3MeC lesion. This strategy provides a simple and versatile tool for the study of the basic biology of DNA repair, clinical diagnosis and therapeutic assessment.
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Affiliation(s)
- Xiangnan Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Xin Yi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Zhimei Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Jianjun He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Zhenkun Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
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22
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Tan YL, Chen H, Wu ZK, He J, Jiang JH. Digital Loop-Mediated Isothermal Amplification-Based Absolute Methylation Quantification Revealed Hypermethylated DAPK1 in Cervical Cancer Patients. Anal Chem 2021; 93:8077-8083. [PMID: 34019386 DOI: 10.1021/acs.analchem.1c01510] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The aberrant methylation of many genes has been reported to be associated with various carcinomas. Accurate detection of the methylation level could provide critical insights into the diagnostic analysis of diseases. Here, a sensitive HpaII-edited absolute droplet loop-mediated isothermal amplification (HEADLAMP) method based on methylation-sensitive restriction enzyme (MSRE) HpaII was developed for the digital quantification of DNA methylation. Methylation levels of the death-associated protein kinase 1 (DAPK1) gene that is associated with many cancers were studied using β-actin as an internal reference. DAPK1 (2.5 pM) with 0.01% methylation (250 aM) can be detected with the conventional HpaII-edited LAMP assay. Using HEADLAMP, as low as 1% methylation level can be distinguished with an estimated limit of detection of 5 aM (ca. 3 copies/μL). Moreover, HEADLAMP can detect low levels of methylated DAPK1 in normal L-02 cells, while the conventional assay cannot. Finally, HEADLAMP was applied to the detection of DAPK1 methylation in 20 clinical tissue samples, which revealed hypermethylated DAPK1 in cervical cancer patients. We envisage potential applications of this robust, specific, and sensitive HEADLAMP assay in epigenetic studies and early clinical diagnosis.
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Affiliation(s)
- Ya-Ling Tan
- State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Hongjian Chen
- State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Zhen-Kun Wu
- State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jianjun He
- State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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23
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Zhao S, Devega R, Francois A, Kidane D. Human ALKBH6 Is Required for Maintenance of Genomic Stability and Promoting Cell Survival During Exposure of Alkylating Agents in Pancreatic Cancer. Front Genet 2021; 12:635808. [PMID: 33897761 PMCID: PMC8058185 DOI: 10.3389/fgene.2021.635808] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/08/2021] [Indexed: 12/21/2022] Open
Abstract
Alpha-ketoglutarate-dependent dioxygenase (ALKBH) is a DNA repair gene involved in the repair of alkylating DNA damage. There are nine types of ALKBH (ALKBH1-8 and FTO) identified in humans. In particular, certain types of ALKBH enzymes are dioxygenases that directly reverse DNA methylation damage via transfer of a methyl group from the DNA adduct onto α-ketoglutarate and release of metabolic products including succinate and formaldehyde. Here, we tested whether ALKBH6 plays a significant role in preventing alkylating DNA damage and decreasing genomic instability in pancreatic cancer cells. Using an E. coli strain deficient with ALKB, we found that ALKBH6 complements ALKB deficiency and increases resistance after alkylating agent treatment. In particular, the loss of ALKBH6 in human pancreatic cancer cells increases alkylating agent-induced DNA damage and significantly decreases cell survival. Furthermore, in silico analysis from The Cancer Genome Atlas (TCGA) database suggests that overexpression of ALKBH6 provides better survival outcomes in patients with pancreatic cancer. Overall, our data suggest that ALKBH6 is required to maintain the integrity of the genome and promote cell survival of pancreatic cancer cells.
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Affiliation(s)
- Shengyuan Zhao
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
| | - Rodan Devega
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
| | - Aaliyah Francois
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
| | - Dawit Kidane
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
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24
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Wang Y, Katanski CD, Watkins C, Pan JN, Dai Q, Jiang Z, Pan T. A high-throughput screening method for evolving a demethylase enzyme with improved and new functionalities. Nucleic Acids Res 2021; 49:e30. [PMID: 33337498 PMCID: PMC7968990 DOI: 10.1093/nar/gkaa1213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/26/2023] Open
Abstract
AlkB is a DNA/RNA repair enzyme that removes base alkylations such as N1-methyladenosine (m1A) or N3-methylcytosine (m3C) from DNA and RNA. The AlkB enzyme has been used as a critical tool to facilitate tRNA sequencing and identification of mRNA modifications. As a tool, AlkB mutants with better reactivity and new functionalities are highly desired; however, previous identification of such AlkB mutants was based on the classical approach of targeted mutagenesis. Here, we introduce a high-throughput screening method to evaluate libraries of AlkB variants for demethylation activity on RNA and DNA substrates. This method is based on a fluorogenic RNA aptamer with an internal modified RNA/DNA residue which can block reverse transcription or introduce mutations leading to loss of fluorescence inherent in the cDNA product. Demethylation by an AlkB variant eliminates the blockage or mutation thereby restores the fluorescence signals. We applied our screening method to sites D135 and R210 in the Escherichia coli AlkB protein and identified a variant with improved activity beyond a previously known hyperactive mutant toward N1-methylguanosine (m1G) in RNA. We also applied our method to O6-methylguanosine (O6mG) modified DNA substrates and identified candidate AlkB variants with demethylating activity. Our study provides a high-throughput screening method for in vitro evolution of any demethylase enzyme.
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Affiliation(s)
- Yuru Wang
- Department of Biochemistry and Molecular Biology, USA.,Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | | | | | - Jessica N Pan
- Department of Biochemistry and Molecular Biology, USA
| | - Qing Dai
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Zhuoxun Jiang
- Department of Biochemistry and Molecular Biology, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, USA
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25
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Gurnari C, Pagliuca S, Visconte V. The Interactome between Metabolism and Gene Mutations in Myeloid Malignancies. Int J Mol Sci 2021; 22:ijms22063135. [PMID: 33808599 PMCID: PMC8003366 DOI: 10.3390/ijms22063135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 12/19/2022] Open
Abstract
The study of metabolic deregulation in myeloid malignancies has led to the investigation of metabolic-targeted therapies considering that cells undergoing leukemic transformation have excessive energy demands for growth and proliferation. However, the most difficult challenge in agents targeting metabolism is to determine a window of therapeutic opportunities between normal and neoplastic cells, considering that all or most of the metabolic pathways important for cancer ontogeny may also regulate physiological cell functions. Targeted therapies have used the properties of leukemic cells to produce altered metabolic products when mutated. This is the case of IDH1/2 mutations generating the abnormal conversion of α-ketoglutarate (KG) to 2-hydroxyglutarate, an oncometabolite inhibiting KG-dependent enzymes, such as the TET family of genes (pivotal in characterizing leukemia cells either by mutations, e.g., TET2, or by altered expression, e.g., TET1/2/3). Additional observations derive from the high sensitivity of leukemic cells to oxidative phosphorylation and its amelioration using BCL-2 inhibitors (Venetoclax) or by disrupting the mitochondrial respiration. More recently, nicotinamide metabolism has been described to mediate resistance to Venetoclax in patients with acute myeloid leukemia. Herein, we will provide an overview of the latest research on the link between metabolic pathways interactome and leukemogenesis with a comprehensive analysis of the metabolic consequences of driver genetic lesions and exemplificative druggable pathways.
