1
|
Liu C, Sun H, Yi Y, Shen W, Li K, Xiao Y, Li F, Li Y, Hou Y, Lu B, Liu W, Meng H, Peng J, Yi C, Wang J. Absolute quantification of single-base m 6A methylation in the mammalian transcriptome using GLORI. Nat Biotechnol 2023; 41:355-366. [PMID: 36302990 DOI: 10.1038/s41587-022-01487-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/24/2022] [Indexed: 12/22/2022]
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification in mammalian cells and the best-studied epitranscriptomic mark. Despite the development of various tools to map m6A, a transcriptome-wide method that enables absolute quantification of m6A at single-base resolution is lacking. Here we use glyoxal and nitrite-mediated deamination of unmethylated adenosines (GLORI) to develop an absolute m6A quantification method that is conceptually similar to bisulfite-sequencing-based quantification of DNA 5-methylcytosine. We apply GLORI to quantify the m6A methylomes of mouse and human cells and reveal clustered m6A modifications with differential distribution and stoichiometry. In addition, we characterize m6A dynamics under stress and examine the quantitative landscape of m6A modification in gene expression regulation. GLORI is an unbiased, convenient method for the absolute quantification of the m6A methylome.
Collapse
Affiliation(s)
- Cong Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Hanxiao Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Yunpeng Yi
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, Jinan, China
| | - Weiguo Shen
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Kai Li
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Ye Xiao
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Fei Li
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Yuchen Li
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yongkang Hou
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Bo Lu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Wenqing Liu
- School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Haowei Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China.
| |
Collapse
|
2
|
Guedes PHG, Brussasco JG, Moço ACR, Moraes DD, Flauzino JMR, Luz LFG, Almeida MTG, Soares MMCN, Oliveira RJ, Madurro JM, Brito-Madurro AG. Ninhydrin as a novel DNA hybridization indicator applied to a highly reusable electrochemical genosensor for Candida auris. Talanta 2021; 235:122694. [PMID: 34517578 DOI: 10.1016/j.talanta.2021.122694] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 12/11/2022]
Abstract
This work reports a simple strategy for Candida auris genomic DNA (gDNA) detection, a multi-resistant fungus associated with nosocomial outbreaks in healthcare settings, presenting high mortality and morbidity rates. The platform was developed using gold electrode sensitized with specific DNA capture probe and ninhydrin as a novel DNA hybridization indicator. The genosensor was able to detect C. auris in urine sample by differential pulse voltammetry and electrochemical impedance spectroscopy. The biosensor's analytical performance was evaluated by differential pulse voltammetry, detecting up to 4.5 pg μL-1 of C. auris gDNA in urine (1:10, V/V). Moreover, the genosensor was reused eight times with no loss in the current signal response. The genosensor showed selectivity and stability, maintaining 100% of its response up to 80 days of storage. In order to analyze interactions of single and double-stranded DNA with ninhydrin, SEM, AFM and molecular dynamics studies followed by docking simulations were performed. Theoretical calculations showed ninhydrin interactions more favorably with dsDNA in an A-T rich binding pocket rather than with the ssDNA. Therefore, the proposed system is a promising electrochemical detection device towards a more accurate detection of C. auris gDNA in biological samples.
Collapse
Affiliation(s)
- Pedro H G Guedes
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - Jéssica G Brussasco
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - Anna C R Moço
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - Dayane D Moraes
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - José M R Flauzino
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - Luiz F G Luz
- Institute of Chemistry, Federal University of Uberlândia, Uberlândia, Brazil
| | | | | | - Ronaldo J Oliveira
- Department of Physics, Institute of Exact, Natural Sciences and Education, Federal University of Triângulo Mineiro, Uberaba, Brazil
| | - João M Madurro
- Institute of Chemistry, Federal University of Uberlândia, Uberlândia, Brazil
| | - Ana G Brito-Madurro
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil.
| |
Collapse
|
3
|
Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
Collapse
Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| |
Collapse
|
4
|
Housh K, Jha JS, Haldar T, Amin SBM, Islam T, Wallace A, Gomina A, Guo X, Nel C, Wyatt JW, Gates KS. Formation and repair of unavoidable, endogenous interstrand cross-links in cellular DNA. DNA Repair (Amst) 2021; 98:103029. [PMID: 33385969 PMCID: PMC8882318 DOI: 10.1016/j.dnarep.2020.103029] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 02/08/2023]
Abstract
Genome integrity is essential for life and, as a result, DNA repair systems evolved to remove unavoidable DNA lesions from cellular DNA. Many forms of life possess the capacity to remove interstrand DNA cross-links (ICLs) from their genome but the identity of the naturally-occurring, endogenous substrates that drove the evolution and retention of these DNA repair systems across a wide range of life forms remains uncertain. In this review, we describe more than a dozen chemical processes by which endogenous ICLs plausibly can be introduced into cellular DNA. The majority involve DNA degradation processes that introduce aldehyde residues into the double helix or reactions of DNA with endogenous low molecular weight aldehyde metabolites. A smaller number of the cross-linking processes involve reactions of DNA radicals generated by oxidation.
Collapse
Affiliation(s)
- Kurt Housh
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Jay S Jha
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Tuhin Haldar
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Saosan Binth Md Amin
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Tanhaul Islam
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Amanda Wallace
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Anuoluwapo Gomina
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Xu Guo
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Christopher Nel
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Jesse W Wyatt
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Kent S Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States; University of Missouri, Department of Biochemistry, Columbia, MO 65211, United States.
| |
Collapse
|
5
|
Wang S, Huang H, Liu J, Wei L, Wu L, Xiong W, Yin P, Tian T, Zhou X. The Manipulation of RNA-Guided Nucleic Acid Cleavage with Ninhydrin Chemistry. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903770. [PMID: 32670753 PMCID: PMC7341091 DOI: 10.1002/advs.201903770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/22/2020] [Indexed: 06/11/2023]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) systems have been established as valuable genome-editing tools. Controlling CRISPR systems has high biological significance and this field has garnered intense interest. There is a considerable need for simple approaches with no need for protein engineering. The CRISPR systems usually require a guide RNA (gRNA) moiety to recruit and direct the nuclease complexes. In this respect, the ninhydrin (1,2,3-indantrione monohydrate) seems to have considerable potential, as yet unexploited, for modifying gRNA. In this study, ninhydrin chemistry is explored for reversible postsynthetic modification of gRNA molecules. It is further shown that ninhydrin chemistry is efficient in modulating two important CRISPR systems. Thus, ninhydrin chemistry exhibits potential applications in future chemical biology studies.
Collapse
Affiliation(s)
- Shao‐Ru Wang
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
- Sauvage Center for Molecular SciencesWuhan UniversityWuhan430072China
- Hubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhan430071China
| | - Hai‐Yan Huang
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
| | - Jian Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Lai Wei
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
| | - Ling‐Yu Wu
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
| | - Wei Xiong
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Tian Tian
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
- Hubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhan430071China
| | - Xiang Zhou
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
- Hubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhan430071China
| |
Collapse
|
6
|
Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ. Nat Methods 2020; 17:515-523. [PMID: 32251394 PMCID: PMC7205578 DOI: 10.1038/s41592-020-0797-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/02/2020] [Indexed: 02/06/2023]
Abstract
Transcription is a highly dynamic process that generates single-stranded DNA (ssDNA) in the genome as ‘transcription bubbles’. Here we describe a kethoxal-assisted single-stranded DNA sequencing (KAS-seq) approach, based on the fast and specific reaction between N3-kethoxal and guanines in ssDNA in live cells and mouse tissues. KAS-seq enables rapid (within 5 min), sensitive, and genome-wide capture and mapping of ssDNA produced by transcriptionally active RNA polymerases or other processes in situ by using as few as 1,000 cells. KAS-seq defines a group of enhancers that are single-stranded, which enrich unique sequence motifs and are associated with specific transcription factor binding and more enhancer-promotor interactions. Under protein condensation inhibition conditions, KAS-seq uncovers a rapid release of RNA polymerase II (Pol II) from a group of promotors. KAS-seq thus facilitates fast, comprehensive, and accurate analysis of transcription dynamics and enhancer activities simultaneously in a low input and high-throughput manner.
