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Wen T, Zhao S, Stingele J, Ravanat JL, Greenberg MM. Quantification of Intracellular DNA-Protein Cross-Links with N7-Methyl-2'-Deoxyguanosine and Their Contribution to Cytotoxicity. Chem Res Toxicol 2024; 37:814-823. [PMID: 38652696 PMCID: PMC11105979 DOI: 10.1021/acs.chemrestox.4c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The major product of DNA-methylating agents, N7-methyl-2'-deoxyguanosine (MdG), is a persistent lesion in vivo, but it is not believed to have a large direct physiological impact. However, MdG reacts with histone proteins to form reversible DNA-protein cross-links (DPCMdG), a family of DNA lesions that can significantly threaten cell survival. In this paper, we developed a tandem mass spectrometry method for quantifying the amounts of MdG and DPCMdG in nuclear DNA by taking advantage of their chemical lability and the concurrent release of N7-methylguanine. Using this method, we determined that DPCMdG is formed in less than 1% yield based upon the levels of MdG in methyl methanesulfonate (MMS)-treated HeLa cells. Despite its low chemical yield, DPCMdG contributes to MMS cytotoxicity. Consequently, cells that lack efficient DPC repair by the DPC protease SPRTN are hypersensitive to MMS. This investigation shows that the downstream chemical and biochemical effects of initially formed DNA damage can have significant biological consequences. With respect to MdG formation, the initial DNA lesion is only the beginning.
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Affiliation(s)
- Tingyu Wen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Shubo Zhao
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000 Grenoble, France
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
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2
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Li J, Cui Z, Fan C, Zhou Y, Ren M, Zhou C. Photo-caged 2-butene-1,4-dial as an efficient, target-specific photo-crosslinker for covalent trapping of DNA-binding proteins. Chem Sci 2023; 14:10884-10891. [PMID: 37829010 PMCID: PMC10566456 DOI: 10.1039/d3sc03719c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023] Open
Abstract
Covalent trapping of DNA-binding proteins via photo-crosslinking is an advantageous method for studying DNA-protein interactions. However, traditional photo-crosslinkers generate highly reactive intermediates that rapidly and non-selectively react with nearby functional groups, resulting in low target-capture yields and high non-target background capture. Herein, we report that photo-caged 2-butene-1,4-dial (PBDA) is an efficient photo-crosslinker for trapping DNA-binding proteins. Photo-irradiation (360 nm) of PBDA-modified DNA generates 2-butene-1,4-dial (BDA), a small, long-lived intermediate that reacts selectively with Lys residues of DNA-binding proteins, leading in minutes to stable DNA-protein crosslinks in up to 70% yield. In addition, BDA exhibits high specificity for target proteins, leading to low non-target background capture. The high photo-crosslinking yield and target specificity make PBDA a powerful tool for studying DNA-protein interactions.
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Affiliation(s)
- Jiahui Li
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University Tianjin 300071 China
| | - Zenghui Cui
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University Tianjin 300071 China
| | - Chaochao Fan
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University Tianjin 300071 China
| | - Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University Tianjin 300071 China
| | - Mengtian Ren
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University Tianjin 300071 China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University Tianjin 300071 China
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3
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Jacinto MP, Greenberg MM. Histone Deacetylase 1 Inhibition by Peptides Containing a DNA Damage-Induced, Nonenzymatic, Histone Covalent Modification. Biochemistry 2023; 62:1388-1393. [PMID: 36972223 PMCID: PMC10124317 DOI: 10.1021/acs.biochem.3c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Treatment of HeLa cells with the DNA damaging agent, bleomycin (BLM), results in the formation of a nonenzymatic 5-methylene-2-pyrrolone histone covalent modification on lysine residues (KMP). KMP is much more electrophilic than other N-acyllysine covalent modifications and post-translational modifications, including N-acetyllysine (KAc). Using histone peptides containing KMP, we show that this modification inhibits the class I histone deacetylase, HDAC1, by reacting with a conserved cysteine (C261) located near the active site. HDAC1 is inhibited by histone peptides whose corresponding N-acetylated sequences are known deacetylation substrates, but not one containing a scrambled sequence. The HDAC1 inhibitor, trichostatin A, competes with covalent modification by the KMP-containing peptides. HDAC1 is also covalently modified by a KMP-containing peptide in a complex milieu. These data indicate that peptides containing KMP are recognized by HDAC1 and are bound in the active site. The effects on HDAC1 indicate that KMP formation in cells may contribute to the biological effects of DNA damaging agents, such as BLM, that form this nonenzymatic covalent modification.
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Affiliation(s)
- Marco Paolo Jacinto
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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4
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Jacinto MP, Heidenreich D, Müller S, Greenberg MM. Covalent Modification of Bromodomain Proteins by Peptides Containing a DNA Damage-Induced, Histone Post-Translational Modification. Chembiochem 2022; 23:e202200373. [PMID: 36173930 PMCID: PMC9675715 DOI: 10.1002/cbic.202200373] [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: 07/01/2022] [Revised: 09/28/2022] [Indexed: 02/03/2023]
Abstract
An electrophilic 5-methylene-2-pyrrolone modification (KMP ) is produced at lysine residues of histone proteins in nucleosome core particles upon reaction with a commonly formed DNA lesion (C4-AP). The nonenzymatic KMP modification is also generated in the histones of HeLa cells treated with the antitumor agent, bleomycin that oxidizes DNA and forms C4-AP. This nonenzymatic covalent histone modification has the same charge as the N-acetyllysine (KAc ) modification but is more electrophilic. In this study we show that KMP -containing histone peptides are recognized by, and covalently modify bromodomain proteins that are KAc readers. Distinct selectivity preferences for covalent bromodomain modification are observed following incubation with KMP -containing peptides of different sequence. MS/MS analysis of 3 covalently modified bromodomain proteins confirmed that Cys adduction was selective. The modified Cys was not always proximal to the KAc binding site, indicating that KMP -containing peptide interaction with bromodomain protein is distinct from the former. Analysis of protein adduction yields as a function of bromodomain pH at which the protein charge is zero (pI) or cysteine solvent accessible surface area are also consistent with non-promiscuous interaction between the proteins and electrophilic peptides. These data suggest that intracellular formation of KMP could affect cellular function and viability by modifying proteins that regulate genetic expression.
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Affiliation(s)
- Marco Paolo Jacinto
- Chemistry, Johns Hopkins University, 3400 N. Charles St., 21218, Baltimore, MD, USA
| | - David Heidenreich
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Marc M Greenberg
- Chemistry, Johns Hopkins University, 3400 N. Charles St., 21218, Baltimore, MD, USA
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5
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Wen T, Yang K, Greenberg MM. Local Alteration of Ionic Strength in a Nucleosome Core Particle and Its Effect on N7-Methyl-2'-deoxyguanosine Depurination. Biochemistry 2022; 61:2221-2228. [PMID: 36136907 PMCID: PMC9670023 DOI: 10.1021/acs.biochem.2c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Positively charged N-terminal histone tails play important roles in maintaining the nucleosome (and chromatin) structure and function. Charge alteration, including those imposed by post-translational modifications, impacts chromatin dynamics, protein binding, and the fate of DNA damage. There is evidence that N-terminal histone tails affect the local ionic environment within a nucleosome core particle (NCP), but this phenomenon is not well understood. Determining the modulation of the local ionic environment within an NCP by histone tails could help uncover the underlying mechanisms of their functions and effects. Utilizing bottom-up syntheses of NCPs containing wild-type or mutated histones and a fluorescent probe that is sensitive to the local ionic environment, we show that interaction with positively charged N-terminal tails increases the local ionic strength near nucleosomal DNA. The effect is diminished by replacing positively charged residues with neutral ones or deleting a tail in its entirety. Replacing the fluorescent probe with the major DNA methylation product, N7-methyl-2'-deoxyguanosine (MdG), revealed changes in the depurination rate constant varying inversely with local ionic strength. These data indicate that the MdG hydrolysis rates depend on and also inform on local ionic strength in an NCP. Overall, histone tail charge contributes to the complexity of the NCP structure and function by modulating the local ionic strength.