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Affiliation(s)
- Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.G.); (S.P.)
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
- Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.G.); (S.P.)
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.G.); (S.P.)
- Correspondence:
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26
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Mustafa M, Ali A, Siddiqui SA, Mir AR, Kausar T, Nayeem SM, Abidi M, Habib S. Biophysical characterization of structural and conformational changes in methylmethane sulfonate modified DNA leading to the frizzled backbone structure and strand breaks in DNA. J Biomol Struct Dyn 2021; 40:7598-7611. [PMID: 33719845 DOI: 10.1080/07391102.2021.1899051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Methyl methanesulfonate (MMS) is a highly toxic DNA-alkylating agent that has a potential to damage the structural integrity of DNA. This work employed multiple biophysical and computational methods to report the MMS mediated structural alterations in the DNA (MMS-DNA). Spectroscopic techniques and gel electrophoresis studies revealed MMS induced exposure of chromophoric groups of DNA; methylation mediated anti→syn conformational change, DNA fragmentation and reduced nucleic acid stability. MMS induced single-stranded regions in the DNA were observed in nuclease S1 assay. FT-IR results indicated MMS mediated loss of the assigned peaks for DNA, partial loss of C-O ribose, loss of deoxyribose region, C-O stretching and bending of the C-OH groups of hexose sugar, a progressive shift in the assigned guanine and adenine peaks, loss of thymine peak, base stacking and presence of C-O-H vibrations of glucose and fructose, indicating direct strand breaks in DNA due to backbone loss. Isothermal titration calorimetry showed MMS-DNA interaction as exothermic with moderate affinity. Dynamic light scattering studies pointed towards methylation followed by the generation of single-stranded regions. Electron microscopy pictured the loss of alignment in parallel base pairs and showed the formation of fibrous aggregates in MMS-DNA. Molecular docking found MMS in close contact with the ribose sugar of DNA backbone having non-bonded interactions. Molecular dynamic simulations confirmed that MMS is capable of interacting with DNA at two levels, one at the level of nitrogenous bases and another at the DNA backbone. The study offers insights into the molecular interaction of MMS and DNA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohd Mustafa
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Asif Ali
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Shahid Ali Siddiqui
- Department of Radiotherapy, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Abdul Rouf Mir
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Tasneem Kausar
- Department of Chemistry, Faculty of Science, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Shahid M Nayeem
- Department of Chemistry, Faculty of Science, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Minhal Abidi
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Safia Habib
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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27
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Waheed SO, Chaturvedi SS, Karabencheva-Christova TG, Christov CZ. Catalytic Mechanism of Human Ten-Eleven Translocation-2 (TET2) Enzyme: Effects of Conformational Changes, Electric Field, and Mutations. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05034] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sodiq O. Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Shobhit S. Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | | | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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28
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Vural S, Palmisano A, Reinhold WC, Pommier Y, Teicher BA, Krushkal J. Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines. Clin Epigenetics 2021; 13:49. [PMID: 33676569 PMCID: PMC7936435 DOI: 10.1186/s13148-021-01026-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/10/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Altered DNA methylation patterns play important roles in cancer development and progression. We examined whether expression levels of genes directly or indirectly involved in DNA methylation and demethylation may be associated with response of cancer cell lines to chemotherapy treatment with a variety of antitumor agents. RESULTS We analyzed 72 genes encoding epigenetic factors directly or indirectly involved in DNA methylation and demethylation processes. We examined association of their pretreatment expression levels with methylation beta-values of individual DNA methylation probes, DNA methylation averaged within gene regions, and average epigenome-wide methylation levels. We analyzed data from 645 cancer cell lines and 23 cancer types from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer datasets. We observed numerous correlations between expression of genes encoding epigenetic factors and response to chemotherapeutic agents. Expression of genes encoding a variety of epigenetic factors, including KDM2B, DNMT1, EHMT2, SETDB1, EZH2, APOBEC3G, and other genes, was correlated with response to multiple agents. DNA methylation of numerous target probes and gene regions was associated with expression of multiple genes encoding epigenetic factors, underscoring complex regulation of epigenome methylation by multiple intersecting molecular pathways. The genes whose expression was associated with methylation of multiple epigenome targets encode DNA methyltransferases, TET DNA methylcytosine dioxygenases, the methylated DNA-binding protein ZBTB38, KDM2B, SETDB1, and other molecular factors which are involved in diverse epigenetic processes affecting DNA methylation. While baseline DNA methylation of numerous epigenome targets was correlated with cell line response to antitumor agents, the complex relationships between the overlapping effects of each epigenetic factor on methylation of specific targets and the importance of such influences in tumor response to individual agents require further investigation. CONCLUSIONS Expression of multiple genes encoding epigenetic factors is associated with drug response and with DNA methylation of numerous epigenome targets that may affect response to therapeutic agents. Our findings suggest complex and interconnected pathways regulating DNA methylation in the epigenome, which may both directly and indirectly affect response to chemotherapy.
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Affiliation(s)
- Suleyman Vural
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - Alida Palmisano
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
- General Dynamics Information Technology (GDIT), 3150 Fairview Park Drive, Falls Church, VA, 22042, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Beverly A Teicher
- Molecular Pharmacology Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA.