Collapse
|
7
|
Hernandez-Castillo C, Termini J, Shuck S. DNA Adducts as Biomarkers To Predict, Prevent, and Diagnose Disease-Application of Analytical Chemistry to Clinical Investigations. Chem Res Toxicol 2020; 33:286-307. [PMID: 31638384 DOI: 10.1021/acs.chemrestox.9b00295] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Characterization of the chemistry, structure, formation, and metabolism of DNA adducts has been one of the most significant contributions to the field of chemical toxicology. This work provides the foundation to develop analytical methods to measure DNA adducts, define their relationship to disease, and establish clinical tests. Monitoring exposure to environmental and endogenous toxicants can predict, diagnose, and track disease as well as guide therapeutic treatment. DNA adducts are one of the most promising biomarkers of toxicant exposure owing to their stability, appearance in numerous biological matrices, and characteristic analytical properties. In addition, DNA adducts can induce mutations to drive disease onset and progression and can serve as surrogate markers of chemical exposure. In this perspective, we highlight significant advances made within the past decade regarding DNA adduct quantitation using mass spectrometry. We hope to expose a broader audience to this field and encourage analytical chemistry laboratories to explore how specific adducts may be related to various pathologies. One of the limiting factors in developing clinical tests to measure DNA adducts is cohort size; ideally, the cohort would allow for model development and then testing of the model to the remaining cohort. The goals of this perspective article are to (1) provide a summary of analyte levels measured using state-of-the-art analytical methods, (2) foster collaboration, and (3) highlight areas in need of further investigation.
Collapse
Affiliation(s)
- Carlos Hernandez-Castillo
- Department of Molecular Medicine , Beckman Research Institute at City of Hope Duarte , California 91010 , United States
| | - John Termini
- Department of Molecular Medicine , Beckman Research Institute at City of Hope Duarte , California 91010 , United States
| | - Sarah Shuck
- Department of Molecular Medicine , Beckman Research Institute at City of Hope Duarte , California 91010 , United States
| |
Collapse
|
8
|
Koliadenko V, Wilanowski T. Additional functions of selected proteins involved in DNA repair. Free Radic Biol Med 2020; 146:1-15. [PMID: 31639437 DOI: 10.1016/j.freeradbiomed.2019.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022]
Abstract
Protein moonlighting is a phenomenon in which a single polypeptide chain can perform a number of different unrelated functions. Here we present our analysis of moonlighting in the case of selected DNA repair proteins which include G:T mismatch-specific thymine DNA glycosylase (TDG), methyl-CpG-binding domain protein 4 (MBD4), apurinic/apyrimidinic endonuclease 1 (APE1), AlkB homologs, poly (ADP-ribose) polymerase 1 (PARP-1) and single-strand selective monofunctional uracil DNA glycosylase 1 (SMUG1). Most of their additional functions are not accidental and clear patterns are emerging. Participation in RNA metabolism is not surprising as bases occurring in RNA are the same or very similar to those in DNA. Other common additional function involves regulation of transcription. This is not unexpected as these proteins bind to specific DNA regions for DNA repair, hence they can also be recruited to regulate transcription. Participation in demethylation and replication of DNA appears logical as well. Some of the multifunctional DNA repair proteins play major roles in many diseases, including cancer. However, their moonlighting might prove a major difficulty in the development of new therapies because it will not be trivial to target a single protein function without affecting its other functions that are not related to the disease.
Collapse
Affiliation(s)
- Vlada Koliadenko
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Wilanowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland.
| |
Collapse
|
9
|
Vilanova B, Fernández D, Casasnovas R, Pomar AM, Alvarez-Idaboy JR, Hernández-Haro N, Grand A, Adrover M, Donoso J, Frau J, Muñoz F, Ortega-Castro J. Formation mechanism of glyoxal-DNA adduct, a DNA cross-link precursor. Int J Biol Macromol 2017; 98:664-675. [PMID: 28192135 DOI: 10.1016/j.ijbiomac.2017.01.140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/30/2017] [Accepted: 01/31/2017] [Indexed: 01/08/2023]
Abstract
DNA nucleobases undergo non-enzymatic glycation to nucleobase adducts which can play important roles in vivo. In this work, we conducted a comprehensive experimental and theoretical kinetic study of the mechanisms of formation of glyoxal-guanine adducts over a wide pH range in order to elucidate the molecular basis for the glycation process. Also, we performed molecular dynamics simulations to investigate how open or cyclic glyoxal-guanine adducts can cause structural changes in an oligonucleotide model. A thermodynamic study of other glycating agents including methylglyoxal, acrolein, crotonaldehyde, 4-hydroxynonenal and 3-deoxyglucosone revealed that, at neutral pH, cyclic adducts were more stable than open adducts; at basic pH, however, the open adducts of 3-deoxyglucosone, methylglyoxal and glyoxal were more stable than their cyclic counterparts. This result can be ascribed to the ability of the adducts to cross-link DNA. The new insights may contribute to improve our understanding of the connection between glycation and DNA cross-linking.
Collapse
Affiliation(s)
- B Vilanova
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain.
| | - D Fernández
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - R Casasnovas
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - A M Pomar
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - J R Alvarez-Idaboy
- Facultad de Química, Departamento de Física y Química Teórica, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico
| | | | - A Grand
- Univ. Greboble Alpes, INAC-SCIB, F-38000 Grenoble, France; CEA, INAC-SyMMES, F-38000 Grenoble, France; Universidad Autónoma de Chile, Carlos Antúnez 1920, 7500566, Providencia, Santiago de, Chile
| | - M Adrover
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - J Donoso
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - J Frau
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - F Muñoz
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - J Ortega-Castro
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| |
Collapse
|
10
|
Mechanistic study of base-pairing small regulatory RNAs in bacteria. Methods 2016; 117:67-76. [PMID: 27693881 DOI: 10.1016/j.ymeth.2016.09.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/22/2016] [Indexed: 11/24/2022] Open
Abstract
In all three kingdoms of life, RNA is not only involved in the expression of genetic information, but also carries out extremely diverse cellular functions. This versatility is essentially due to the fact that RNA molecules can exploit the power of base pairing to allow them to fold into a wide variety of structures through which they can perform diverse roles, but also to selectively target and bind to other nucleic acids. This is true in particular for bacterial small regulatory RNAs that act by imperfect base-pairing with target mRNAs, and thereby control their expression through different mechanisms. Here we outline an overview of in vivo and in vitro approaches that are currently used to gain mechanistic insights into how these sRNAs control gene expression in bacteria.
Collapse
|
11
|
Lee C, Kim J, Kwon M, Lee K, Min H, Kim SH, Kim D, Lee N, Kim J, Kim D, Ko C, Park C. Screening for Escherichia coli K-12 genes conferring glyoxal resistance or sensitivity by transposon insertions. FEMS Microbiol Lett 2016; 363:fnw199. [PMID: 27535647 DOI: 10.1093/femsle/fnw199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2016] [Indexed: 12/14/2022] Open
Abstract
Glyoxal (GO) belongs to the reactive electrophilic species generated in vivo in all organisms. In order to identify targets of GO and their response mechanisms, we attempted to screen for GO-sensitive mutants by random insertions of TnphoA-132. The genes responsible for GO susceptibility were functionally classified as the following: (i) tRNA modification; trmE, gidA and truA, (ii) DNA repair; recA and recC, (iii) toxin-antitoxin; mqsA and (iv) redox metabolism; yqhD and caiC In addition, an insertion in the crp gene, encoding the cAMP responsive transcription factor, exhibits a GO-resistant phenotype, which is consistent with the phenotype of adenylate cyclase (cya) mutant showing GO resistance. This suggests that global regulation involving cAMP is operated in a stress response to GO. To further characterize the CRP-regulated genes directly associated with GO resistance, we created double mutants deficient in both crp and one of the candidate genes including yqhD, gloA and sodB The results indicate that these genes are negatively regulated by CRP as confirmed by real-time RT-PCR. We propose that tRNA as well as DNA are the targets of GO and that toxin/antitoxin, antioxidant and cAMP are involved in cellular response to GO.