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Affiliation(s)
- Tingyu Wen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Kun Yang
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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Jacinto MP, Fried SD, Greenberg MM. Intracellular Formation of a DNA Damage-Induced, Histone Post-Translational Modification Following Bleomycin Treatment. J Am Chem Soc 2022; 144:7600-7605. [PMID: 35467863 PMCID: PMC9121625 DOI: 10.1021/jacs.2c02880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Evaluating the significance of various forms of DNA damage is complicated by discoveries that some lesions inactivate repair enzymes or produce more deleterious forms of damage. Histone lysines within nucleosomes react with the commonly produced C4'-oxidized abasic site (C4-AP) to concomitantly yield an electrophilic modification (KMP) on lysine and DNA strand scission. We developed a chemoproteomic approach to identify KMP in HeLa cells. More than 60 000 KMP-modified histones are produced per cell. Using LC-MS/MS, we detected KMP at 17 of the 57 lysine residues distributed throughout the four core histone proteins. Therefore, KMP constitutes a DNA damage-induced, nonenzymatic histone post-translational modification. KMP formation suggests that downstream processes resulting from DNA damage could have ramifications on cells.
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Affiliation(s)
- Marco Paolo Jacinto
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Stephen D. Fried
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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7
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Ren M, Greenberg MM, Zhou C. Participation of Histones in DNA Damage and Repair within Nucleosome Core Particles: Mechanism and Applications. Acc Chem Res 2022; 55:1059-1073. [PMID: 35271268 PMCID: PMC8983524 DOI: 10.1021/acs.accounts.2c00041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA is damaged by various endogenous and exogenous sources, leading to a diverse group of reactive intermediates that yield a complex mixture of products. The initially formed products are often metastable and can react to yield lesions that are more biologically deleterious. Mechanistic studies are frequently carried out on free DNA as the substrate. The observations do not necessarily reflect the reaction environment inside human cells where genomic DNA is condensed as chromatin in the nucleus. Chromatin is made up of monomeric structural units called nucleosomes, which are comprised of DNA wrapped around an octameric core of histone proteins (two copies each of histones H2A, H2B, H3, and H4).This account presents a summary of our work in the past decade on the mechanistic studies of DNA damage and repair in reconstituted nucleosome core particles (NCPs). A series of metastable lesions and reactive intermediates, such as abasic sites (AP), N7-methyl-2'-deoxyguanosine (MdG), and 2'-deoxyadenosin-N6-yl radical (dA•), have been independently generated in a site-specific manner in bottom-up-synthesized NCPs. Detailed mechanistic studies on these NCPs revealed that histones actively participate in DNA damage and repair processes in diverse ways. For instance, nucleophilic residues in the flexible histone N-terminal tails, such as Lys and N-terminal α-amine, react with electrophilic DNA damage and reactive intermediates. In some cases, transient intermediates are produced, leading to the promotion or suppression of damage and repair processes. In other examples, reactions with histones yield reversible or stable DNA-protein cross-links (DPCs). Histones also utilize acidic and basic residues, such as histidine and aspartic acid, to catalyze DNA strand cleavage through general acid/base catalysis. Alternatively, a Tyr in histone plays a vital role in nucleosomal DNA damage and repair via radical transfer. Finally, the reactivity discovered during the mechanistic studies has facilitated the development of new reagents and methods with applications in biotechnology.This research has enriched our knowledge of the roles of histone proteins in DNA damage and repair and their contributions to epigenetics and may have significant biological implications. The residues in histone N-terminal tails that react with DNA lesions also play pivotal roles in regulating the structure and function of chromatin, indicating that there may be cross-talk between DNA damage and repair in eukaryotic cells and epigenetic regulation. Also, in view of the biased amino acid composition of histones, these results provide hints about how the proteins have evolved to minimize their deleterious effects but maximize beneficial ones for maintaining genome integrity. Finally, previously unreported DPCs and histone post-translational modifications have been discovered through this research. The effects of these newly identified lesions on the structure and function of chromatin and their fates inside cells remain to be elucidated.
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Affiliation(s)
- Mengtian Ren
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
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8
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Tagad A, Singh RK, Patwari GN. Binary Matrix Method to Enumerate, Hierarchically Order, and Structurally Classify Peptide Aggregation. J Chem Inf Model 2022; 62:1585-1594. [PMID: 35232014 DOI: 10.1021/acs.jcim.2c00069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein aggregation is a common and complex phenomenon in biological processes, yet a robust analysis of this aggregation process remains elusive. The commonly used methods such as center-of-mass to center-of-mass (COM-COM) distance, the radius of gyration (Rg), hydrogen bonding (HB), and solvent accessible surface area do not quantify the aggregation accurately. Herein, a new and robust method that uses an aggregation matrix (AM) approach to investigate peptide aggregation in a MD simulation trajectory is presented. An nxn two-dimensional AM is created by using the interpeptide Cα-Cα cutoff distances, which are binarily encoded (0 or 1). These aggregation matrices are analyzed to enumerate, hierarchically order, and structurally classify the aggregates. Comparison of the present AM method suggests that it is superior to the HB method since it can incorporate nonspecific interactions and the Rg and COM-COM methods since the cutoff distance is independent of the length of the peptide. More importantly, the present method can structurally classify the peptide aggregates, which the conventional Rg, COM-COM, and HB methods fail to do. The unique selling point of this method is its ability to structurally classify peptide aggregates using two-dimensional matrices.
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Affiliation(s)
- Amol Tagad
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Reman Kumar Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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9
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Zhou Y, Lu K, Li Q, Fan C, Zhou C. C4'-Fluorinated Oligodeoxynucleotides: Synthesis, Stability, Structural Studies. Chemistry 2021; 27:14738-14746. [PMID: 34432342 DOI: 10.1002/chem.202102561] [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: 07/14/2021] [Indexed: 11/06/2022]
Abstract
Fluoro-substitution on the ribose moiety (e. g., 2'-F-deoxyribonucleotide) represents a popular way to modulate the ribose conformation and, hence, the structure and function of nucleic acids. In the present study, we synthesized 4'-F-deoxythymidine (4'-F T) and introduced it to oligodeoxyribonucleotides (ODNs). Though scission of the glycosylic bond of 4'-F T followed by strand cleavage occurred to some extent under alkaline conditions, the 4'-F T-modified ODNs were rather stable in neutral buffers. NMR studies showed that like 2'-F-deoxyribonucleoside, 4'-F T exists predominantly in the North conformation not only in the nucleoside form but also in the context of ODN strands. Circular dichroism spectroscopy, thermal denaturing and RNase H1 footprinting studies of 4'-F T-modified ODN/cDNA and ODN/cRNA duplexes indicated that the North conformation tendency of 4'-F T is maintained in the duplexes, leading to a local structural perturbation. Collectively, 4'-F-deoxyribonucleotide structurally resembles the 2'-F-deoxyribonucleotide but imparts less structural perturbation to the duplex than the latter.