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29
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Wu Y, Yang X, Jiang G, Zhang H, Ge L, Chen F, Li J, Liu H, Wang H. 5'-tRF-GlyGCC: a tRNA-derived small RNA as a novel biomarker for colorectal cancer diagnosis. Genome Med 2021; 13:20. [PMID: 33563322 PMCID: PMC7874477 DOI: 10.1186/s13073-021-00833-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 01/14/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND tRNA-derived small RNAs (tDRs), which are widely distributed in human tissues including blood and urine, play an important role in the progression of cancer. However, the expression of tDRs in colorectal cancer (CRC) plasma and their potential diagnostic values have not been systematically explored. METHODS The expression profiles of tDRs in plasma of CRC and health controls (HCs) are investigated by small RNA sequencing. The level and diagnostic value of 5'-tRF-GlyGCC are evaluated by quantitative PCR in plasma samples from 105 CRC patients and 90 HCs. The mechanisms responsible for biogenesis of 5'-tRF-GlyGCC are checked by in vitro and in vivo models. RESULTS 5'-tRF-GlyGCC is dramatically increased in plasma of CRC patients compared to that of HCs. The area under curve (AUC) for 5'-tRF-GlyGCC in CRC group is 0.882. The combination of carcinoembryonic antigen (CEA) and carbohydrate antigen 199 (CA199) with 5'-tRF-GlyGCC improves the AUC to 0.926. Consistently, the expression levels of 5'-tRF-GlyGCC in CRC cells and xenograft tissues are significantly greater than that in their corresponding controls. Blood cells co-cultured with CRC cells or mice xenografted with CRC tumors show increased levels of 5'-tRF-GlyGCC. In addition, we find that the increased expression of 5'-tRF-GlyGCC is dependent on the upregulation of AlkB homolog 3 (ALKBH3), a tRNA demethylase which can promote tRNA cleaving to generate tDRs. CONCLUSIONS The level of 5'-tRF-GlyGCC in plasma is a promising diagnostic biomarker for CRC diagnosis.
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MESH Headings
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/blood
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics
- Animals
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Cell Line, Tumor
- Colorectal Neoplasms/blood
- Colorectal Neoplasms/diagnosis
- Colorectal Neoplasms/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Male
- Mice, Inbred BALB C
- RNA, Transfer/blood
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Yingmin Wu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, Guangdong, China
| | - Xiangling Yang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, Guangdong, China
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, Guangdong, China
| | - Guanmin Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong, China
| | - Haisheng Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, Guangdong, China
| | - Lichen Ge
- Department of Clinical Laboratory, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Feng Chen
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, Guangdong, China
| | - Jiexin Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, Guangdong, China.
| | - Huanliang Liu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, Guangdong, China.
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, Guangdong, China.
| | - Hongsheng Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, Guangdong, China.
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30
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Guan Y, Greenberg EF, Hasipek M, Chen S, Liu X, Kerr CM, Gackowski D, Zarakowska E, Radivoyevitch T, Gu X, Willard B, Visconte V, Makishima H, Nazha A, Mukherji M, Sekeres MA, Saunthararajah Y, Oliński R, Xu M, Maciejewski JP, Jha BK. Context dependent effects of ascorbic acid treatment in TET2 mutant myeloid neoplasia. Commun Biol 2020; 3:493. [PMID: 32895473 PMCID: PMC7477582 DOI: 10.1038/s42003-020-01220-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
Loss-of-function TET2 mutations (TET2MT) are common in myeloid neoplasia. TET2, a DNA dioxygenase, requires 2-oxoglutarate and Fe(II) to oxidize 5-methylcytosine. TET2MT thus result in hypermethylation and transcriptional repression. Ascorbic acid (AA) increases dioxygenase activity by facilitating Fe(III)/Fe(II) redox reaction and may alleviate some biological consequences of TET2MT by restoring dioxygenase activity. Here, we report the utility of AA in the prevention of TET2MT myeloid neoplasia (MN), clarify the mechanistic underpinning of the TET2-AA interactions, and demonstrate that the ability of AA to restore TET2 activity in cells depends on N- and C-terminal lysine acetylation and nature of TET2MT. Consequently, pharmacologic modulation of acetyltransferases and histone deacetylases may regulate TET dioxygenase-dependent AA effects. Thus, our study highlights the contribution of factors that may enhance or attenuate AA effects on TET2 and provides a rationale for novel therapeutic approaches including combinations of AA with class I/II HDAC inhibitor or sirtuin activators in TET2MT leukemia. Using TET2- and ascorbic acid deficient model systems Guan et al show that long term treatment with ascorbic acid delays myeloid neoplasia in mice and reveal a complex interplay of post-translational modification of lysine residues that modulate TET2 activity in neoplastic evolution.
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Affiliation(s)
- Yihong Guan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Edward F Greenberg
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Leukemia Program, Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Metis Hasipek
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Shi Chen
- Department of Cell System & Anatomy, University of Texas Health at San Antonio, San Antonio, TX, 78229, USA.,Sylvester Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Xiaochen Liu
- Department of Cell System & Anatomy, University of Texas Health at San Antonio, San Antonio, TX, 78229, USA
| | - Cassandra M Kerr
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-095, Bydgoszcz, Poland
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-095, Bydgoszcz, Poland
| | - Tomas Radivoyevitch
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaorong Gu
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Belinda Willard
- Proteomics and Metabolomics Core, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hideki Makishima
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Aziz Nazha
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Leukemia Program, Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Mikkael A Sekeres
- Leukemia Program, Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ryszard Oliński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-095, Bydgoszcz, Poland
| | - Mingjiang Xu
- Department of Cell System & Anatomy, University of Texas Health at San Antonio, San Antonio, TX, 78229, USA.,Sylvester Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA. .,Leukemia Program, Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Babal K Jha
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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31
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Waheed S, Ramanan R, Chaturvedi SS, Lehnert N, Schofield CJ, Christov CZ, Karabencheva-Christova TG. Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair. ACS CENTRAL SCIENCE 2020; 6:795-814. [PMID: 32490196 PMCID: PMC7256942 DOI: 10.1021/acscentsci.0c00312] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Indexed: 05/08/2023]
Abstract
AlkB and its human homologue AlkBH2 are Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases that repair alkylated DNA bases occurring as a consequence of reactions with mutagenic agents. We used molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) methods to investigate how structural dynamics influences the selectivity and mechanisms of the AlkB- and AlkBH2-catalyzed demethylation of 3-methylcytosine (m3C) in single (ssDNA) and double (dsDNA) stranded DNA. Dynamics studies reveal the importance of the flexibility in both the protein and DNA components in determining the preferences of AlkB for ssDNA and of AlkBH2 for dsDNA. Correlated motions, including of a hydrophobic β-hairpin, are involved in substrate binding in AlkBH2-dsDNA. The calculations reveal that 2OG rearrangement prior to binding of dioxygen to the active site Fe is preferred over a ferryl rearrangement to form a catalytically productive Fe(IV)=O intermediate. Hydrogen atom transfer proceeds via a σ-channel in AlkBH2-dsDNA and AlkB-dsDNA; in AlkB-ssDNA, there is a competition between σ- and π-channels, implying that the nature of the complexed DNA has potential to alter molecular orbital interactions during the substrate oxidation. Our results reveal the importance of the overall protein-DNA complex in determining selectivity and how the nature of the substrate impacts the mechanism.