Collapse
Affiliation(s)
- Changhan Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Jihong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Minsuk Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Kihyun Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Haeyoung Min
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Seong Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Dongkyu Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Nayoung Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Jiyeun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Doyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Changmin Ko
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Chankyu Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| |
Collapse
|
12
|
Jahnz-Wechmann Z, Framski GR, Januszczyk PA, Boryski J. Base-Modified Nucleosides: Etheno Derivatives. Front Chem 2016; 4:19. [PMID: 27200341 PMCID: PMC4848297 DOI: 10.3389/fchem.2016.00019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/07/2016] [Indexed: 11/13/2022] Open
Abstract
This review presents synthesis and chemistry of nucleoside analogs, possessing an additional fused, heterocyclic ring of the "etheno" type, such as 1,N(6)-ethenoadenosine, 1,N(4)-ethenocytidine, 1,N(2)-ethenoguanosine, and other related derivatives. Formation of ethenonucleosides, in the presence of α-halocarbonyl reagents and their mechanism, stability, and degradation, reactions of substitution and transglycosylation, as well as their application in the nucleoside synthesis, have been described. Some of the discussed compounds may be applied as chemotherapeutic agents in antiviral and anticancer treatment, acting as pro-nucleosides of already known, biologically active nucleoside analogs.
Collapse
Affiliation(s)
| | - Grzegorz R Framski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan, Poland
| | - Piotr A Januszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan, Poland
| | - Jerzy Boryski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan, Poland
| |
Collapse
|
13
|
Jahnz-Wechmann Z, Framski G, Januszczyk P, Boryski J. Bioactive fused heterocycles: Nucleoside analogs with an additional ring. Eur J Med Chem 2015; 97:388-96. [DOI: 10.1016/j.ejmech.2014.12.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/05/2014] [Accepted: 12/17/2014] [Indexed: 11/25/2022]
|
14
|
Uchiyama S, Ohta K, Inaba Y, Kunugita N. Determination of carbonyl compounds generated from the E-cigarette using coupled silica cartridges impregnated with hydroquinone and 2,4-dinitrophenylhydrazine, followed by high-performance liquid chromatography. ANAL SCI 2014; 29:1219-22. [PMID: 24334991 DOI: 10.2116/analsci.29.1219] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Carbonyl compounds in E-cigarette smoke mist were measured using coupled silica cartridges impregnated with hydroquinone and 2,4-dinitrophenylhydrazine, followed by high-performance liquid chromatography. A total of 363 E-cigarettes (13 brands) were examined. Four of the 13 E-cigarette brands did not generate any carbonyl compounds, while the other nine E-cigarette brands generated various carbonyl compounds. However, the carbonyl concentrations of the E-cigarette products did not show typical distributions, and the mean values were largely different from the median values. It was elucidated that E-cigarettes incidentally generate high concentrations of carbonyl compounds.
Collapse
|
15
|
Abstract
The discovery of the enzymatic formation of lactic acid from methylglyoxal dates back to 1913 and was believed to be associated with one enzyme termed ketonaldehydemutase or glyoxalase, the latter designation prevailed. However, in 1951 it was shown that two enzymes were needed and that glutathione was the required catalytic co-factor. The concept of a metabolic pathway defined by two enzymes emerged at this time. Its association to detoxification and anti-glycation defence are its presently accepted roles, since methylglyoxal exerts irreversible effects on protein structure and function, associated with misfolding. This functional defence role has been the rationale behind the possible use of the glyoxalase pathway as a therapeutic target, since its inhibition might lead to an increased methylglyoxal concentration and cellular damage. However, metabolic pathway analysis showed that glyoxalase effects on methylglyoxal concentration are likely to be negligible and several organisms, from mammals to yeast and protozoan parasites, show no phenotype in the absence of one or both glyoxalase enzymes. The aim of the present review is to show the evolution of thought regarding the glyoxalase pathway since its discovery 100 years ago, the current knowledge on the glyoxalase enzymes and their recognized role in the control of glycation processes.
Collapse
|
16
|
Calderón-Montaño JM, Burgos-Morón E, Orta ML, Pastor N, Perez-Guerrero C, Austin CA, Mateos S, López-Lázaro M. Guanidine-reactive agent phenylglyoxal induces DNA damage and cancer cell death. Pharmacol Rep 2012; 64:1515-25. [DOI: 10.1016/s1734-1140(12)70949-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 06/28/2012] [Indexed: 01/03/2023]
|
17
|
More SS, Raza A, Vince R. The butter flavorant, diacetyl, forms a covalent adduct with 2-deoxyguanosine, uncoils DNA, and leads to cell death. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:3311-3317. [PMID: 22385266 DOI: 10.1021/jf300180e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Diacetyl (DA), a natural butter flavorant, is a causative agent for the lung disease obliterative bronchiolitis. Mutagenic properties of 1,2-dicarbonyls have previously been empirically linked to their possible interaction with DNA nucleobases. This study for the first time identifies chemically the adduct of DA with 2-deoxyguanosine. Selective reactivity of DA with 5'-TTTGTTTTT-3' over 5'-TTTTTTTTT-3' indicated its propensity to modify specifically the guanosine residue. Treatment of plasmid DNA, pBR322, with DA induced changes in electrophoretic mobility that are typical of ternary structure disruption. Such DNA nucleobase interaction of DA translated into increased apoptosis in DA-treated SH-SY5Y cells in a dose-dependent manner (IC(50) = 0.114 ± 0.0421 mM). The traditional carbonyl scavengers metformin, 2-thiobarbituric acid, and d-penicillamine protected cells from DA toxicity in proportion to their rates of reaction with DA, with d-penicillamine causing a maximal increase in the IC(50) to 5.23 ± 0.0992 mM when co-incubated with DA.
Collapse
Affiliation(s)
- Swati S More
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | | | |
Collapse
|
18
|
Parr C, Pierce SE, Smith SI, Brodbelt JS. Investigation of the Reactivity of Oligodeoxynucleotides with Glyoxal and KMnO(4) Chemical Probes by Electrospray Ionization Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 304:115-123. [PMID: 21743793 PMCID: PMC3130548 DOI: 10.1016/j.ijms.2010.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The reactions of two well-known chemical probes, glyoxal and potassium permanganate (KMnO(4)), with oligodeoxynucleotides were monitored by electrospray ionization (ESI) mass spectrometry to evaluate the influence of the sequence of DNA, its secondary structure, and interactions with associated ligands on the reactivity of the two probes. Glyoxal, a guanine-reactive probe, incorporated a mass shift of 58 Da, and potassium permanganate (KMnO(4)) is a thymine-reactive probe that resulted in a mass shift of 34 Da. The reactions depended on the accessibility of the nucleobases, and the peak abundances of the adducts in the ESI-mass spectra were used to quantify the extent of the chemical probe reactions. In this study, both mixed-base sequences were studied as well as control sequences in which one reactive site was located at the terminus or center of the oligodeoxynucleotide while the surrounding bases were a second, different nucleobase. In addition, the reactions of the chemical probes with non-covalent complexes formed between DNA and either actinomycin D or ethidium bromide, both known to interact with single strand DNA, were evaluated.