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Affiliation(s)
- Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Kuan Lu
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Qiang Li
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chaochao Fan
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
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10
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Bignon E, Gillet N, Jiang T, Morell C, Dumont E. A Dynamic View of the Interaction of Histone Tails with Clustered Abasic Sites in a Nucleosome Core Particle. J Phys Chem Lett 2021; 12:6014-6019. [PMID: 34165307 DOI: 10.1021/acs.jpclett.1c01058] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Apurinic/apyrimidinic sites are the most common forms of DNA damage under physiological conditions, yet their structural and dynamical behavior within nucleosome core particles has just begun to be investigated and is dramatically different from that of abasic sites in B-DNA. Clusters of two or more abasic sites are repaired even less efficiently and hence constitute hot spots of high mutagenicity notably due to enhanced double-strand break formation. On the basis of an X-ray structure of a 146 bp DNA wrapped onto a histone core, we investigate the structural behavior of two bistranded abasic sites positioned at mutational hot spots during microsecond-range molecular dynamics simulations. Our simulations allow us to probe interactions of histone tails at clustered abasic site locations, with a definitive assignment of the key residues involved in the NCP-catalyzed formation of DNA-protein cross-linking in line with recent experimental findings, and pave the way for a systematic assessment of the response of histone tails to DNA lesions.
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Affiliation(s)
- Emmanuelle Bignon
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, F69342 Lyon, France
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280 CNRS, Université Claude Bernard Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Natacha Gillet
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, F69342 Lyon, France
| | - Tao Jiang
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, F69342 Lyon, France
| | - Christophe Morell
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280 CNRS, Université Claude Bernard Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Elise Dumont
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, F69342 Lyon, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
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11
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Abstract
The field of epigenetics has exploded over the last two decades, revealing an astonishing level of complexity in the way genetic information is stored and accessed in eukaryotes. This expansion of knowledge, which is very much ongoing, has been made possible by the availability of evermore sensitive and precise molecular tools. This review focuses on the increasingly important role that chemistry plays in this burgeoning field. In an effort to make these contributions more accessible to the nonspecialist, we group available chemical approaches into those that allow the covalent structure of the protein and DNA components of chromatin to be manipulated, those that allow the activity of myriad factors that act on chromatin to be controlled, and those that allow the covalent structure and folding of chromatin to be characterized. The application of these tools is illustrated through a series of case studies that highlight how the molecular precision afforded by chemistry is being used to establish causal biochemical relationships at the heart of epigenetic regulation.
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Affiliation(s)
- John D Bagert
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Tom W Muir
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
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12
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Ren M, Shang M, Wang H, Xi Z, Zhou C. Histones participate in base excision repair of 8-oxodGuo by transiently cross-linking with active repair intermediates in nucleosome core particles. Nucleic Acids Res 2021; 49:257-268. [PMID: 33290564 PMCID: PMC7797075 DOI: 10.1093/nar/gkaa1153] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 12/20/2022] Open
Abstract
8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) is a biomarker of oxidative DNA damage and can be repaired by hOGG1 and APE1 via the base excision repair (BER) pathway. In this work, we studied coordinated BER of 8-oxodGuo by hOGG1 and APE1 in nucleosome core particles and found that histones transiently formed DNA-protein cross-links (DPCs) with active repair intermediates such as 3'-phospho-α,β-unsaturated aldehyde (PUA) and 5'-deoxyribosephosphate (dRP). The effects of histone participation could be beneficial or deleterious to the BER process, depending on the circumstances. In the absence of APE1, histones enhanced the AP lyase activity of hOGG1 by cross-linking with 3'-PUA. However, the formed histone-PUA DPCs hampered the subsequent repair process. In the presence of APE1, both the AP lyase activity of hOGG1 and the formation of histone-PUA DPCs were suppressed. In this case, histones could catalyse removal of the 5'-dRP by transiently cross-linking with the active intermediate. That is, histones promoted the repair by acting as 5'-dRP lyases. Our findings demonstrate that histones participate in multiple steps of 8-oxodGuo repair in nucleosome core particles, highlighting the diverse roles that histones may play during DNA repair in eukaryotic cells.
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Affiliation(s)
- Mengtian Ren
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Mengdi Shang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Huawei Wang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
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13
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Bignon E, Claerbout VEP, Jiang T, Morell C, Gillet N, Dumont E. Nucleosomal embedding reshapes the dynamics of abasic sites. Sci Rep 2020; 10:17314. [PMID: 33057206 PMCID: PMC7560594 DOI: 10.1038/s41598-020-73997-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/31/2020] [Indexed: 12/16/2022] Open
Abstract
Apurinic/apyrimidinic (AP) sites are the most common DNA lesions, which benefit from a most efficient repair by the base excision pathway. The impact of losing a nucleobase on the conformation and dynamics of B-DNA is well characterized. Yet AP sites seem to present an entirely different chemistry in nucleosomal DNA, with lifetimes reduced up to 100-fold, and the much increased formation of covalent DNA-protein cross-links leading to strand breaks, refractory to repair. We report microsecond range, all-atom molecular dynamics simulations that capture the conformational dynamics of AP sites and their tetrahydrofuran analogs at two symmetrical positions within a nucleosome core particle, starting from a recent crystal structure. Different behaviours between the deoxyribo-based and tetrahydrofuran-type abasic sites are evidenced. The two solvent-exposed lesion sites present contrasted extrahelicities, revealing the crucial role of the position of a defect around the histone core. Our all-atom simulations also identify and quantify the frequency of several spontaneous, non-covalent interactions between AP and positively-charged residues from the histones H2A and H2B tails that prefigure DNA-protein cross-links. Such an in silico mapping of DNA-protein cross-links gives important insights for further experimental studies involving mutagenesis and truncation of histone tails to unravel mechanisms of DPCs formation.
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Affiliation(s)
- Emmanuelle Bignon
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France. .,Institut des Sciences Analytiques, UMR 5280, Université de Lyon 1 (UCBL) CNRS, Lyon, France.
| | - Victor E P Claerbout
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Tao Jiang
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Christophe Morell
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon 1 (UCBL) CNRS, Lyon, France
| | - Natacha Gillet
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Elise Dumont
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France. .,Institut Universitaire de France, 5 rue Descartes, 75005, Paris, France.
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14
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Zang C, Wang H, Li T, Zhang Y, Li J, Shang M, Du J, Xi Z, Zhou C. A light-responsive, self-immolative linker for controlled drug delivery via peptide- and protein-drug conjugates. Chem Sci 2019; 10:8973-8980. [PMID: 31762977 PMCID: PMC6857671 DOI: 10.1039/c9sc03016f] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/08/2019] [Indexed: 01/01/2023] Open
Abstract
Photoirradiation of the PC4AP linker generates an active intermediate that reacts intramolecularly with a primary amine on the carrier peptide/protein, leading to rapid release of the drug without generating any toxic side products.
When designing prodrugs, choosing an appropriate linker is the key to achieving efficient, controlled drug delivery. Herein, we report the use of a photocaged C4′-oxidized abasic site (PC4AP) as a light-responsive, self-immolative linker. Any amine- or hydroxyl-bearing drug can be loaded onto the linker via a carbamate or carbonate bond, and the linker is then conjugated to a carrier peptide or protein via an alkyl chain. The PC4AP linker is stable under physiologically relevant conditions. However, photodecaging of the linker generates an active intermediate that reacts intramolecularly with a primary amine (the ε-amine of a lysine residue and the N-terminal amine) on the carrier, leading to rapid and efficient release of the drug via an addition–elimination cascade, without generating any toxic side products. We demonstrated that the use of this self-immolative linker to conjugate the anticancer drug doxorubicin to a cell-penetrating peptide or an antibody enabled targeted, controlled delivery of the drug to cells. Our results suggest that the linker can be used with a broad range of carriers, such as cell-penetrating peptides, proteins, antibodies, and amine-functionalized polymers, and thus will find a wide range of practical applications.