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Affiliation(s)
- Sodiq
O. Waheed
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Rajeev Ramanan
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Shobhit S. Chaturvedi
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Nicolai Lehnert
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Christopher J. Schofield
- The
Chemistry Research Laboratory, The Department of Chemistry, Mansfield
Road, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christo Z. Christov
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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32
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Baldwin MR, Admiraal SJ, O'Brien PJ. Transient kinetic analysis of oxidative dealkylation by the direct reversal DNA repair enzyme AlkB. J Biol Chem 2020; 295:7317-7326. [PMID: 32284330 PMCID: PMC7247310 DOI: 10.1074/jbc.ra120.013517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/10/2020] [Indexed: 11/06/2022] Open
Abstract
AlkB is a bacterial Fe(II)- and 2-oxoglutarate-dependent dioxygenase that repairs a wide range of alkylated nucleobases in DNA and RNA as part of the adaptive response to exogenous nucleic acid-alkylating agents. Although there has been longstanding interest in the structure and specificity of Escherichia coli AlkB and its homologs, difficulties in assaying their repair activities have limited our understanding of their substrate specificities and kinetic mechanisms. Here, we used quantitative kinetic approaches to determine the transient kinetics of recognition and repair of alkylated DNA by AlkB. These experiments revealed that AlkB is a much faster alkylation repair enzyme than previously reported and that it is significantly faster than DNA repair glycosylases that recognize and excise some of the same base lesions. We observed that whereas 1,N6-ethenoadenine can be repaired by AlkB with similar efficiencies in both single- and double-stranded DNA, 1-methyladenine is preferentially repaired in single-stranded DNA. Our results lay the groundwork for future studies of AlkB and its human homologs ALKBH2 and ALKBH3.
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Affiliation(s)
- Michael R Baldwin
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - Suzanne J Admiraal
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - Patrick J O'Brien
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600.
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33
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Cornelissen NV, Michailidou F, Muttach F, Rau K, Rentmeister A. Nucleoside-modified AdoMet analogues for differential methyltransferase targeting. Chem Commun (Camb) 2020; 56:2115-2118. [PMID: 31970375 PMCID: PMC7030947 DOI: 10.1039/c9cc07807j] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Methyltransferases (MTases) modify a wide range of biomolecules using S-adenosyl-l-methionine (AdoMet) as the cosubstrate. Synthetic AdoMet analogues are powerful tools to site-specifically introduce a variety of functional groups and exhibit potential to be converted only by distinct MTases. Extending the size of the substituent at the sulfur/selenium atom provides selectivity among MTases but is insufficient to discriminate between promiscuous MTases. We present a panel of AdoMet analogues differing in the nucleoside moiety (NM-AdoMets). These NM-AdoMets were efficiently produced by a previously uncharacterized methionine adenosyltransferase (MAT) from methionine and ATP analogues, such as ITP and N6-propargyl-ATP. The N6-modification changed the relative activity of three representative MTases up to 13-fold resulting in discrimination of substrates for the methyl transfer and could also be combined with transfer of allyl and propargyl groups.
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Affiliation(s)
- Nicolas V Cornelissen
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Freideriki Michailidou
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Fabian Muttach
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Kristina Rau
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
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34
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Kanazhevskaya LY, Smyshlyaev DA, Alekseeva IV, Fedorova OS. Conformational Dynamics of Dioxygenase AlkB and DNA in the Course of Catalytically Active Enzyme–Substrate Complex Formation. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019060190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Liu ZQ. Bridging free radical chemistry with drug discovery: A promising way for finding novel drugs efficiently. Eur J Med Chem 2019; 189:112020. [PMID: 32006794 DOI: 10.1016/j.ejmech.2019.112020] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/06/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023]
Abstract
Many diseases have been regarded to correlate with the in vivo oxidative damages, which are caused by overproduced free radicals from metabolic process or reactive oxygen species (ROS). This background motivates chemists to explore free radical reactions and to design a number of antioxidants, but whether free radical chemistry can be applied to accelerate the efficacy of the drug discovery is still underrepresented. Herein, in light of recent findings as well as kinetics on free radical reaction, the discipline of free radical chemistry is introduced to be a novel tool for finding potential drugs from antioxidant libraries accumulated during the study on free radical chemistry. These antioxidants provide with such abundant types of structural skeleton that might be employed to inhibit oxidations in different biological microenvironments. Although the in vitro characterization on the antioxidative property exerts a potential role of an antioxidant as a prodrug, the in vivo investigation on the property for quenching free radicals will make a final decision for the antioxidant whether it is worthy to be further explored pharmacologically. Therefore, it is reasonable to expect that bridging free radical chemistry with the pharmacological research will provide with a succinct way for finding novel drugs efficiently.
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Affiliation(s)
- Zai-Qun Liu
- Department of Organic Chemistry, College of Chemistry, Jilin University, No.2519 Jiefang Road, Changchun, 130021, People's Republic of China.
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36
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Xing SC, Mi JD, Chen JY, Xiao L, Wu YB, Liang JB, Zhang LH, Liao XD. The metabolism and morphology mutation response of probiotic Bacillus coagulans for lead stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133490. [PMID: 31635006 DOI: 10.1016/j.scitotenv.2019.07.296] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/10/2019] [Accepted: 07/18/2019] [Indexed: 05/20/2023]
Abstract
Lead is among the most common toxic heavy metals and its contamination is of great public concern. Bacillus coagulans is the probiotic which can be considered as the lead absorption sorbent to apply in the lead contaminant water directly or indirectly. A better understanding of the lead resistance and tolerance mechanisms of B. coagulans would help further its development and utilization. Wild-type Bacillus coagulans strain R11 isolated from a lead mine, was acclimated to lead-containing culture media over 85 passages, producing two lead-adapted strains, and the two strains shown higher lead intracellular accumulation ability (38.56-fold and 19.36-fold) and reducing ability (6.94-fold and 7.44-fold) than that of wild type. Whole genome sequencing, genome resequencing, and comparative transcriptomics identified lead resistance and tolerance process significantly involved in these genes which regulated glutathione and sulfur metabolism, flagellar formation and metal ion transport pathways in the lead-adapted strains, elucidating the relationships among the mechanisms regulating lead deposition, deoxidation, and motility and the evolved tolerance to lead. In addition, the B. coagulans mutants tended to form flagellar and chemotaxis systems to avoid lead ions rather than export it, suggesting a new resistance strategy. Based on the present results, the optimum lead concentration in environment should be considered when employed B. coagulans as the lead sorbent, due to the bacteria growth ability decreased in high lead concentration and physiology morphology changed could reduce the lead removal effectiveness. The identified deoxidization and compound secretion genes and pathways in B. coagulans R11 also are potential genetic engineering candidates for synthesizing glutathione, cysteine, methionine, and selenocompounds.