Collapse
Affiliation(s)
- Carol Parr
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
| | | | | | | |
Collapse
|
19
|
Lai C, Lin G, Wang W, Luo H. Absolute configurations and stability of cyclic guanosine mono-adducts with glyoxal and methylglyoxal. Chirality 2011; 23:487-94. [DOI: 10.1002/chir.20875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Accepted: 04/14/2010] [Indexed: 11/08/2022]
|
20
|
Raza A, Vince R. Dehydroascorbic acid adducts of guanosine residues: possible biological implications. Chembiochem 2011; 12:1015-7. [PMID: 21425230 DOI: 10.1002/cbic.201000748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Indexed: 11/08/2022]
Affiliation(s)
- Abbas Raza
- Center for Drug Design, University of Minnesota, Minneapolis, 55455, USA
| | | |
Collapse
|
21
|
Steen KA, Malhotra A, Weeks KM. Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease. J Am Chem Soc 2010; 132:9940-3. [PMID: 20597503 DOI: 10.1021/ja103781u] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a powerful approach for characterizing RNA structure and dynamics at single-nucleotide resolution. However, SHAPE technology is limited, sometimes severely, because primer extension detection obscures structural information for approximately 15 nts at the 5' end and 40-60 nts at the 3' end of the RNA. Moreover, detection by primer extension is more complex than the actual structure-selective chemical interrogation step. Here we quantify covalent adducts in RNA directly by adduct-inhibited exoribonuclease degradation. RNA 2'-O-adducts block processivity of a 3'-->5' exoribonuclease, RNase R, to produce fragments that terminate three nucleotides 3' of the modification site. We analyzed the structure of the native thiamine pyrophosphate (TPP) riboswitch aptamer domain and identified large changes in local nucleotide dynamics and global RNA structure upon ligand binding. In addition to numerous changes that can be attributed to ligand recognition, we identify a single nucleotide bulge register shift, distant from the binding site, that stabilizes the ligand-bound structure. Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) should prove broadly useful for facile structural analysis of small noncoding RNAs and for RNAs that have functionally critical structures at their 5' and 3' ends.
Collapse
Affiliation(s)
- Kady-Ann Steen
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | | | | |
Collapse
|
22
|
Wang H, Cao H, Wang Y. Quantification of N2-carboxymethyl-2'-deoxyguanosine in calf thymus DNA and cultured human kidney epithelial cells by capillary high-performance liquid chromatography-tandem mass spectrometry coupled with stable isotope dilution method. Chem Res Toxicol 2010; 23:74-81. [PMID: 19968260 DOI: 10.1021/tx900286c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glyoxal is generated endogenously from the degradation of glucose and the oxidation of carbohydrates, lipids, and the 2-deoxyribose moieties of DNA. Glyoxal is also widely used in industry and is present in cigarette smoke and food. Glyoxal can conjugate with nucleobases and proteins to give advanced glycation end products. N(2)-Carboxymethyl-2'-deoxyguanosine (N(2)-CMdG) and the cyclic 1,N(2)-glyoxal-dG are the major glyoxal adducts formed in DNA. In this study, we first assessed the stabilities of these two adducts. It turned out that 1,N(2)-glyoxal-dG was very unstable, with more than 70% of the adduct being decomposed to dG upon a 24 h incubation at 37 degrees C in phosphate-buffered saline. However, N(2)-CMdG was very stable; less than 0.5% of the lesion was degraded to dG after a 7 day incubation under the same conditions. We further developed a sensitive capillary liquid chromatography-electrospray ionization-tandem mass spectrometry coupled with a stable isotope dilution method and quantified the formation of N(2)-CMdG in calf thymus DNA and 293T human kidney epithelial cells that were exposed to glyoxal and in calf thymus DNA treated with d-glucose. Our results showed that N(2)-CMdG was produced at 2-134 lesions per 10(6) nucleosides in calf thymus DNA when the surrounding glyoxal concentration was increased from 10 to 500 microM and approximately 3-27 lesions per 10(7) nucleosides, while the D-glucose concentration changed from 2 to 50 mM. Furthermore, N(2)-CMdG was induced endogenously in 293T human kidney epithelial cells and exposure to glyoxal further stimulated the formation of this lesion; the level of this adduct ranged from 7 to 15 lesions per 10(8) nucleosides, while the glyoxal concentration increased from 10 microM to 1.25 mM. Collectively, our results suggested that N(2)-CMdG might serve as a biomarker for glyoxal exposure.
Collapse
Affiliation(s)
- Hongxia Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, USA
| | | | | |
Collapse
|
23
|
Mortimer SA, Johnson JS, Weeks KM. Quantitative analysis of RNA solvent accessibility by N-silylation of guanosine. Biochemistry 2009; 48:2109-14. [PMID: 19226117 DOI: 10.1021/bi801939g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An important unmet experimental objective is to analyze local RNA structure in a way that is strictly governed by solvent accessibility. Essentially all chemical probes currently used to evaluate RNA (and DNA) structure via formation of stable covalent adducts employ carbon-based electrophiles, which undergo nucleophilic attack from limited spatial orientations and via highly polar transition states. Reaction by these classical electrophiles is therefore gated by both solvent accessibility and additional electrostatic factors. In contrast, silicon electrophiles react via their d-orbitals and consequently can undergo nucleophilic attack from many spatial orientations. In this work, we explore the use of silanes to react indiscriminately with RNA such that the primary factor governing reactivity is solvent accessibility. We show that N,N-(dimethylamino)dimethylchlorosilane (DMAS-Cl) reacts at the guanosine N2 position to yield a near-perfect measure (r >or= 0.82) of solvent accessibility in an RNA with a complex tertiary structure. This silane-based chemistry represents a direct and quantitative approach for probing solvent accessibility at the base pairing face of guanosine in RNA.
Collapse
Affiliation(s)
- Stefanie A Mortimer
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | | | | |
Collapse
|
24
|
Chen HJC, Chen YC. Analysis of glyoxal-induced DNA cross-links by capillary liquid chromatography nanospray ionization tandem mass spectrometry. Chem Res Toxicol 2009; 22:1334-41. [PMID: 19527002 DOI: 10.1021/tx900129e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glyoxal (gx) is an alpha-dicarbonyl species derived endogenously from the metabolism of carbohydrates or nitrosamines and from oxidation of lipids and nucleic acids. It is also widely distributed in foods and the environment. Glyoxal reacts with biomolecules, causing cross-links of proteins and DNA. The cross-linked products of glyoxal with 2'-deoxyribonucleosides have been characterized as dG-gx-dC, dG-gx-dG, and dG-gx-dA. We herein develop a highly specific and sensitive capillary liquid chromatography nanospray ionization tandem mass spectrometry (capLC-NSI/MS/MS) assay for the simultaneous quantification of these three DNA cross-links using a triple-quadrupole mass spectrometer. The sample pretreatment procedures included enzyme hydrolysis of DNA and adduct enrichment by a reversed phase solid phase extraction column. We compared two enzyme hydrolysis conditions, and significantly different adduct levels were observed. This assay achieved attomole sensitivity with detection limits of 12-75 amol injecting each cross-link standard on-column. After calf thymus DNA was incubated with 1.0 mM of glyoxal at 37 degrees C for 30 days, the levels of dG-gx-dC, dG-gx-dG, and dG-gx-dA in this sample were determined as 6.52, 0.80, and 2.74 in 10(5) normal nucleotides, respectively, by capLC-NSI/MS/MS analysis after hydrolysis under optimized conditions. The identity of these cross-links in glyoxal-treated DNA was confirmed by MS(2) and MS(3) scan spectra using a linear ion trap mass spectrometer. In 20 microg of human placental DNA hydrolysate, the levels of dG-gx-dC, dG-gx-dG, and dG-gx-dA were quantified as 2.49, 1.26, and 3.50 in 10(8) normal nucleotides, respectively. These DNA cross-links, if not repaired, can be mutagenic, and they represent a type of damage to the integrity of DNA structure due to exposure of glyoxal.
Collapse
Affiliation(s)
- Hauh-Jyun Candy Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan.
| | | |
Collapse
|
25
|
Abdulnur SF. Interactions of methylglyoxal with methylamine. CIBA FOUNDATION SYMPOSIUM 2008:195-209. [PMID: 259499 DOI: 10.1002/9780470720493.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ab initio quantum mechanical calculations are used to study the interactions of the aldehydic group of methylglyoxal with the NH2 groups of protein side-chains, using methylamine as a representative molecule. The hydrogen-bonding interaction, C = O...H - N, results in an electronic charge transfer from methylglyoxal to methylamine in both the ground and first excited triplet states. In this latter state a slight possibility is found for the H atom in the hydrogen bond to tunnel from methylglyoxal to methylamine, leading to the possible formation of two free radical fragments. The approach of methylamine to methylglyoxal in the stacked conformation C...N to form a hemiacetal, associated with electron charge transfer from methylamine to methylglyoxal, is energetically unfavourable in vacuum. The concomitant tunnelling of a proton from a proton-donating solvent molecule to the aldehydic oxygen of methylglyoxal is shown to make this approach favourable. The relative stability of the keto and enol forms of methylglyoxal is also investigated, the keto form being found the more stable in vacuum.