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Affiliation(s)
- Chuanlong Zang
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
| | - Huawei Wang
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
| | - Tiantian Li
- School of Pharmaceutical Sciences , Tsinghua University , 30 Shuangqing Rd. , Beijing 100084 , China
| | - Yingqian Zhang
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
| | - Jiahui Li
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
| | - Mengdi Shang
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
| | - Juanjuan Du
- School of Pharmaceutical Sciences , Tsinghua University , 30 Shuangqing Rd. , Beijing 100084 , China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
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15
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Abstract
Repair of damaged DNA plays a crucial role in maintaining genomic integrity and normal cell function. The base excision repair (BER) pathway is primarily responsible for removing modified nucleobases that would otherwise cause deleterious and mutagenic consequences and lead to disease. The BER process is initiated by a DNA glycosylase, which recognizes and excises the target nucleobase lesion, and is completed via downstream enzymes acting in a well-coordinated manner. A majority of our current understanding about how BER enzymes function comes from in vitro studies using free duplex DNA as a simplified model. In eukaryotes, however, BER is challenged by the packaging of genomic DNA into chromatin. The fundamental structural repeating unit of chromatin is the nucleosome, which presents a more complex substrate context than free duplex DNA for repair. In this chapter, we discuss how BER enzymes, particularly glycosylases, engage in the context of packaged DNA with insights obtained from both in vivo and in vitro studies. Furthermore, we review factors and mechanisms that can modify chromatin architecture and/or influence DNA accessibility to BER machinery, such as the geometric location of the damage site, nucleosomal DNA unwrapping, histone post-translational modifications, histone variant incorporation, and chromatin remodeling.
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Affiliation(s)
- Chuxuan Li
- Department of Chemistry, Brown University, Providence, RI, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI, United States.
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16
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Ren M, Cheng Y, Duan Q, Zhou C. Transesterification Reaction and the Repair of Embedded Ribonucleotides in DNA Are Suppressed upon the Assembly of DNA into Nucleosome Core Particles †. Chem Res Toxicol 2019; 32:926-934. [PMID: 30990021 DOI: 10.1021/acs.chemrestox.9b00059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ribonucleotides can be incorporated into DNA through many different cellular processes, and abundant amounts of ribonucleotides are detected in genomic DNA. Embedded ribonucleotides lead to genomic instability through either spontaneous ribonucleotide cleavage via internal transesterification or by inducing mutagenesis, recombination, and chromosome rearrangements. Ribonucleotides misincorporated in genomic DNA can be removed by the ribonucleotide excision repair (RER) pathway in which RNase HII initiates the repair by cleaving the 5'-phosphate of the ribonucleotide. Herein, based on in vitro reconstituted nucleosome core particles (NCPs) containing a single ribonucleotide at different positions, we studied the kinetics of ribonucleotide cleavage via the internal transesterification reaction and repair of the ribonucleotides by RNase HII in NCPs. Our results show that ribonucleotide cleavage via the internal transesterification in NCPs is suppressed compared to that in free DNA. DNA bending and structural rigidity account for the suppressed ribonucleotide cleavage in NCPs. Ribonucleotide repair by RNase HII in NCPs exhibits a strong correlation between the translational and rotational positions of the ribonucleotides. An embedded ribonucleotide located at the entry site while facing outward in NCP is repaired as efficiently as that in free DNA. However, the repair of those located in the central part of NCPs and facing inward are inhibited by up to 273-fold relative to those in free dsDNA. The difference in repair efficiency appears to arise from their different accessibility to repair enzymes in NCPs. This study reveals that a ribonucleotide misincorporated in DNA assembled into NCPs is protected against cleavage. Hence, the spontaneous cleavage of the misincorporated ribonucleotides under physiological conditions is not an essential threat to the stability of chromatin DNA. Instead, their decreased repair efficiency in NCPs may result in numerous and persistent ribonucleotides in genomic DNA, which could exert other deleterious effects on DNA such as mutagenesis and recombination.
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Affiliation(s)
- Mengtian Ren
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Yiran Cheng
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Qian Duan
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
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17
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Yang K, Prasse C, Greenberg MM. Effect of Histone Lysine Methylation on DNA Lesion Reactivity in Nucleosome Core Particles. Chem Res Toxicol 2019; 32:910-916. [PMID: 30916939 DOI: 10.1021/acs.chemrestox.9b00049] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lysine methylation is a common post-translational histone modification that regulates transcription and gene expression. The lysine residues in the histone tail also react with damaged nucleotides in chromatin, including abasic sites and N7-methyl-2'-deoxyguanosine, the major product of DNA methylating agents. Lysine monomethylation transforms the ε-amine into a secondary amine, which could be more nucleophilic and/or basic than the ε-amine in lysine, and therefore more reactive with damaged DNA. The effect of lysine methylation on the reactivity with abasic sites and N7-methyl-2'-deoxyguanosine was examined in nucleosome core particles using a methylated lysine analogue derived from cysteine. ε-Amine methylation increases the rate constant for abasic site reaction within nucleosome core particles. Reactivity at the two positions examined increased less than twofold. Mechanistic experiments indicate that faster β-elimination from an intermediate iminium ion accounts for accelerated abasic reactivity. The rate constants for nucleophilic attack (Schiff base/iminium ion formation) by the lysine and methylated lysine analogues are indistinguishable. Similarly, the rate constants describing nucleophilic attack by the lysine and methylated lysine analogues on β-2'-fluoro-N7-methyl-2'-deoxyguanosine to form DNA-protein cross-links are also within experimental error of one another. These data indicate that abasic site containing DNA will be destabilized by lysine methylation. However, these experiments do not indicate that DNA-protein cross-link formation, a recently discovered form of damage resulting from N7-guanine methylation, will be affected by this post-translational modification.
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Affiliation(s)
- Kun Yang
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Carsten Prasse
- Department of Environmental Health and Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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18
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19
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Rana A, Yang K, Greenberg MM. Reactivity of the Major Product of C5'-Oxidative DNA Damage in Nucleosome Core Particles. Chembiochem 2019; 20:672-676. [PMID: 30444560 DOI: 10.1002/cbic.201800663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 11/11/2022]
Abstract
The major pathway for DNA damage following hydrogen atom abstraction from the C5'-position results in direct strand scission and concomitant formation of a 5'-aldehyde-containing nucleotide (e.g., T-al). We determined that the half-life of alkali-labile T-al in free DNA under physiological conditions varies from 5-12 days. T-al reactivity was examined at three positions within nucleosome core particles (NCPs). β-Elimination increased >2.5-fold when T-al was proximal to the lysine-rich histone H4 tail. No difference in reactivity between free DNA and NCPs was observed when T-al was distal from the histone tails. The position-dependent involvement of histone tails in T-al elimination was gleaned from experiments with sodium cyanoborohydride and histone protein variants. The enhancement of T-al elimination in NCPs is significantly smaller than previously observed for abasic sites. Computational studies comparing elimination from T-al and abasic sites indicate that the barrier for the rate-determining step in the latter is 2.6 kcal mol-1 lower and is stabilized by a hydrogen bond between the C4-hydroxy group and phosphate leaving group. The long lifetime for T-al in NCPs, combined with what is known about its repair suggests that this DNA lesion might pose significant challenges within cells.
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Affiliation(s)
- Anup Rana
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kun Yang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
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20
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Ravasco JMJM, Faustino H, Trindade A, Gois PMP. Bioconjugation with Maleimides: A Useful Tool for Chemical Biology. Chemistry 2018; 25:43-59. [PMID: 30095185 DOI: 10.1002/chem.201803174] [Citation(s) in RCA: 301] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Indexed: 02/06/2023]
Abstract
Maleimide chemistry stands out in the bioconjugation toolbox by virtue of its synthetic accessibility, excellent reactivity, and practicability. The second-generation of clinically approved antibody-drug conjugates (ADC) and much of the current ADC pipeline in clinical trials contain the maleimide linkage. However, thiosuccinimide linkages are now known to be less robust than once thought, and ergo, are correlated with suboptimal pharmacodynamics, pharmacokinetics, and safety profiles in some ADC constructs. Rational design of novel generations of maleimides and maleimide-type reagents have been reported to address the shortcomings of classical maleimides, allowing for the formation of robust bioconjugate linkages. This review highlights the main strategies for rational reagent design that have allowed irreversible bioconjugations in cysteines, reversible labelling strategies and disulfide re-bridging.