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Affiliation(s)
- Si-Cheng Xing
- College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642, Guangdong, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642, Guangdong, China
| | - Jian-Dui Mi
- College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642, Guangdong, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642, Guangdong, China
| | - Jing-Yuan Chen
- College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642, Guangdong, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642, Guangdong, China
| | - Lei Xiao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642, Guangdong, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642, Guangdong, China
| | - Yin-Bao Wu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642, Guangdong, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642, Guangdong, China
| | - Juan Boo Liang
- Laboratory of Sustainable Animal Production and Biodiversity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical AgroBioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Xin-Di Liao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642, Guangdong, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642, Guangdong, China.
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Bian K, Lenz SAP, Tang Q, Chen F, Qi R, Jost M, Drennan CL, Essigmann JM, Wetmore SD, Li D. DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro. Nucleic Acids Res 2019; 47:5522-5529. [PMID: 31114894 PMCID: PMC6582317 DOI: 10.1093/nar/gkz395] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/25/2019] [Accepted: 05/03/2019] [Indexed: 01/08/2023] Open
Abstract
5-Methylcytosine (5mC) in DNA CpG islands is an important epigenetic biomarker for mammalian gene regulation. It is oxidized to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) by the ten-eleven translocation (TET) family enzymes, which are α-ketoglutarate (α-KG)/Fe(II)-dependent dioxygenases. In this work, we demonstrate that the epigenetic marker 5mC is modified to 5hmC, 5fC, and 5caC in vitro by another class of α-KG/Fe(II)-dependent proteins—the DNA repair enzymes in the AlkB family, which include ALKBH2, ALKBH3 in huamn and AlkB in Escherichia coli. Theoretical calculations indicate that these enzymes may bind 5mC in the syn-conformation, placing the methyl group comparable to 3-methylcytosine, the prototypic substrate of AlkB. This is the first demonstration of the AlkB proteins to oxidize a methyl group attached to carbon, instead of nitrogen, on a DNA base. These observations suggest a broader role in epigenetics for these DNA repair proteins.
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Affiliation(s)
- Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Fangyi Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Rui Qi
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - John M Essigmann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
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38
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Chen Z, Qi M, Shen B, Luo G, Wu Y, Li J, Lu Z, Zheng Z, Dai Q, Wang H. Transfer RNA demethylase ALKBH3 promotes cancer progression via induction of tRNA-derived small RNAs. Nucleic Acids Res 2019; 47:2533-2545. [PMID: 30541109 PMCID: PMC6411830 DOI: 10.1093/nar/gky1250] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/16/2018] [Accepted: 12/03/2018] [Indexed: 12/11/2022] Open
Abstract
Transfer RNA is heavily modified and plays a central role in protein synthesis and cellular functions. Here we demonstrate that ALKBH3 is a 1-methyladenosine (m1A) and 3-methylcytidine (m3C) demethylase of tRNA. ALKBH3 can promote cancer cell proliferation, migration and invasion. In vivo study confirms the regulation effects of ALKBH3 on growth of tumor xenograft. The m1A demethylated tRNA is more sensitive to angiogenin (ANG) cleavage, followed by generating tRNA-derived small RNAs (tDRs) around the anticodon regions. tDRs are conserved among species, which strengthen the ribosome assembly and prevent apoptosis triggered by cytochrome c (Cyt c). Our discovery opens a potential and novel paradigm of tRNA demethylase, which regulates biological functions via generation of tDRs.
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Affiliation(s)
- Zhuojia Chen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.,Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Meijie Qi
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Guanzheng Luo
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingmin Wu
- Department of Microbial and Biochemical Pharmacy, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiexin Li
- Department of Microbial and Biochemical Pharmacy, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhike Lu
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Zhong Zheng
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Hongsheng Wang
- Department of Microbial and Biochemical Pharmacy, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
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Pagano A, de Sousa Araújo S, Macovei A, Dondi D, Lazzaroni S, Balestrazzi A. Metabolic and gene expression hallmarks of seed germination uncovered by sodium butyrate in Medicago truncatula. PLANT, CELL & ENVIRONMENT 2019; 42:259-269. [PMID: 29756644 DOI: 10.1111/pce.13342] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/03/2018] [Accepted: 05/05/2018] [Indexed: 05/20/2023]
Abstract
Because high-quality seeds are essential for successful crop production in challenging environments, understanding the molecular bases of seed vigour will lead to advances in seed technology. Histone deacetylase inhibitors, promoting histone hyperacetylation, are used as tools to explore aspects still uncovered of the abiotic stress response in plants. The aim of this work was to investigate novel signatures of seed germination in Medicago truncatula, using the histone deacetylase inhibitor sodium butyrate (NaB) as stress agent. NaB-treated and untreated seeds collected at 2 and 8 hr of imbibition and at the radicle protrusion stage underwent molecular phenotyping and nontargeted metabolome profiling. Quantitative enrichment analysis revealed the influence of NaB on seed nucleotide, amino acid, lipid, and carbohydrate metabolism. Up-regulation of antioxidant and polyamine biosynthesis genes occurred in response to NaB. DNA damage evidenced in NaB-treated seeds correlated with up-regulation of base-excision repair genes. Changes in N1 -methyladenosine and N1 -methylguanine were associated with up-regulation of MtALKBH1 (alkylation repair homolog) gene. N2 ,N2 -dimethylguanosine and 5-methylcytidine, tRNA modifications involved in the post-transcriptional regulation of DNA damage response, were also accumulated in NaB-treated seeds at the radicle protrusion stage. The observed changes in seed metabolism can provide novel potential metabolic hallmarks of germination.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, Pavia, 27100, Italy
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Avenida da República, Estação Agronómica Nacional, Oeiras, 2780-157, Portugal
| | - Anca Macovei
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, Pavia, 27100, Italy
| | - Daniele Dondi
- Department of Chemistry, University of Pavia, Viale Taramelli 12, Pavia, 27100, Italy
| | - Simone Lazzaroni
- Department of Chemistry, University of Pavia, Viale Taramelli 12, Pavia, 27100, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, Pavia, 27100, Italy
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40
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Thapar R, Bacolla A, Oyeniran C, Brickner JR, Chinnam NB, Mosammaparast N, Tainer JA. RNA Modifications: Reversal Mechanisms and Cancer. Biochemistry 2018; 58:312-329. [PMID: 30346748 DOI: 10.1021/acs.biochem.8b00949] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An emerging molecular understanding of RNA alkylation and its removal is transforming our knowledge of RNA biology and its interplay with cancer chemotherapy responses. DNA modifications are known to perform critical functions depending on the genome template, including gene expression, DNA replication timing, and DNA damage protection, yet current results suggest that the chemical diversity of DNA modifications pales in comparison to those on RNA. More than 150 RNA modifications have been identified to date, and their complete functional implications are still being unveiled. These include intrinsic roles such as proper processing and RNA maturation; emerging evidence has furthermore uncovered RNA modification "readers", seemingly analogous to those identified for histone modifications. These modification recognition factors may regulate mRNA stability, localization, and interaction with translation machinery, affecting gene expression. Not surprisingly, tumors differentially modulate factors involved in expressing these marks, contributing to both tumorigenesis and responses to alkylating chemotherapy. Here we describe the current understanding of RNA modifications and their removal, with a focus primarily on methylation and alkylation as functionally relevant changes to the transcriptome. Intriguingly, some of the same RNA modifications elicited by physiological processes are also produced by alkylating agents, thus blurring the lines between what is a physiological mark and a damage-induced modification. Furthermore, we find that a high level of gene expression of enzymes with RNA dealkylation activity is a sensitive readout for poor survival in four different cancer types, underscoring the likely importance of examining RNA dealkylation mechanisms to cancer biology and for cancer treatment and prognosis.