Collapse
|
26
|
Pluskota-Karwatka D, Pawłowicz AJ, Tomas M, Kronberg L. Formation of adducts in the reaction of glyoxal with 2′-deoxyguanosine and with calf thymus DNA. Bioorg Chem 2008; 36:57-64. [PMID: 18078668 DOI: 10.1016/j.bioorg.2007.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 10/10/2007] [Accepted: 10/10/2007] [Indexed: 11/27/2022]
|
27
|
Bidmon C, Frischmann M, Pischetsrieder M. Analysis of DNA-bound advanced glycation end-products by LC and mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 855:51-8. [PMID: 17161667 DOI: 10.1016/j.jchromb.2006.11.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 11/15/2006] [Accepted: 11/21/2006] [Indexed: 11/18/2022]
Abstract
Sugars and sugar degradation products readily react in vitro with guanine derivatives, resulting in the formation of DNA-bound advanced glycation end-products (DNA-AGEs). The two diastereomers of N(2)-(1-carboxyethyl)-2'-deoxyguanosine (CEdG(A,B)) and the cyclic adduct of methylglyoxal and 2'-deoxyguanosine (mdG) (N(2)-7-bis(1-hydroxy-2-oxopropyl)-2'-deoxyguanosine have also been detected in cultured cells and/or in vivo. LC-MS/MS methods have been developed to analyze sensitively DNA adducts in vitro and in vivo. In this paper, the chemical structures of possible DNA-AGEs and the application of LC-MS/MS to measure DNA-AGEs are reviewed.
Collapse
Affiliation(s)
- Clemens Bidmon
- Institute of Pharmacy and Food Chemistry, University of Erlangen-Nuremberg, Erlangen, Germany
| | | | | |
Collapse
|
28
|
Palani PV, Lin NS. Northern analysis of viral plus- and minus-strand RNAs. CURRENT PROTOCOLS IN MICROBIOLOGY 2007; Chapter 16:Unit 16E.3. [PMID: 18770617 DOI: 10.1002/9780471729259.mc16e03s4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Replication is a fundamental activity of viruses. Replication of positive-sense RNA viruses involves the synthesis of complementary minus-strand intermediates from the parental RNA template followed by synthesis of nascent plus strands. Negative-sense RNA genome and double-stranded RNA are copied into positive-sense mRNA before translation. To detect and estimate the abundance of plus- and minus-strand viral transcripts in the infected samples, northern analysis is the most commonly used method.
Collapse
|
29
|
Yu E, Fabris D. Toward multiplexing the application of solvent accessibility probes for the investigation of RNA three-dimensional structures by electrospray ionization-Fourier transform mass spectrometry. Anal Biochem 2005; 334:356-66. [PMID: 15494143 DOI: 10.1016/j.ab.2004.07.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2004] [Indexed: 11/16/2022]
Abstract
Multiple solvent accessibility probes can be applied simultaneously to investigate the three-dimensional structure of complex RNA substrates when electrospray ionization-Fourier transform mass spectrometry (ESI-FTMS) is employed in place of polyacrylamide gel electrophoresis (PAGE). We show that classic chemical probes, such as dimethylsulfate, kethoxal, and 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate, can be combined in probing mixtures designed to assess the full spectrum of base pairing and steric protection for the most abundant ribonucleotides included in RNA. After probe-independent hydrolysis of the alkylated substrate, the mixture of oligonucleotide products is mass mapped by ESI-FTMS analysis, which enables the unambiguous identification of probed bases from the unique mass signatures provided by the different chemical modifiers. In this bottom-up approach, any theoretical limit to the size of the possible target RNA will be determined by the effectiveness of the hydrolysis procedure rather than by the performance of the detection technique. Control experiments performed on the stem-loop 4 of human immunodeficiency virus type 1 have shown no adverse interactions between the reagents combined in the probing cocktails. No significant discrepancies between the alkylation patterns offered by the cocktails and the individual reagents could be detected, indicating that multiplexing the probe application does not necessarily lead to structural distortion but provides valid data on base accessibility and protection. To demonstrate the ruggedness of this approach, optimized cocktails were finally employed to assess the stability of the folded structure of mouse mammary tumor virus pseudoknot in the presence of different amounts of Mg2+. Multiplexing the probe application constitutes an essential step toward high-throughput applications, which will take advantage of a strategy that maximizes the information attainable from a single experiment, while minimizing time and sample consumption over PAGE-based methods.
Collapse
Affiliation(s)
- Eizadora Yu
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | | |
Collapse
|
30
|
Ruohola AM, Koissi N, Andersson S, Lepistö I, Neuvonen K, Mikkola S, Lönnberg H. Reactions of 9-substituted guanines with bromomalondialdehyde in aqueous solution predominantly yield glyoxal-derived adducts. Org Biomol Chem 2004; 2:1943-50. [PMID: 15227548 DOI: 10.1039/b405117c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reactions of 9-ethylguanine, 2'-deoxyguanosine and guanosine with bromomalondialdehyde in aqueous buffers over a wide pH-range were studied. The main products were isolated and characterized by (1)H and (13)C NMR and mass spectroscopy. The final products formed under acidic and basic conditions were different, but they shared the common feature of being derived from glyoxal. Among the 1 : 1 adducts, 1,N(2)-(trans-1,2-dihydroxyethano)guanine adduct (6) predominated at pH < 6 and N(2)-carboxymethylguanine adduct (10a,b) at pH > 7. In addition to these, an N(2)-(4,5-dihydroxy-1,3-dioxolan-2-yl)methylene adduct (11a,b) and an N(2)-carboxymethyl-1,N(2)-(trans-1,2-dihydroxyethano)guanine adduct (12) were obtained at pH 10. The results of kinetic experiments suggest that bromomalondialdehyde is significantly decomposed to formic acid and glycolaldehyde under the conditions required to obtain guanine adducts. Glycolaldehyde is oxidized to glyoxal, which then modifies the guanine base more readily than bromomalondialdehyde. Besides the glyoxal-derived adducts, 1,N(2)-ethenoguanine (5a-c) and N(2),3-ethenoguanine adducts (4a-c) were formed as minor products, and a transient accumulation of two unstable intermediates, tentatively identified as 1,N(2)-(1,2,2,3-tetrahydroxypropano)(8) and 1,N(2)-(2-formyl-1,2,3-trihydroxypropano)(9) adducts, was observed.
Collapse
Affiliation(s)
- Anne-Mari Ruohola
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | | | | | | | | | | | | |
Collapse
|
31
|
Abstract
Exocyclic DNA adducts are mutagenic lesions that can be formed by both exogenous and endogenous mutagens/carcinogens. These adducts are structurally analogs but can differ in certain features such as ring size, conjugation, planarity and substitution. Although the information on the biological role of the repair activities for these adducts is largely unknown, considerable progress has been made on their reaction mechanisms, substrate specificities and kinetic properties that are affected by adduct structures. At least four different mechanisms appear to have evolved for the removal of specific exocyclic adducts. These include base excision repair, nucleotide excision repair, mismatch repair, and AP endonuclease-mediated repair. This overview highlights the recent progress in such areas with emphasis on structure-activity relationships. It is also apparent that more information is needed for a better understanding of the biological and structural implications of exocyclic adducts and their repair.