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Affiliation(s)
- João M J M Ravasco
- Bioorganic Chemistry Department, Research Institute for Medicines, (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Hélio Faustino
- Bioorganic Chemistry Department, Research Institute for Medicines, (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Alexandre Trindade
- Bioorganic Chemistry Department, Research Institute for Medicines, (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal.,School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Pedro M P Gois
- Bioorganic Chemistry Department, Research Institute for Medicines, (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
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21
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Bai J, Zhang Y, Xi Z, Greenberg MM, Zhou C. Oxidation of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Leads to Substantial DNA-Histone Cross-Links within Nucleosome Core Particles. Chem Res Toxicol 2018; 31:1364-1372. [PMID: 30412392 DOI: 10.1021/acs.chemrestox.8b00244] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
8-Oxo-7,8-dihydro-2'-deoxyguanosine(8-oxodGuo) is a common primary product of cellular oxidative DNA damage. 8-OxodGuo is more readily oxidized than 2'-deoxyguanosine (dG); a two-electron oxidation generates a highly reactive intermediate (OGox), which forms covalent adducts with nucleophiles, including OH-, free amines, and the side chains of amino acids such as lysine. We determined here that K3Fe(CN)6 oxidation of 8-oxodGuo in nucleosome core particles (NCPs) produces high yields, quantitative (i.e., 100%) in some cases, of DNA-protein cross-links (DPCs). The efficiency of DPC formation was closely related to 8-oxodGuo base pairing and location within the NCP and was only slightly decreased by adding the DNA-protective polyamine spermine to the system. Using NCPs that contained histone mutants, we determined that DPCs result predominantly from OGox trapping by the N-terminal histone amine. The DPCs were stable under physiological conditions and therefore could have important biological consequences. For instance, the essentially quantitative yield of DPCs at some positions within NCPs would reduce the yield of the mutagenic DNA lesions spiroiminodihydantoin and guanidinohydantoin produced from the common intermediate OGox, which in turn would affect mutation signatures of oxidative stress in a position-dependent manner. In summary, our findings indicate that site-specific incorporation of 8-oxodGuo into NCPs, followed by its oxidation, leads to DPCs with an efficiency depending on 8-oxodGuo location and orientation. Given that 8-oxodGuo formation is widespread in genomic DNA and that DPC formation is highly efficient, DPCs may occur in eukaryotic cells and may affect several important biological processes.
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Affiliation(s)
- Jing Bai
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Yingqian Zhang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , 3400 N. Charles Street , Baltimore , Maryland 21218 , United States
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300071 , China
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22
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Yang K, Greenberg MM. Histone Tail Sequences Balance Their Role in Genetic Regulation and the Need To Protect DNA against Destruction in Nucleosome Core Particles Containing Abasic Sites. Chembiochem 2018; 20:78-82. [PMID: 30307690 DOI: 10.1002/cbic.201800559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Indexed: 12/14/2022]
Abstract
Abasic sites (AP) are produced 10 000 times per day in a single cell. Strand cleavage at AP is accelerated ≈100-fold within a nucleosome core particle (NCP) compared to free DNA. The lysine-rich N-terminal tails of histone proteins catalyze single-strand breaks through a mechanism used by base-excision-repair enzymes, despite the general dearth of glutamic acid, aspartic acid, and histidine-the amino acids that are typically responsible for deprotonation of Schiff base intermediates. Incorporating glutamic acid, aspartic acid, or histidine proximal to lysine residues in histone N-terminal tails increases AP reactivity as much as sixfold. The rate acceleration is due to more facile DNA cleavage of Schiff-base intermediates. These observations raise the possibility that histone proteins could have evolved to minimize the presence of histidine, glutamic acid, and aspartic acid in their lysine-rich N-terminal tails to guard against enhancing the toxic effects of DNA damage.
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Affiliation(s)
- Kun Yang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
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23
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Histone tails decrease N7-methyl-2'-deoxyguanosine depurination and yield DNA-protein cross-links in nucleosome core particles and cells. Proc Natl Acad Sci U S A 2018; 115:E11212-E11220. [PMID: 30429328 DOI: 10.1073/pnas.1813338115] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Monofunctional alkylating agents preferentially react at the N7 position of 2'-deoxyguanosine in duplex DNA. Methylated DNA, such as that produced by methyl methanesulfonate (MMS) and temozolomide, exists for days in organisms. The predominant consequence of N7-methyl-2'-deoxyguanosine (MdG) is widely believed to be abasic site (AP) formation via hydrolysis, a process that is slow in free DNA. Examination of MdG reactivity within nucleosome core particles (NCPs) provided two general observations. MdG depurination rate constants are reduced in NCPs compared with when the identical DNA sequence is free in solution. The magnitude of the decrease correlates with proximity to the positively charged histone tails, and experiments in NCPs containing histone variants reveal that positively charged amino acids are responsible for the decreased rate of abasic site formation from MdG. In addition, the lysine-rich histone tails form DNA-protein cross-links (DPCs) with MdG. Cross-link formation is reversible and is ascribed to nucleophilic attack at the C8 position of MdG. DPC and retarded abasic site formation are observed in NCPs randomly damaged by MMS, indicating that these are general processes. Histone-MdG cross-links were also detected by mass spectrometry in chromatin isolated from V79 Chinese hamster lung cells treated with MMS. The formation of DPCs following damage by a monofunctional alkylating agent has not been reported previously. These observations reveal the possibility that such DPCs may contribute to the cytotoxicity of monofunctional alkylating agents, such as MMS, N-methyl-N-nitrosourea, and temozolomide.
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24
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Laverty DJ, Greenberg MM. Expanded Substrate Scope of DNA Polymerase θ and DNA Polymerase β: Lyase Activity on 5'-Overhangs and Clustered Lesions. Biochemistry 2018; 57:6119-6127. [PMID: 30299084 PMCID: PMC6200648 DOI: 10.1021/acs.biochem.8b00911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA polymerase θ (Pol θ) is a multifunctional enzyme with double-strand break (DSB) repair, translesion synthesis, and lyase activities. Pol θ lyase activity on ternary substrates containing a 5'-dRP that are produced during base excision repair of abasic sites (AP) is weak compared to that of DNA polymerase β (Pol β), a polymerase integrally involved in base excision repair. This led us to explore whether Pol θ utilizes its lyase activity to remove 5'-dRP and incise abasic sites from alternative substrates that might be produced during DNA damage and repair. We found that Pol θ exhibited lyase activity on abasic lesions near DSB termini and on clustered lesions. To calibrate the Pol θ activity, Pol β reactivity was examined with the same substrates. Pol β excised 5'-dRP from within a 5'-overhang 80 times faster than did Pol θ. Pol θ and Pol β also incised AP within clustered lesions but showed opposite preferences with respect to the polarity of the lesions. AP lesions in 5'-overhangs were typically excised by Pol β 35-50 times faster than those in a duplex substrate but 15-20-fold more slowly than 5'-dRP in a ternary complex. This is the first report of Pol θ exhibiting lyase activity within an unincised strand. These results suggest that bifunctional polymerases may exhibit lyase activity on a greater variety of substrates than previously recognized. A role in DSB repair could potentially be beneficial, while the aberrant activity exhibited on clustered lesions may be deleterious because of their conversion to DSBs.