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Affiliation(s)
- Roopa Thapar
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Clement Oyeniran
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Joshua R Brickner
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Naga Babu Chinnam
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - John A Tainer
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
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41
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Purslow JA, Venditti V. 1H, 15N, 13C backbone resonance assignment of human Alkbh5. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:297-301. [PMID: 29858729 DOI: 10.1007/s12104-018-9826-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant and reversible post-transcriptional modification in eukaryotic mRNA and long non-coding RNA (lncRNA). The central role of m6A in various physiological processes has generated considerable biological and pharmacological interest. Alkbh5 (AlkB homologue 5) belongs to the AlkB family and is a non-heme Fe(II)/α-ketoglutarate-dependent dioxygenase that selectively catalyzes the oxidative demethylation of m6A. Herein, we report the backbone 1H, 15N, 13C chemical shift assignment of a fully active, 26 kDa construct of human Alkbh5. Experiments were acquired at 25 °C by heteronuclear multidimensional NMR spectroscopy. Collectively, 92% of all backbone resonances were assigned, with 195 out of a possible 212 residues assigned in the 1H-15N TROSY spectrum. Using the program TALOS+, a secondary structure prediction was generated from the assigned backbone resonance that is consistent with the previously reported X-ray structure of the enzyme. The reported assignment will permit investigations of the protein structural dynamics anticipated to provide crucial insight regarding fundamental aspects in the recognition and enzyme regulation processes.
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Affiliation(s)
- Jeffrey A Purslow
- Department of Chemistry, Iowa State University, Hach Hall, 2438 Pammel Drive, Ames, IA, 50011, USA
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University, Hach Hall, 2438 Pammel Drive, Ames, IA, 50011, USA.
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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42
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Liu X, Wu J, Shi W, Shi W, Liu H, Wu X. Lead Induces Genotoxicity via Oxidative Stress and Promoter Methylation of DNA Repair Genes in Human Lymphoblastoid TK6 Cells. Med Sci Monit 2018; 24:4295-4304. [PMID: 29933360 PMCID: PMC6045917 DOI: 10.12659/msm.908425] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Lead (Pb) is a widely used metal in modern industry and is regarded as a health hazard. Although lead-induced genotoxicity has been confirmed, the direct evidence that lead induces genotoxicity in human cells and its related mechanisms has not been fully elucidated. In this study, for the first time, we evaluated the genotoxicity induced by lead in human lymphoblastoid TK6 cells. Material/Methods The TK6 cells were incubated with various concentrations of Pb(Ac)2 for 6 h, 12 h, or 24 h. Cell viability was detected by CCK8 assay. Various biochemical markers were assessed by specific kits. Immunofluorescence assay was used to detect γ-H2AX foci formation. The promoter methylation was assessed by methylation-specific PCR. The protein levels were determined by Western blot assay. Results The results showed that after exposure to lead, cell viability was obviously decreased and γ-H2AX foci formation was significantly enhanced in TK6 cells. Moreover, the levels of 8-OHdG, ROS, MDA, and GSSG were increased, while the GSH level and SOD activity were decreased in lead-treated TK6 cells. The activation of the Nrf2-ARE signaling pathway was involved in lead-induced oxidative stress in TK6 cells. Finally, the expressions of DNA repair genes XRCC1, hOGG-1, BRCA1, and XPD were inhibited via enhancing their promoter methylation in TK6 cells after exposure to lead. Conclusions Taken together, our study provides the first published evidence that lead exposure results in DNA damage via promoting oxidative stress and the promoter methylation of DNA repair genes in human lymphoblastoid TK6 cells.