Collapse
Affiliation(s)
- Bo Hang
- Department of Molecular Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA.
| |
Collapse
|
32
|
Mistry N, Podmore I, Cooke M, Butler P, Griffiths H, Herbert K, Lunec J. Novel monoclonal antibody recognition of oxidative DNA damage adduct, deoxycytidine-glyoxal. J Transl Med 2003; 83:241-50. [PMID: 12594238 DOI: 10.1097/01.lab.0000053915.88556.ed] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Glyoxal, a reactive aldehyde, is a decomposition product of lipid hydroperoxides, oxidative deoxyribose breakdown, or autoxidation of sugars, such as glucose. It readily forms DNA adducts, generating potential carcinogens such as glyoxalated deoxycytidine (gdC). A major drawback in assessing gdC formation in cellular DNA has been methodologic sensitivity. We have developed an mAb that specifically recognizes gdC. Balb/c mice were immunized with DNA, oxidatively modified by UVC/hydrogen peroxide in the presence of endogenous metal ions. Although UVC is not normally considered an oxidizing agent, a UVC/hydrogen peroxide combination may lead to glyoxalated bases arising from hydroxyl radical damage to deoxyribose. This damaging system was used to induce numerous oxidative lesions including glyoxal DNA modifications, from which resulted a number of clones. Clone F3/9/H2/G5 showed increased reactivity toward glyoxal-modified DNA greater than that of the immunizing antigen. ELISA unequivocally showed Ab recognition toward gdC, which was confirmed by gas chromatography-mass spectrometry of the derivatized adduct after formic acid hydrolysis to the modified base. Binding of Ab F3/9 with glyoxalated and untreated oligomers containing deoxycytidine, deoxyguanosine, thymidine, and deoxyadenosine assessed by ELISA produced significant recognition (p > 0.0001) of glyoxal-modified deoxycytidine greater than that of untreated oligomer. Additionally, inhibition ELISA studies using the glyoxalated and native deoxycytidine oligomer showed increased recognition for gdC with more than a 5-fold difference in IC(50) values. DNA modified with increasing levels of iron (II)/EDTA produced a dose-dependent increase in Ab F3/9 binding. This was reduced in the presence of catalase or aminoguanidine. We have validated the potential of gdC as a marker of oxidative DNA damage and showed negligible cross-reactivity with 8-oxo-2'-deoxyguanosine or malondialdehyde-modified DNA as well as its utility in immunocytochemistry. Formation of the gdC adduct may involve intermediate structures; however, our results strongly suggest Ab F3/9 has major specificity for the predominant product, 5-hydroxyacetyl-dC.
Collapse
Affiliation(s)
- Nalini Mistry
- Oxidative Stress Group, Department of Clinical Biochemistry, University Hospitals of Leicester National Heath Service Trust, Leicester, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
33
|
Vanin E, Burkhard SJ, Kaiser II. p
-azidophenylglyoxal: a heterobifunctional photosensitive reagent. FEBS Lett 2001. [DOI: 10.1016/0014-5793(81)80060-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
34
|
Murata-Kamiya N, Kamiya H. Methylglyoxal, an endogenous aldehyde, crosslinks DNA polymerase and the substrate DNA. Nucleic Acids Res 2001; 29:3433-8. [PMID: 11504881 PMCID: PMC55850 DOI: 10.1093/nar/29.16.3433] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2001] [Revised: 06/29/2001] [Accepted: 06/29/2001] [Indexed: 11/14/2022] Open
Abstract
Methylglyoxal, a known endogenous and environmental mutagen, is a reactive alpha-ketoaldehyde that can modify both DNA and proteins. To investigate the possibility that methylglyoxal induces a crosslink between DNA and DNA polymerase, we treated a 'primed template' DNA and the exonuclease-deficient Klenow fragment (KF(exo-)) of DNA polymerase I with methylglyoxal in vitro. When the reaction mixtures were analyzed by SDS-PAGE, we found that methylglyoxal induced a DNA-KF(exo-) crosslink. The specific binding complex of KF(exo-) and 'primed template' DNA was necessary for formation of the DNA-KF(exo-) crosslink. Methylglyoxal reacted with guanine residues in the single-stranded portion of the template DNA. When 2'-deoxyguanosine was incubated with Nalpha-acetyllysine or N-acetylcysteine in the presence of methylglyoxal, a crosslinked product was formed. No other amino acid derivatives tested could generate a crosslinked product. These results suggest that methylglyoxal crosslinks a guanine residue of the substrate DNA and lysine and cysteine residues near the binding site of the DNA polymerase during DNA synthesis and that DNA replication is severely inhibited by the methylglyoxal-induced DNA-DNA polymerase crosslink.
Collapse
Affiliation(s)
- N Murata-Kamiya
- Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan
| | | |
Collapse
|
35
|
Martins AM, Mendes P, Cordeiro C, Freire AP. In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:3930-6. [PMID: 11453985 DOI: 10.1046/j.1432-1327.2001.02304.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The kinetics of glyoxalase I [(R)-S-lactoylglutathione methylglyoxal-lyase; EC 4.4.1.5] and glyoxalase II (S-2-hydroxyacylglutathione hydrolase; EC 3.1.2.6) from Saccharomyces cerevisiae was studied in situ, in digitonin permeabilized cells, using two different approaches: initial rate analysis and progress curves analysis. Initial rate analysis was performed by hyperbolic regression of initial rates using the program HYPERFIT. Glyoxalase I exhibited saturation kinetics on 0.05-2.5 mM hemithioacetal concentration range, with kinetic parameters Km 0.53 +/- 0.07 mM and V (3.18 +/- 0.16) x 10(-2) mM.min(-1). Glyoxalase II also showed saturation kinetics in the SD-lactoylglutathione concentration range of 0.15-3 mM and Km 0.32 +/- 0.13 mM and V (1.03 +/- 0.10) x 10(-3) mM.min(-1) were obtained. The kinetic parameters of both enzymes were also estimated by nonlinear regression of progress curves using the raw absorbance data and integrated differential rate equations with the program GEPASI. Several optimization methods were used to minimize the sum of squares of residuals. The best parameter fit for the glyoxalase I reaction was obtained with a single curve analysis, using the irreversible Michaelis-Menten model. The kinetic parameters obtained, Km 0.62 +/- 0.18 mM and V (2.86 +/- 0.01) x 10(-2) mM.min(-1), were in agreement with those obtained by initial rate analysis. The results obtained for glyoxalase II, using either the irreversible Michaelis-Menten model or a phenomenological reversible hyperbolic model, showed a high correlation of residuals with time and/or high values of standard deviation associated with Km. The possible causes for the discrepancy between data obtained from initial rate analysis and progress curve analysis, for glyoxalase II, are discussed.
Collapse
Affiliation(s)
- A M Martins
- Grupo de Enzimologia, Centro de Estudos de Bioquímica e Fisiologia, Faculdade de Ciências da Universidade de Lisboa, Portugal
| | | | | | | |
Collapse
|
36
|
Fidanza N, Valiensi J, Peruchena N. Conformational and topological analysis of the charge density in guanine-α-dicarbonyl adducts at AM1 level. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0166-1280(00)00355-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
37
|
Fischer B, Kabha E, Gendron FP, Beaudoin AR. Synthesis, mechanism and fluorescence properties of 8-(aryl)-3-beta-D-ribofuranosylimidazo[2,1-i]purine 5'-phosphate derivatives. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:1033-54. [PMID: 10893720 DOI: 10.1080/15257770008033041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The synthesis of new fluorescent nucleotides is described. This synthesis comprises two parallel reactions, the Kornblum oxidation and imidazole formation, which lead to 8-(aryl)-3-beta-D-ribofuranosylimidazo[2,1-i]purine 5'-phosphates 2 from AMP or ATP. A detailed mechanism is proposed based on monitoring the reaction by 1H- and 13C-NMR spectroscopy, MS, FAB, HPLC, and pH meter. The spectral and fluorescent properties of the new derivatives at various pH values are described. Excitation and emission maxima for 3 were observed at 290 and 420 nm, respectively, in both basic and neutral media. In acidic media, the emission maximum shifted to 410 nm, however, the fluorescence intensity increased 1.5-fold. ATP analogues 2b and 3b exhibited relative stability regarding hydrolysis by type II ATPDase. Compound 3b is relatively chemically stable at pH 10.4 and 7.4.