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Affiliation(s)
- Daniel J. Laverty
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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25
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Abstract
A facile, one-pot synthetic method for the synthesis of 5-methylene-2-pyrrolones (5MPs) from inexpensive furfuryl acetate is described. Bromine oxidation and trapping of the in situ generated 1,4-dicarbonyl compound by a primary amine provided the corresponding 5MPs in 50-69% yield.
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Affiliation(s)
- Marco Paolo Jacinto
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Patricio Pichling
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
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26
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Wang R, Yang K, Banerjee S, Greenberg MM. Rotational Effects within Nucleosome Core Particles on Abasic Site Reactivity. Biochemistry 2018; 57:3945-3952. [PMID: 29894168 DOI: 10.1021/acs.biochem.8b00493] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
An abasic (AP) site is a ubiquitous DNA lesion that is produced via several cellular processes. Although AP sites are cytotoxic and mutagenic, cells are protected from them by different DNA damage tolerance and repair pathways, including base excision repair (BER). AP lesions are alkali-labile, but the half-life for strand scission is several weeks in free DNA at around neutral pH. The AP lifetime is reduced ∼100-fold in nucleosome core particles (NCPs) because the histone proteins promote strand scission. The reactivity of other DNA lesions to BER enzymes and exogenous reagents is highly dependent upon rotational positioning within the NCP. We examined strand scission at AP sites as a function of rotational position over approximately one helical turn of DNA. The rate constant for strand scission at AP varies ∼4-fold, a range of reactivity much smaller than that observed for processes that involve reaction with diffusible reagents in solution. In addition, the change in rate constant does not exhibit an obvious pattern with respect to rotational position. The small dependence of reactivity on rotational position is attributed to interactions with histone proteins. A molecular model based upon NCP X-ray crystal structures indicates that histone protein tails access AP sites via the major or minor groove and are therefore not limited to regions where one particular groove is exposed to solvent. Determining the roles of individual proteins is difficult because of the unstructured nature of the histone tails and the chemical mechanism, which involves reversible Schiff base formation, followed by irreversible elimination.
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Affiliation(s)
- Ruixiang Wang
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Kun Yang
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Samya Banerjee
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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27
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Li F, Zhang Y, Bai J, Greenberg MM, Xi Z, Zhou C. 5-Formylcytosine Yields DNA-Protein Cross-Links in Nucleosome Core Particles. J Am Chem Soc 2017; 139:10617-10620. [PMID: 28742335 DOI: 10.1021/jacs.7b05495] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In situ generation of 5-formylcytosine (5fC) in nucleosome core particles (NCPs) reveals that 5fC leads to essential DNA-protein cross-links (DPCs). Mechanistic studies using chemical models and mutated histones demonstrate that DPCs form reversibly between the formyl function of 5fC and primary amines on histones. These results suggest that DPC formation from 5fC in chromatin occurs in addition to its role in DNA demethylation.
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Affiliation(s)
- Fengchao Li
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Yingqian Zhang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Jing Bai
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300071, China
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28
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Zhang Y, Zhou X, Xie Y, Greenberg MM, Xi Z, Zhou C. Thiol Specific and Tracelessly Removable Bioconjugation via Michael Addition to 5-Methylene Pyrrolones. J Am Chem Soc 2017; 139:6146-6151. [PMID: 28407468 DOI: 10.1021/jacs.7b00670] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
5-Methylene pyrrolones (5MPs) are highly thiol-specific and tracelessly removable bioconjugation tools. 5MPs are readily prepared from primary amines in one step. 5MPs exhibit significantly improved stability under physiologically relevant conditions and cysteine specificity compared to commonly used analogues, maleimides. Michael addition of thiol to 5MPs occurs rapidly, cleanly, and does not generate a stereocenter. The conjugates efficiently release thiols via retro-Michael reaction in alkaline buffer (pH 9.5) or via thiol exchange at pH 7.5. This unique property makes 5MPs valuable for the controlled release of conjugated cargo and temporary thiol protection. The utilization of 5MPs for protein immobilization and pull-down of active complexes is illustrated using E. coli. acetohydroxyacid synthase isozyme I.
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Affiliation(s)
- Yingqian Zhang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Xiaoping Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Yonghui Xie
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
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29
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Banerjee S, Chakraborty S, Jacinto MP, Paul MD, Balster MV, Greenberg MM. Probing Enhanced Double-Strand Break Formation at Abasic Sites within Clustered Lesions in Nucleosome Core Particles. Biochemistry 2016; 56:14-21. [PMID: 28005342 DOI: 10.1021/acs.biochem.6b01144] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA is rapidly cleaved under mild alkaline conditions at apyrimidinic/apurinic sites, but the half-life is several weeks in phosphate buffer (pH 7.5). However, abasic sites are ∼100-fold more reactive within nucleosome core particles (NCPs). Histone proteins catalyze the strand scission, and at superhelical location 1.5, the histone H4 tail is largely responsible for the accelerated cleavage. The rate constant for strand scission at an abasic site is enhanced further in a nucleosome core particle when it is part of a bistranded lesion containing a proximal strand break. Cleavage of this form results in a highly deleterious double-strand break. This acceleration is dependent upon the position of the abasic lesion in the NCP and its structure. The enhancement in cleavage rate at an apurinic/apyrimidinic site rapidly drops off as the distance between the strand break and abasic site increases and is negligible once the two forms of damage are separated by 7 bp. However, the enhancement of the rate of double-strand break formation increases when the size of the gap is increased from one to two nucleotides. In contrast, the cleavage rate enhancement at 2-deoxyribonolactone within bistranded lesions is more modest, and it is similar in free DNA and nucleosome core particles. We postulate that the enhanced rate of double-strand break formation at bistranded lesions containing apurinic/apyrimidinic sites within nucleosome core particles is a general phenomenon and is due to increased DNA flexibility.
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Affiliation(s)
- Samya Banerjee
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Supratim Chakraborty
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Marco Paolo Jacinto
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Michael D Paul
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Morgan V Balster
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
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30
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Gatanaga C, Yang B, Inadomi Y, Usui K, Ota C, Katayama T, Suemune H, Aso M. Site-Specific Turn-On Fluorescent Labeling of DNA-Interacting Protein Using Oligodeoxynucleotides That Modify Lysines To Produce 5,6-Dimethoxy 3-Methyleneisoindolin-1-one. ACS Chem Biol 2016; 11:2216-21. [PMID: 27253874 DOI: 10.1021/acschembio.6b00090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have developed oligodeoxynucleotides (ODNs) that modify primary amines to produce 5,6-dimethoxy 3-methyleneisoindolin-1-one. Compared to the oxygen isosteric fluorophore, 4,5-dimethoxyphthalimide, this methyleneisoindolinone was more stable and exhibited an 85 nm blue-shifted fluorescent emission (λmax at 425 nm) with an intensity comparable to that of the phthalimide. Reaction of the DNA-binding domain of Escherichia coli DnaA protein with an ODN containing its binding sequence efficiently afforded a modified fluorescent protein at a specific lysine residue in the proximity of the ODN. A full-length DnaA protein was also successfully fluorescently labeled. These results demonstrate the potential utility of the ODNs developed in this study for the fluorescent labeling of DNA-interacting protein at the lysine residue of interest.