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Affiliation(s)
- Xiangquan Liu
- Department of Nutrition and Food Safety, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China (mainland)
| | - Jingying Wu
- Department of Preventive Medicine, Fuzhou Center for Disease Control and Prevention, Fuzhou, Fujian, China (mainland)
| | - Wenyan Shi
- Department of Clinical Nutrition, Shenzhen Third People's Hospital, Shenzhen, Guangdong, China (mainland)
| | - Wenhua Shi
- Department of Occupational Health, Fuzhou Center for Disease Control and Prevention, Fuzhou, Fujian, China (mainland)
| | - Hekun Liu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China (mainland)
| | - Xiaonan Wu
- Department of Nutrition and Food Safety, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China (mainland)
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43
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Liu M, Chen X, Chen T, Yin SF. A facile and general acid-catalyzed deuteration at methyl groups of N-heteroarylmethanes. Org Biomol Chem 2018; 15:2507-2511. [PMID: 28266672 DOI: 10.1039/c7ob00062f] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A facile and general Brønsted acid-catalyzed deuteration at the methyl group of N-heteroarylmethanes was achieved through a dearomatic enamine intermediate under relatively mild reaction conditions. Both 2-methyl and 4-methyl groups in quinolines were deuterated with high deuterium incorporation. Pyridines, benzo[d]thiazoles, indoles and imines including these clinical drugs were also deuterated efficiently at the methyl groups. This reaction could be conducted on a large scale (500 mmol), showing its good potential for use in large-scale synthesis.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Xue Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Tieqiao Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Shuang-Feng Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
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44
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Lenz SAP, Wetmore SD. QM/MM Study of the Reaction Catalyzed by Alkyladenine DNA Glycosylase: Examination of the Substrate Specificity of a DNA Repair Enzyme. J Phys Chem B 2017; 121:11096-11108. [PMID: 29148771 DOI: 10.1021/acs.jpcb.7b09646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human alkyladenine DNA glycosylase (AAG) functions as part of the base excision repair pathway to excise structurally diverse oxidized and alkylated DNA purines. Specifically, AAG uses a water molecule activated by a general base and a nonspecific active site lined with aromatic residues to cleave the N-glycosidic bond. Despite broad substrate specificity, AAG does not target the natural purines (adenine (A) and guanine (G)). Using the ONIOM(QM:MM) methodology, we provide fundamental atomic level details of AAG bound to DNA-containing a neutral substrate (hypoxanthine (Hx)), a nonsubstrate (G), or a cationic substrate (7-methylguanine (7MeG)) and probe changes in the reaction pathway that occur when AAG targets different nucleotides. We reveal that subtle differences in protein-DNA contacts upon binding different substrates within the flexible AAG active site can significantly affect the deglycosylation reaction. Notably, we predict that AAG excises Hx in a concerted mechanism that is facilitated through correct alignment of the (E125) general base due to hydrogen bonding with a neighboring aromatic amino acid (Y127). Hx departure is further stabilized by π-π interactions with aromatic amino acids and hydrogen bonds with active site water. Despite possessing a similar structure to Hx, G is not excised since the additional exocyclic amino group leads to misalignment of the general base due to disruption of the key E125-Y127 hydrogen bond, the catalytically unfavorable placement of water within the active site, and weakened π-contacts between aromatic amino acids and the nucleobase. In contrast, cationic 7MeG does not occupy the same position within the AAG active site as G due to steric clashes with the additional N7 methyl group, which results in the correct alignment of the general base and permits nucleobase excision as observed for neutral Hx. Overall, our structural data rationalizes the observed substrate specificity of AAG and contributes to our fundamental understanding of enzymes with flexible active sites and broad substrate specificities.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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45
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Duan HC, Wei LH, Zhang C, Wang Y, Chen L, Lu Z, Chen PR, He C, Jia G. ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition. THE PLANT CELL 2017; 29:2995-3011. [PMID: 29180595 PMCID: PMC5757257 DOI: 10.1105/tpc.16.00912] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 10/17/2017] [Accepted: 11/24/2017] [Indexed: 05/18/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant, internal, posttranscriptional modification in mRNA among all higher eukaryotes. In mammals, this modification is reversible and plays broad roles in the regulation of mRNA metabolism and processing. Despite its importance, previous studies on the role and mechanism of m6A methylation in Arabidopsis thaliana have been limited. Here, we report that ALKBH10B is a demethylase that oxidatively reverses m6A methylation in mRNA in vitro and in vivo. Depletion of ALKBH10B in the alkbh10b mutant delays flowering and represses vegetative growth. Complementation with wild-type ALKBH10B, but not a catalytically inactive mutant (ALKBH10B H366A/E368A), rescues these effects in alkbh10b-1 mutant plants, suggesting the observed phenotypes are controlled by the catalytic action of ALKBH10B We show that ALKBH10B-mediated mRNA demethylation affects the stability of target transcripts, thereby influencing floral transition. We identified 1190 m6A hypermethylated transcripts in the alkbh10b-1 mutant involved in plant development. The discovery and characterization of the archetypical RNA demethylase in Arabidopsis sheds light on the occurrence and functional role(s) of reversible mRNA methylation in plants and defines the role of m6A RNA modification in Arabidopsis floral transition.
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Affiliation(s)
- Hong-Chao Duan
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lian-Huan Wei
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chi Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ye Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lin Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhike Lu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chuan He
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- National Engineering Research Center of Pesticide (Tianjin), Nankai University, Tianjin 300071, China
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46
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Huang D, Guo X, Peng Z, Zeng G, Xu P, Gong X, Deng R, Xue W, Wang R, Yi H, Liu C. White rot fungi and advanced combined biotechnology with nanomaterials: promising tools for endocrine-disrupting compounds biotransformation. Crit Rev Biotechnol 2017; 38:671-689. [PMID: 29082760 DOI: 10.1080/07388551.2017.1386613] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Endocrine-disrupting compounds (EDCs) can interfere with endocrine systems and bio-accumulate through the food chain and even decrease biodiversity in contaminated areas. This review discusses a critical overview of recent research progress in the biotransformation of EDCs (including polychlorinated biphenyl and nonylphenol, and suspected EDCs such as heavy metals and sulfonamide antibiotics) by white rot fungi (WRF) based on techniques with an emphasis on summarizing and analyzing fungal molecular, metabolic and genetic mechanisms. Not only intracellular metabolism which seems to perform essential roles in the ability of WRF to transform EDCs, but also advanced applications are deeply discussed. This review mainly reveals the removal pathway of heavy metal and antibiotic pollutants because the single pollution almost did not exist in a real environment while the combined pollution has become more serious and close to people's life. The trends in WRF technology and its related advanced applications which use the combined technology, including biocatalysis of WRF and adsorption of nanomaterials, to degrade EDCs have also been introduced. Furthermore, challenges and future research needs EDCs biotransformation by WRF are also discussed. This research, referring to metabolic mechanisms and the combined technology of WRF with nanomaterials, undoubtedly contributes to the applications of biotechnology. This review will be of great benefit to an understanding of the trends in biotechnology for the removal of EDCs.