Collapse
Affiliation(s)
- B Fischer
- Department of Chemistry, Gonda-Goldscmied Medical Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | | | | | | |
Collapse
|
38
|
Seidel W, Pischetsrieder M. Immunochemical detection of N2-[1-(1-carboxy)ethyl]guanosine, an advanced glycation end product formed by the reaction of DNA and reducing sugars or L-ascorbic acid in vitro. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1425:478-84. [PMID: 9838211 DOI: 10.1016/s0304-4165(98)00101-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the Maillard reaction, free amino groups of proteins and nucleic acids react with reducing sugars to form advanced glycation end products (AGE). A major product found in reaction mixtures of guanosine and glucose is N2-[1-(1-carboxy)ethyl]guanosine (CEG), which, therefore, can be used as a marker of advanced glycation of DNA. An enzyme-linked immunosorbent assay (ELISA) was developed to detect and to semi-quantitate nonenzymatic glycosylation of DNA. A polyclonal antiserum was raised against CEG linked to keyhole limpet hemocyanin. A protocol for a competitive ELISA was developed, and the antiserum was tested for crossreactivity. Several unmodified nucleotides and N2-modified guanosine derivatives showed no or negligible crossreactivity. Only very similar structures like N2-(carboxymethyl)guanosine and N2-(1-carboxy-3-hydroxypropyl)guanosine, which have been identified as reaction products of glucose or l-ascorbic acid and guanosine, display significant binding activity. The signal can be totally repressed by free CEG, yet protein-bound CEG is a stronger inhibitor. DNA incubated with d-glucose, dihydroxyacetone, l-ascorbic or l-dehydroascorbic acid shows a signal inhibition indicating the formation of CEG in vitro. The competitive ELISA procedure proved to be a sensitive method which can be used to detect glycation of DNA in vivo.
Collapse
Affiliation(s)
- W Seidel
- Institut für Pharmazie, Abteilung Lebensmittelchemie, Ludwig-Maximilians-Universität München, Sophienstrasse 10, 80333 Munich, Germany
| | | |
Collapse
|
39
|
Leng F, Graves D, Chaires JB. Chemical cross-linking of ethidium to DNA by glyoxal. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1442:71-81. [PMID: 9767119 DOI: 10.1016/s0167-4781(98)00122-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ethidium was found to be efficiently cross-linked to DNA by glyoxal. Kinetic studies showed that the rate of the cross-linking reaction is strongly dependent on the glyoxal concentration. Comparative studies using a series of phenanthridines and acridines showed that NH2 groups at both the 2 and 7 positions on the phenanthridine ring are necessary for efficient cross-linking. Studies using synthetic polydeoxynucleotides showed that the 2-amino group of guanine is absolutely required for cross-linking. Fluorescence contact energy transfer and relative viscosity experiments showed that the cross-linked drug remains intercalated into DNA. DNA gel electrophoresis and melting studies demonstrated that cross-linked ethidium does not dissociate the DNA double helix to single strands.
Collapse
Affiliation(s)
- F Leng
- Department of Biochemistry, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216-4505, USA
| | | | | |
Collapse
|
40
|
Murata-Kamiya N, Kamiya H, Kaji H, Kasai H. Nucleotide excision repair proteins may be involved in the fixation of glyoxal-induced mutagenesis in Escherichia coli. Biochem Biophys Res Commun 1998; 248:412-7. [PMID: 9675151 DOI: 10.1006/bbrc.1998.8973] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To investigate the influence of nucleotide excision repair (NER) on glyoxal-induced mutations, we treated wild-type and NER-deficient (uvrC) Escherichia coli strains with glyoxal, and analyzed mutations in the chromosomal lacI gene. In both strains, the cell death and the mutation frequency increased according to the dose of glyoxal added to the culture medium, and cell death was induced to a similar level in both strains. Interestingly, the frequency of glyoxal-induced mutations in the wild-type strain was higher than that in the uvrC strain. Particularly, the frequency of base-pair substitutions was 4.7-fold higher in the wild-type strain. In the wild-type strain, G:C-->T:A transversions were predominant, followed by G:C-->A:T and A:T-->T:A mutations. In the uvrC strain, G:C-->A:T transitions were predominant, followed by G:C-->T:A transversions. All the base-pair substitutions except for G:C-->A:T transitions were >4-fold higher in the wild-type strain than in the uvrC strain. These results suggest that NER may be involved in the fixation of glyoxal-induced base-pair substitutions.
Collapse
Affiliation(s)
- N Murata-Kamiya
- Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1, Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan
| | | | | | | |
Collapse
|
41
|
Møller P, Wallin H. Adduct formation, mutagenesis and nucleotide excision repair of DNA damage produced by reactive oxygen species and lipid peroxidation product. Mutat Res 1998; 410:271-90. [PMID: 9630671 DOI: 10.1016/s1383-5742(97)00041-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reactive oxygen species are formed constantly in living organisms, as products of the normal metabolism, or as a result of many different environmental influences. Here we review the knowledge of formation of DNA damage, the mutations caused by reactive oxygen species and the role of the excision repair processes, that protect the organism from oxidative DNA damage. In particular, we have focused on recent studies that demonstrate the important role of nucleotide excision repair. We propose two major roles of nucleotide excision repair as 1) a backup when base excision repair of small oxidative lesions becomes saturated, and as 2) a primary repair pathway for DNA damage produced by lipid peroxidation products.
Collapse
Affiliation(s)
- P Møller
- National Institute of Occupational Health, Lerso Parkallé 105, DK-2100 Copenhagen O, Denmark.
| | | |
Collapse
|
42
|
Balzer M, Wagner R. A chemical modification method for the structural analysis of RNA and RNA-protein complexes within living cells. Anal Biochem 1998; 256:240-2. [PMID: 9473284 DOI: 10.1006/abio.1997.2499] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
MESH Headings
- Aldehydes/metabolism
- Bacterial Proteins/chemistry
- Bacterial Proteins/metabolism
- Butanones
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Macromolecular Substances
- Mutation
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/metabolism
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/metabolism
Collapse
Affiliation(s)
- M Balzer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
| | | |
Collapse
|
43
|
Murata-Kamiya N, Kamiya H, Kaji H, Kasai H. Mutational specificity of glyoxal, a product of DNA oxidation, in the lacI gene of wild-type Escherichia coli W3110. Mutat Res 1997; 377:255-62. [PMID: 9247622 DOI: 10.1016/s0027-5107(97)00083-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
To determine the mutation spectrum of glyoxal, which is produced from DNA by oxygen free-radicals, we analyzed the chromosomal lacI gene of mutants induced by treatment of a wild-type Escherichia coli strain with glyoxal. The cell death and the mutation frequency increased according to the concentration of glyoxal added to the culture medium. The majority of the spontaneous mutations (82%) and that of the glyoxal-induced mutations (50%) were the addition or deletion of a 5'-TGGC-3' sequence at positions 623-634, which was reported to be a mutational hot spot in the lacI gene. In the glyoxal-induced mutants, however, the ratio of base-pair substitutions was increased (35%). Although all types of base-pair substitutions were detected, 78% of the base-pair substitutions occurred at G:C sites. Among them, G:C-->A:T transitions were predominant, followed by G:C-->T:A transversions. These mutations appeared to be distributed randomly within the lacI gene. These results suggest that glyoxal-induced mutations may correlate to mutations induced by oxygen free-radicals.
Collapse
Affiliation(s)
- N Murata-Kamiya
- Department of Health Policy and Management, University of Occupational and Environmental Health, Kitakyushu, Japan
| | | | | | | |
Collapse
|
44
|
Murata-Kamiya N, Kaji H, Kasai H. Types of mutations induced by glyoxal, a major oxidative DNA-damage product, in Salmonella typhimurium. Mutat Res 1997; 377:13-6. [PMID: 9219574 DOI: 10.1016/s0027-5107(97)00016-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have analyzed the types of mutations induced by glyoxal, a major oxidative DNA-damage product, in Salmonella typhimurium. A set of six strains, TA7001 to TA7006, was used to detect base-pair substitutions, and the TA98 strain was employed to detect frameshift mutations. Glyoxal did not induce mutations at A:T base pairs. The majority of the mutations induced by glyoxal were base-pair substitutions at G:C base pairs, and a small level of frameshift mutations was detected in the TA98 strain.