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Affiliation(s)
- Chiemi Gatanaga
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Bo Yang
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuka Inadomi
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazuteru Usui
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Chiyoe Ota
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tsutomu Katayama
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hiroshi Suemune
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mariko Aso
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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31
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Olszewska A, Pohl R, Brázdová M, Fojta M, Hocek M. Chloroacetamide-Linked Nucleotides and DNA for Cross-Linking with Peptides and Proteins. Bioconjug Chem 2016; 27:2089-94. [PMID: 27479485 DOI: 10.1021/acs.bioconjchem.6b00342] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nucleotides, 2'-deoxyribonucleoside triphosphates (dNTPs), and DNA probes bearing reactive chloroacetamido group linked to nucleobase (cytosine or 7-deazadaenine) through a propargyl tether were prepared and tested in cross-linking with cysteine- or histidine-containing peptides and proteins. The chloroacetamide-modifed dNTPs proved to be good substrates for DNA polymerases in the enzymatic synthesis of modified DNA probes. Modified nucleotides and DNA reacted efficiently with cysteine and cysteine-containing peptides, whereas the reaction with histidine was sluggish and low yielding. The modified DNA efficiently cross-linked with p53 protein through alkylation of cysteine and showed potential for cross-linking with histidine (in C277H mutant of p53).
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Affiliation(s)
- Agata Olszewska
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Marie Brázdová
- Institute of Biophysics, Czech Academy of Sciences , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, Czech Academy of Sciences , Kralovopolska 135, 612 65 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University , Kamenice 753/5, CZ-625 00 Brno, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague , Hlavova 8, 12843 Prague 2, Czech Republic
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32
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Greenberg MM. Reactivity of Nucleic Acid Radicals. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2016; 50:119-202. [PMID: 28529390 DOI: 10.1016/bs.apoc.2016.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.
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33
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Ali A, Wagner JR. Isomerization of 5-Hydroxy-5-methylhydantoin 2′-Deoxynucleoside into α-Furanose, β-Furanose, α-Pyranose, and β-Pyranose Anomers. Chem Res Toxicol 2015; 29:65-74. [DOI: 10.1021/acs.chemrestox.5b00406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anum Ali
- Département de Médecine
Nucléaire et de Radiobiologie, Faculté de Médecine
et des Sciences de la Santé, Université de Sherbrooke, 3001,
12e Avenue Nord, Sherbrooke, Québec, Canada J1H 5N4
| | - J. Richard Wagner
- Département de Médecine
Nucléaire et de Radiobiologie, Faculté de Médecine
et des Sciences de la Santé, Université de Sherbrooke, 3001,
12e Avenue Nord, Sherbrooke, Québec, Canada J1H 5N4
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34
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Abstract
How DNA damaged is formed, recognized, and repaired in chromatin is an area of intense study. To better understand the structure activity relationships of damaged chromatin, mono and dinucleosomes containing site-specific damage have been prepared and studied. This review will focus on the design, synthesis, and characterization of model systems of damaged chromatin for structural, physical, and enzymatic studies.
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35
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Weng L, Greenberg MM. Rapid Histone-Catalyzed DNA Lesion Excision and Accompanying Protein Modification in Nucleosomes and Nucleosome Core Particles. J Am Chem Soc 2015; 137:11022-31. [PMID: 26290445 DOI: 10.1021/jacs.5b05478] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
C5'-Hydrogen atoms are frequently abstracted during DNA oxidation. The oxidized abasic lesion 5'-(2-phosphoryl-1,4-dioxobutane) (DOB) is an electrophilic product of the C5'-radical. DOB is a potent irreversible inhibitor of DNA polymerase β, and forms interstrand cross-links in free DNA. We examined the reactivity of DOB within nucleosomes and nucleosome core particles (NCPs), the monomeric component of chromatin. Depending upon the position at which DOB is generated within a NCP, it is excised from nucleosomal DNA at a rate 275-1500-fold faster than that in free DNA. The half-life of DOB (7.0-16.8 min) in NCPs is shorter than any other abasic lesion. DOB's lifetime in NCPs is also significantly shorter than the estimated lifetime of an abasic site within a cell, suggesting that the observed chemistry would occur intracellularly. Histones also catalyze DOB excision when the lesion is present in the DNA linker region of a nucleosome. Schiff-base formation between DOB and histone proteins is detected in nucleosomes and NCPs, resulting in pyrrolone formation at the lysine residues. The lysines modified by DOB are often post-translationally modified. Consequently, the histone modifications described herein could affect the regulation of gene expression and may provide a chemical basis for the cytotoxicity of the DNA damaging agents that produce this lesion.
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Affiliation(s)
- Liwei Weng
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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36
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Kalaitzakis D, Kouridaki A, Noutsias D, Montagnon T, Vassilikogiannakis G. Methylene Blue as a Photosensitizer and Redox Agent: Synthesis of 5-Hydroxy-1H-pyrrol-2(5H)-ones from Furans. Angew Chem Int Ed Engl 2015; 54:6283-7. [DOI: 10.1002/anie.201500744] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/09/2015] [Indexed: 11/11/2022]
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37
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Kalaitzakis D, Kouridaki A, Noutsias D, Montagnon T, Vassilikogiannakis G. Methylene Blue as a Photosensitizer and Redox Agent: Synthesis of 5-Hydroxy-1H-pyrrol-2(5H)-ones from Furans. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500744] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Weng L, Zhou C, Greenberg MM. Probing interactions between lysine residues in histone tails and nucleosomal DNA via product and kinetic analysis. ACS Chem Biol 2015; 10:622-30. [PMID: 25475712 PMCID: PMC4336632 DOI: 10.1021/cb500737y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
The
histone proteins in nucleosome core particles are known to
catalyze DNA cleavage at abasic and oxidized abasic sites, which are
produced by antitumor antibiotics and as a consequence of other modalities
of DNA damage. The lysine rich histone tails whose post-translational
modifications regulate genetic expression in cells are mainly responsible
for this chemistry. Cleavage at a C4′-oxidized abasic site
(C4-AP) concomitantly results in modification of lysine residues in
histone tails. Using LC-MS/MS, we demonstrate here that that Lys8,
-12, -16, and -20 of histone H4 were modified when C4-AP was incorporated
at a hot spot (superhelical location 1.5) for DNA damage within a
nucleosome core particle. A new DNA–protein cross-linking method
that provides a more quantitative analysis of individual amino acid
reactivity is also described. DNA–protein cross-links were
produced by an irreversible reaction between a nucleic acid electrophile
that was produced following oxidatively induced rearrangement of a
phenyl selenide derivative of thymidine (3) and nucleophilic
residues within proteins. In addition to providing high yields of
DNA–protein cross-links, kinetic analysis of the cross-linking
reaction yielded rate constants that enabled ranking the contributions
by individual or groups of amino acids. Cross-linking from 3 at superhelical location 1.5 revealed the following order of reactivity
for the nucleophilic amino acids in the histone H4 tail: His18 >
Lys16
> Lys20 ≈ Lys8, Lys12 > Lys5. Cross-linking via 3 will be generally useful for investigating DNA–protein
interactions.
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Affiliation(s)
- Liwei Weng
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Chuanzheng Zhou
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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39
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Oxidatively induced DNA damage and its repair in cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:212-45. [PMID: 25795122 DOI: 10.1016/j.mrrev.2014.11.002] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 12/28/2022]
Abstract
Oxidatively induced DNA damage is caused in living organisms by endogenous and exogenous reactive species. DNA lesions resulting from this type of damage are mutagenic and cytotoxic and, if not repaired, can cause genetic instability that may lead to disease processes including carcinogenesis. Living organisms possess DNA repair mechanisms that include a variety of pathways to repair multiple DNA lesions. Mutations and polymorphisms also occur in DNA repair genes adversely affecting DNA repair systems. Cancer tissues overexpress DNA repair proteins and thus develop greater DNA repair capacity than normal tissues. Increased DNA repair in tumors that removes DNA lesions before they become toxic is a major mechanism for development of resistance to therapy, affecting patient survival. Accumulated evidence suggests that DNA repair capacity may be a predictive biomarker for patient response to therapy. Thus, knowledge of DNA protein expressions in normal and cancerous tissues may help predict and guide development of treatments and yield the best therapeutic response. DNA repair proteins constitute targets for inhibitors to overcome the resistance of tumors to therapy. Inhibitors of DNA repair for combination therapy or as single agents for monotherapy may help selectively kill tumors, potentially leading to personalized therapy. Numerous inhibitors have been developed and are being tested in clinical trials. The efficacy of some inhibitors in therapy has been demonstrated in patients. Further development of inhibitors of DNA repair proteins is globally underway to help eradicate cancer.