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Affiliation(s)
- Danlian Huang
- a College of Environmental Science and Engineering, Hunan University , Changsha , China.,b Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education , Changsha , China
| | - Xueying Guo
- a College of Environmental Science and Engineering, Hunan University , Changsha , China.,b Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education , Changsha , China
| | - Zhiwei Peng
- a College of Environmental Science and Engineering, Hunan University , Changsha , China.,b Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education , Changsha , China
| | - Guangming Zeng
- a College of Environmental Science and Engineering, Hunan University , Changsha , China.,b Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education , Changsha , China
| | - Piao Xu
- a College of Environmental Science and Engineering, Hunan University , Changsha , China.,b Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education , Changsha , China
| | - Xiaomin Gong
- a College of Environmental Science and Engineering, Hunan University , Changsha , China.,b Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education , Changsha , China
| | - Rui Deng
- a College of Environmental Science and Engineering, Hunan University , Changsha , China.,b Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education , Changsha , China
| | - Wenjing Xue
- a College of Environmental Science and Engineering, Hunan University , Changsha , China.,b Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education , Changsha , China
| | - Rongzhong Wang
- a College of Environmental Science and Engineering, Hunan University , Changsha , China.,b Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education , Changsha , China
| | - Huan Yi
- a College of Environmental Science and Engineering, Hunan University , Changsha , China.,b Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education , Changsha , China
| | - Caihong Liu
- a College of Environmental Science and Engineering, Hunan University , Changsha , China.,b Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education , Changsha , China
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47
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Torabifard H, Cisneros GA. Computational investigation of O 2 diffusion through an intra-molecular tunnel in AlkB; influence of polarization on O 2 transport. Chem Sci 2017; 8:6230-6238. [PMID: 28989656 PMCID: PMC5628400 DOI: 10.1039/c7sc00997f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022] Open
Abstract
E. Coli AlkB catalyzes the direct dealkylation of various alkylated bases in damaged DNA. The diffusion of molecular oxygen to the active site in AlkB is an essential step for the oxidative dealkylation activity. Despite detailed studies on the stepwise oxidation mechanism of AlkB, there is no conclusive picture of how O2 molecules reach the active site of the protein. Yu et al. (Nature, 439, 879) proposed the existence of an intra-molecular tunnel based on their initial crystal structures of AlkB. We have employed computational simulations to investigate possible migration pathways inside AlkB for O2 molecules. Extensive molecular dynamics (MD) simulations, including explicit ligand sampling and potential of mean force (PMF) calculations, have been performed to provide a microscopic description of the O2 delivery pathway in AlkB. Analysis of intra-molecular tunnels using the CAVER software indicates two possible pathways for O2 to diffuse into the AlkB active site. Explicit ligand sampling simulations suggests that only one of these tunnels provides a viable route. The free energy path for an oxygen molecule to travel along each of these tunnels has been determined with AMBER and AMOEBA. Both PMFs indicate passive transport of O2 from the surface of the protein. However, the inclusion of explicit polarization shows a very large barrier for diffusion of the co-substrate out of the active site, compared with the non-polarizable potential. In addition, our results suggest that the mutation of a conserved residue along the tunnel, Y178, has dramatic effects on the dynamics of AlkB and on the transport of O2 along the tunnel.
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Affiliation(s)
- Hedieh Torabifard
- Department of Chemistry , Wayne State University , Detroit , MI 48202 , USA
| | - G Andrés Cisneros
- Department of Chemistry , University of North Texas , Denton , TX 76203 , USA .
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48
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Riml C, Lusser A, Ennifar E, Micura R. Synthesis, Thermodynamic Properties, and Crystal Structure of RNA Oligonucleotides Containing 5-Hydroxymethylcytosine. J Org Chem 2017; 82:7939-7945. [PMID: 28707898 DOI: 10.1021/acs.joc.7b01171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
5-Hydroxymethylcytosine (hm5C) is an RNA modification that has attracted significant interest because of the finding that RNA hydroxymethylation can favor mRNA translation. For insight into the mechanistic details of hm5C function to be obtained, the availability of RNAs containing this modification at defined positions that can be used for in vitro studies is highly desirable. In this work, we present an eight-step route to 5-hydroxymethylcytidine (hm5rC) phosphoramidite for solid-phase synthesis of modified RNA oligonucleotides. Furthermore, we examined the effects of hm5rC on RNA duplex stability and its impact on structure formation using the sarcin-ricin loop (SRL) motif. Thermal denaturation experiments revealed that hm5rC increases RNA duplex stability. By contrast, when cytosine within an UNCG tetraloop motif was replaced by hm5rC, the thermodynamic stability of the corresponding hairpin fold was attenuated. Importantly, incorporation of hm5rC into the SRL motif resulted in an RNA crystal structure at 0.85 Å resolution. Besides changes in the hydration pattern at the site of modification, a slight opening of the hm5rC-G pair compared to the unmodified C-G in the native structure was revealed.
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Affiliation(s)
- Christian Riml
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck , 6020 Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck , 6020 Innsbruck, Austria
| | - Eric Ennifar
- Université de Strasbourg, CNRS , Architecture et Réactivité des ARN, UPR 9002, 67000 Strasbourg, France
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck , 6020 Innsbruck, Austria
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49
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Chen F, Bian K, Tang Q, Fedeles BI, Singh V, Humulock ZT, Essigmann JM, Li D. Oncometabolites d- and l-2-Hydroxyglutarate Inhibit the AlkB Family DNA Repair Enzymes under Physiological Conditions. Chem Res Toxicol 2017; 30:1102-1110. [PMID: 28269980 DOI: 10.1021/acs.chemrestox.7b00009] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Cancer-associated mutations often lead to perturbed cellular energy metabolism and accumulation of potentially harmful oncometabolites. One example is the chiral molecule 2-hydroxyglutarate (2HG); its two stereoisomers (d- and l-2HG) have been found at abnormally high concentrations in tumors featuring anomalous metabolic pathways. 2HG has been demonstrated to competitively inhibit several α-ketoglutarate (αKG)- and non-heme iron-dependent dioxygenases, including some of the AlkB family DNA repair enzymes, such as ALKBH2 and ALKBH3. However, previous studies have only provided the IC50 values of d-2HG on the enzymes, and the results have not been correlated to physiologically relevant concentrations of 2HG and αKG in cancer cells. In this work, we performed detailed kinetic analyses of DNA repair reactions catalyzed by ALKBH2, ALKBH3, and the bacterial AlkB in the presence of d- and l-2HG in both double- and single-stranded DNA contexts. We determined the kinetic parameters of inhibition, including kcat, KM, and Ki. We also correlated the relative concentrations of 2HG and αKG previously measured in tumor cells with the inhibitory effect of 2HG on the AlkB family enzymes. Both d- and l-2HG significantly inhibited the human DNA repair enzymes ALKBH2 and ALKBH3 at pathologically relevant concentrations (73-88% for d-2HG and 31-58% for l-2HG inhibition). This work provides a new perspective that the elevation of the d- or l-2HG concentration in cancer cells may contribute to an increased mutation rate by inhibiting the DNA repair performed by the AlkB family enzymes and thus exacerbate the genesis and progression of tumors.
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Affiliation(s)
- Fangyi Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Bogdan I Fedeles
- Department of Biological Engineering, Department of Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Vipender Singh
- Department of Biological Engineering, Department of Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Zachary T Humulock
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - John M Essigmann
- Department of Biological Engineering, Department of Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
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50
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Three structurally related Copper complexes with two isomers: DNA/BSA binding ability, DNA cleavage activity and excellent cytotoxicity. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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