Collapse
Affiliation(s)
- N Murata-Kamiya
- Department of Health Policy and Management, University of Occupational and Environmental Health, Kitakyushu, Japan
| | | | | |
Collapse
|
45
|
Murata-Kamiya N, Kamiya H, Kaji H, Kasai H. Glyoxal, a major product of DNA oxidation, induces mutations at G:C sites on a shuttle vector plasmid replicated in mammalian cells. Nucleic Acids Res 1997; 25:1897-902. [PMID: 9115355 PMCID: PMC146688 DOI: 10.1093/nar/25.10.1897] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Glyoxal is a major product of DNA oxidation in which Fenton-type oxygen free radical-forming systems are involved. To determine the mutation spectrum of glyoxal in mammalian cells and to compare the spectrum with those observed in other experimental systems, we analyzed mutations in a bacterial suppressor tRNA gene (supF) in the shuttle vector plasmid pMY189. We treated pMY189 with glyoxal and immediately transfected it into simian COS-7 cells. The cytotoxicity and mutation frequency increased according to the dose of glyoxal. The majority of glyoxal-induced mutations (48%) were single-base substitutions. Eighty three percent of the single-base substitutions occurred at G:C base pairs. Among them, G:C-->T:A transversions were predominant, followed by G:C-->C:G transversions and G:C-->A:T transitions. A:T-->T:A transversions were also observed. Mutational hotspots within the supF gene were detected. These results suggest that glyoxal may play an important role in mutagenesis induced by oxygen free radicals.
Collapse
Affiliation(s)
- N Murata-Kamiya
- Department of Health Policy and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807, Japan
| | | | | | | |
Collapse
|
46
|
Bartsch H. DNA adducts in human carcinogenesis: etiological relevance and structure-activity relationship. Mutat Res 1996; 340:67-79. [PMID: 8692183 DOI: 10.1016/s0165-1110(96)90040-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Sensitive methods for quantifying DNA adducts from (i) benzo[a]pyrene (BP), (ii) alkylation exposure, and (iii) etheno(epsilon)-DNA adduct-forming chemicals were developed and applied to humans and animal models. The aims were to identify hitherto unknown sources and mechanisms of exogenous and endogenous DNA damage, to examine the effect of drug polymorphism on BP adduct levels, and to develop QSAR between tumorigenic potency, heritable genetic damage and structural elements of alkylating carcinogens (Vogel and Nivard (1994) Mutation Res., 395, 13-32). (i) BP-DNA adducts: An HPLC/fluorimetry assay suitable for measuring (+)-anti-BP-diol-epoxide (BPDE) adducts in human tissues and white blood cells (WBC) was developed (Alexandrov et al. (1992) Cancer Res., 52, 6248-6253). In smokers, a positive correlation was found between pulmonary CYP1A1-related catalytic activity (AHH) and the level of lung BPDE-DNA adducts. In coke oven workers, an enhancing effect of smoking on BPDE-adduct levels in WBC was demonstrated (Rojas et al. (1995) Carcinogenesis, 16, 1373-1376). (ii) 3-Alkyladenines (3-alkAde): Alkylating carcinogens form 3-alkAde adducts in DNA which depurinate to yield 3-alkAde in urine, for which a detection method was developed (Friesen et al. (1991) Chem. Res. Toxicol., 4, 102-106; Prevost et al. (1990) Carcinogenesis, 11, 1747-1751), using immunoaffinity purification and GC-MS analysis. The usefulness of 3-alkAde analysis for the determination of the whole-body dose of alkylating agents derived from exogenous and endogenous sources was demonstrated. (iii) Etheno-DNA adduct-forming agents: Etheno(epsilon)-DNA base adducts (epsilon A, epsilon dC, epsilon dG) are promutagenic DNA lesions that are formed by occupational (vinyl halides) and environmental (urethane) carcinogens. An ultrasensitive detection method was developed (Nair et al. (1995) Carcinogenesis, 16, 613-617), based on immunoaffinity purification and 32P-postlabelling of epsilon-nucleoside 3'-monophosphates. Liver DNA from unexposed rats, mice and from human samples contained background levels of epsilon dA and epsilon dC (Bartsch et al. (1994) Drug. Metab. Rev., 26, 349-371). As formation of epsilon dA and epsilon dC adducts by lipid peroxidation products was demonstrated (El Ghissassi et al. (1995) Chem. Res. Toxicol., 8, 278-283), they may serve as markers for oxidative stress. Results from testing this hypothesis are presented.
Collapse
Affiliation(s)
- H Bartsch
- German Cancer Research Center (DKFZ), Division of Toxicology and Cancer Risk Factors, Heidelberg, Germany
| |
Collapse
|
47
|
Beijer B, Gr⊘tli M, Douglas ME, Sproat BS. Simplified and Cost Effective Syntheses of Fully Protected Phosphoramidite Monomers Suitable for the Assembly of Oligo(2′-O-allylribonucleotides). ACTA ACUST UNITED AC 1994. [DOI: 10.1080/15257779408010672] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
48
|
Abstract
Although the interest is growing towards glyoxalases and methylglyoxal, their role in metabolism is still an enigma. In this paper, the effects of methylglyoxal in both in vivo and in vitro mammalian systems are reviewed and correlated with its interaction with macromolecules (nucleic acids, proteins). The theories on the role of methylglyoxal and glyoxalases are also discussed. Recently, data obtained have focused attention on the possible role of disturbed methylglyoxal metabolism in the development of diabetic complications and it is hoped that the contribution of methylglyoxal to pathological events can be ascertained in the near future.
Collapse
Affiliation(s)
- M P Kalapos
- Semmelweis University Medical School, First Institute of Biochemistry, Budapest, Hungary
| |
Collapse
|
49
|
Rodríguez Mellado JM, Ruiz Montoya M. Correlations between chemical reactivity and mutagenic activity against S. typhimurium TA100 for alpha-dicarbonyl compounds as a proof of the mutagenic mechanism. Mutat Res 1994; 304:261-4. [PMID: 7506369 DOI: 10.1016/0027-5107(94)90218-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The mutagenic activities in the Ames test against S. typhimurium TA100 for a series of alpha-dicarbonyl compounds are examined together with the formation constants of the adducts formed between such compounds and guanine and guanosine. Correlations between the equilibrium constants, the apparent reaction enthalpies, and the mutagenic activity are presented. These correlations imply that the mutagenic activity is related to the chemical reactivity of the dicarbonyl compounds with the puric bases.
Collapse
Affiliation(s)
- J M Rodríguez Mellado
- Departamento de Química Física y Termodinámica Aplicada, Facultad de Ciencias, Universidad de Córdoba, Spain
| | | |
Collapse
|
50
|
Hou YM, Westhof E, Giegé R. An unusual RNA tertiary interaction has a role for the specific aminoacylation of a transfer RNA. Proc Natl Acad Sci U S A 1993; 90:6776-80. [PMID: 8341698 PMCID: PMC47015 DOI: 10.1073/pnas.90.14.6776] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The nucleotides in a tRNA that specifically interact with the cognate aminoacyl-tRNA synthetase have been found largely located in the helical stems, the anticodon, or the discriminator base, where they vary from one tRNA to another. The conserved and semiconserved nucleotides that are responsible for the tRNA tertiary structure have been shown to have little role in synthetase recognition. Here we report that aminoacylation of Escherichia coli tRNA(Cys) depends on the anticodon, the discriminator base, and a tertiary interaction between the semiconserved nucleotides at positions 15 and 48. While all other tRNAs contain a purine at position 15 and a complementary pyrimidine at position 48 that establish the tertiary interaction known as the Levitt pair, E. coli tRNA(Cys) has guanosine -15 and -48. Replacement of guanosine -15 or -48 with cytidine virtually eliminates aminoacylation. Structural analyses with chemical probes suggest that guanosine -15 and -48 interact through hydrogen bonds between the exocyclic N-2 and ring N-3 to stabilize the joining of the two long helical stems of the tRNA. This tertiary interaction is different from the traditional base pairing scheme in the Levitt pair, where hydrogen bonds would form between N-1 and O-6. Our results provide evidence for a role of RNA tertiary structure in synthetase recognition.
Collapse
Affiliation(s)
- Y M Hou
- Unité de Recherche Propre Structures des Macromolécules Biologiques et Mecanismes de Reconnaissance, Centre National de la Recherche Scientifique, Strasbourg, France
| | | | | |
Collapse
|