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40
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Ghosh S, Greenberg MM. Synthesis of cross-linked DNA containing oxidized abasic site analogues. J Org Chem 2014; 79:5948-57. [PMID: 24949656 PMCID: PMC4084848 DOI: 10.1021/jo500944g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA interstrand cross-links are an important family of DNA damage that block replication and transcription. Recently, it was discovered that oxidized abasic sites react with the opposing strand of DNA to produce interstrand cross-links. Some of the cross-links between 2'-deoxyadenosine and the oxidized abasic sites, 5'-(2-phosphoryl-1,4-dioxobutane) (DOB) and the C4-hydroxylated abasic site (C4-AP), are formed reversibly. Chemical instability hinders biochemical, structural, and physicochemical characterization of these cross-linked duplexes. To overcome these limitations, we developed methods for preparing stabilized analogues of DOB and C4-AP cross-links via solid-phase oligonucleotide synthesis. Oligonucleotides of any sequence are attainable by synthesizing phosphoramidites in which the hydroxyl groups of the cross-linked product were orthogonally protected using photochemically labile and hydrazine labile groups. Selective unmasking of a single hydroxyl group precedes solid-phase synthesis of one arm of the cross-linked DNA. The method is compatible with commercially available phosphoramidites and other oligonucleotide synthesis reagents. Cross-linked duplexes containing as many as 54 nt were synthesized on solid-phase supports. Subsequent enzyme ligation of one cross-link product provided a 60 bp duplex, which is suitable for nucleotide excision repair studies.
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Affiliation(s)
- Souradyuti Ghosh
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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41
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Abstract
![]()
Although
DNA binding proteins shield the genetic material from
diffusible reactive oxygen species by reacting with them, the resulting
protein (peroxyl) radicals can oxidize the bound DNA. To explore this
possible DNA damage by protein radicals, histone H4 proteins containing
an azoalkane radical precursor at defined sites were prepared. Photolysis
of a nucleosome core particle containing the modified protein produces
DNA damage that is consistent with selective C4′-oxidation.
The nucleotide(s) damaged is highly dependent on proximity to the
protein radical. These experiments provide insight into the effects
of oxidative stress on protein-bound DNA, revealing an additional
layer of complexity concerning nucleic acid damage.
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Affiliation(s)
- Chuanzheng Zhou
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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42
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Greenberg MM. Looking beneath the surface to determine what makes DNA damage deleterious. Curr Opin Chem Biol 2014; 21:48-55. [PMID: 24762292 DOI: 10.1016/j.cbpa.2014.03.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/21/2014] [Accepted: 03/25/2014] [Indexed: 02/07/2023]
Abstract
Apurinic/apyrimidinic and oxidized abasic sites are chemically reactive DNA lesions that are produced by a variety of damaging agents. The effects of these molecules that lack a Watson-Crick base on polymerase enzymes are well documented. More recently, multiple consequences of the electrophilic nature of abasic lesions have been revealed. Members of this family of DNA lesions have been shown to inactivate repair enzymes and undergo spontaneous transformation into more deleterious forms of damage. Abasic site reactivity provides insight into the chemical basis for the cytotoxicity of DNA damaging agents that produce them and are valuable examples of how looking beneath the surface of seemingly simple molecules can reveal biologically relevant chemical complexity.
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Affiliation(s)
- Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400N, Charles Street, Baltimore, MD 21218, United States.
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43
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Greenberg MM. Abasic and oxidized abasic site reactivity in DNA: enzyme inhibition, cross-linking, and nucleosome catalyzed reactions. Acc Chem Res 2014; 47:646-55. [PMID: 24369694 DOI: 10.1021/ar400229d] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Abasic lesions are a family of DNA modifications that lack Watson-Crick bases. The parent member of this family, the apurinic/apyrimidinic lesion (AP), occurs as an intermediate during DNA repair, following nucleobase alkylation, and from random hydrolysis of native nucleotides. In a given day, each cell produces between 10000 and 50000 AP lesions. A variety of oxidants including γ-radiolysis produce oxidized abasic sites, such as C4-AP, from the deoxyribose backbone. A number of potent, cytotoxic antitumor agents, such as bleomycin and the enediynes (e.g., calicheamicin, esperamicin, and neocarzinostatin) also lead to oxidized abasic sites in DNA. The absence of Watson-Crick bases prevents DNA polymerases from properly determining which nucleotide to incorporate opposite abasic lesions. Consequently, several studies have revealed that (oxidized) abasic sites are highly mutagenic. Abasic lesions are also chemically unstable, are prone to strand scission, and possess electrophilic carbonyl groups. However, researchers have only uncovered the consequences of the inherent reactivity of these electrophiles within the past decade. The development of solid phase synthesis methods for oligonucleotides that both place abasic sites in defined positions and circumvent their inherent alkaline lability has facilitated this research. Chemically synthesized oligonucleotides containing abasic lesions provide substrates that have allowed researchers to discover a range of interesting chemical properties of potential biological importance. For instance, abasic lesions form DNA-DNA interstrand cross-links, a particularly important family of DNA damage because they block replication and transcription absolutely. In addition, bacterial repair enzymes can convert an interstrand cross-link derived from C4-AP into a double-strand break, the most deleterious form of DNA damage. Oxidized abasic lesions can also inhibit DNA repair enzymes that remove damaged nucleotides. DNA polymerase β, an enzyme that is irreversibly inactivated, is vitally important in base excision repair and is overproduced in some tumor cells. Nucleosome core particles, the monomeric components that make up chromatin, accentuate the chemical instability of abasic lesions. In experiments using synthetic nucleosome core particles containing abasic sites, the histone proteins catalyze strand cleavage at the sites that incorporate these lesions. Furthermore, in the presence of the C4-AP lesion, strand scission is accompanied by modification of the histone protein. The reactivity of (oxidized) abasic lesions illustrates how seemingly simple nucleic acid modifications can have significant biochemical effects and may provide a chemical basis for the cytotoxicity of the chemotherapeutic agents that produce them.
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Affiliation(s)
- Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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44
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Volle C, Dalal Y. Histone variants: the tricksters of the chromatin world. Curr Opin Genet Dev 2014; 25:8-14,138. [PMID: 24463272 DOI: 10.1016/j.gde.2013.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 11/05/2013] [Indexed: 12/26/2022]
Abstract
The eukaryotic genome exists in vivo at an equimolar ratio with histones, thus forming a polymer composed of DNA and histone proteins. Each nucleosomal unit in this polymer provides versatile capabilities and dynamic range. Substitutions of the individual components of the histone core with structurally distinct histone variants and covalent modifications alter the local fabric of the chromatin fiber, resulting in epigenetic changes that can be regulated by the cell. In this review, we highlight recent advances in the study of histone variant structure, assembly, and inheritance, their influence on nucleosome positioning, and their cumulative effect upon gene expression, DNA repair and the progression of disease. We also highlight fundamental questions that remain unanswered regarding the behavior of histone variants and their influence on cellular function in the normal and diseased states.
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Affiliation(s)
- Catherine Volle
- Chromatin Structure and Epigenetic Mechanisms Team, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yamini Dalal
- Chromatin Structure and Epigenetic Mechanisms Team, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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