1
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Sales AH, Kolbanovskiy M, Geacintov NE, Chen KM, Sun YW, El-Bayoumy K. Treatment of Human HeLa Cells with Black Raspberry Extracts Enhances the Removal of DNA Lesions by the Nucleotide Excision Repair Mechanism. Antioxidants (Basel) 2022; 11:2110. [PMID: 36358482 PMCID: PMC9686895 DOI: 10.3390/antiox11112110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
As demonstrated by us earlier and by other researchers, a diet containing freeze-dried black raspberries (BRB) inhibits DNA damage and carcinogenesis in animal models. We tested the hypothesis that the inhibition of DNA damage by BRB is due, in part, to the enhancement of DNA repair capacity evaluated in the human HeLa cell extract system, an established in vitro system for the assessment of cellular DNA repair activity. The pre-treatment of intact HeLa cells with BRB extracts (BRBE) enhances the nucleotide excision repair (NER) of a bulky deoxyguanosine adduct derived from the polycyclic aromatic carcinogen benzo[a]pyrene (BP-dG) by ~24%. The NER activity of an oxidatively-derived non-bulky DNA lesion, guanidinohydantoin (Gh), is also enhanced by ~24%, while its base excision repair activity is enhanced by only ~6%. Western Blot experiments indicate that the expression of selected, NER factors is also increased by BRBE treatment by ~73% (XPA), ~55% (XPB), while its effects on XPD was modest (<14%). These results demonstrate that BRBE significantly enhances the NER yields of a bulky and a non-bulky DNA lesion, and that this effect is correlated with an enhancement of expression of the critically important NER factor XPA and the helicase XPB, but not the helicase XPD.
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Affiliation(s)
- Ana H. Sales
- Department of Chemistry, New York University, New York, NY 10003, USA
| | | | | | - Kun-Ming Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Yuan-Wan Sun
- Department of Biochemistry and Molecular Biology, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Karam El-Bayoumy
- Department of Biochemistry and Molecular Biology, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
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2
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Kowalczyk K, Roszak J, Sobańska Z, Stępnik M. Review of mechanisms of genotoxic action of dibenzo[def,p]chrysene (formerly dibenzo[a,l]pyrene). TOXIN REV 2022. [DOI: 10.1080/15569543.2022.2124419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
| | - J. Roszak
- Department of Translational Research, Nofer Institute of Occupational Medicine, Łódź, Poland
| | - Z. Sobańska
- Department of Translational Research, Nofer Institute of Occupational Medicine, Łódź, Poland
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3
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Ten TB, Zvoda V, Sarangi MK, Kuznetsov SV, Ansari A. "Flexible hinge" dynamics in mismatched DNA revealed by fluorescence correlation spectroscopy. J Biol Phys 2022; 48:253-272. [PMID: 35451661 PMCID: PMC9411374 DOI: 10.1007/s10867-022-09607-x] [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: 10/31/2021] [Accepted: 03/22/2022] [Indexed: 10/18/2022] Open
Abstract
Altered unwinding/bending fluctuations at DNA lesion sites are implicated as plausible mechanisms for damage sensing by DNA-repair proteins. These dynamics are expected to occur on similar timescales as one-dimensional (1D) diffusion of proteins on DNA if effective in stalling these proteins as they scan DNA. We examined the flexibility and dynamics of DNA oligomers containing 3 base pair (bp) mismatched sites specifically recognized in vitro by nucleotide excision repair protein Rad4 (yeast ortholog of mammalian XPC). A previous Forster resonance energy transfer (FRET) study mapped DNA conformational distributions with cytosine analog FRET pair primarily sensitive to DNA twisting/unwinding deformations (Chakraborty et al. Nucleic Acids Res. 46: 1240-1255 (2018)). These studies revealed B-DNA conformations for nonspecific (matched) constructs but significant unwinding for mismatched constructs specifically recognized by Rad4, even in the absence of Rad4. The timescales of these unwinding fluctuations, however, remained elusive. Here, we labeled DNA with Atto550/Atto647N FRET dyes suitable for fluorescence correlation spectroscopy (FCS). With these probes, we detected higher FRET in specific, mismatched DNA compared with matched DNA, reaffirming unwinding/bending deformations in mismatched DNA. FCS unveiled the dynamics of these spontaneous deformations at ~ 300 µs with no fluctuations detected for matched DNA within the ~ 600 ns-10 ms FCS time window. These studies are the first to visualize anomalous unwinding/bending fluctuations in mismatched DNA on timescales that overlap with the < 500 µs "stepping" times of repair proteins on DNA. Such "flexible hinge" dynamics at lesion sites could arrest a diffusing protein to facilitate damage interrogation and recognition.
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Affiliation(s)
- Timour B Ten
- Department of Physics (M/C 273), University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Viktoriya Zvoda
- Department of Physics (M/C 273), University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Manas K Sarangi
- Department of Physics (M/C 273), University of Illinois at Chicago, Chicago, IL, 60607, USA
- Present Address: Department of Physics, Indian Institute of Technology, Patna, 801103, India
| | - Serguei V Kuznetsov
- Department of Physics (M/C 273), University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Anjum Ansari
- Department of Physics (M/C 273), University of Illinois at Chicago, Chicago, IL, 60607, USA.
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4
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Wilson KA, Jeong YER, Wetmore SD. Multiscale computational investigations of the translesion synthesis bypass of tobacco-derived DNA adducts: critical insights that complement experimental biochemical studies. Phys Chem Chem Phys 2022; 24:10667-10683. [PMID: 35502640 DOI: 10.1039/d2cp00481j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Among the numerous agents that damage DNA, tobacco products remain one of the most lethal and result in the most diverse set of DNA lesions. This perspective aims to provide an overview of computational work conducted to complement experimental biochemical studies on the mutagenicity of adducts derived from the most potent tobacco carcinogen, namely 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (nicotine-derived nitrosaminoketone or NNK). Lesions ranging from the smallest methylated thymine derivatives to the larger, flexible pyridyloxobutyl (POB) guanine adducts are considered. Insights are obtained from density functional theory (DFT) calculations and molecular dynamics (MD) simulations into the damaged nucleobase and nucleoside structures, the accommodation of the lesions in the active site of key human polymerases, the intrinsic base pairing potentials of the adducts, and dNTP incorporation opposite the lesions. Overall, the computational data provide atomic level information that can rationalize the differential mutagenic properties of tobacco-derived lesions and uncover important insights into the impact of adduct size, nucleobase, position, and chemical composition of the bulky moiety.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute (ARRTI) and Southern Alberta Genome Sciences Center (SAGSC), University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Ye Eun Rebecca Jeong
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute (ARRTI) and Southern Alberta Genome Sciences Center (SAGSC), University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute (ARRTI) and Southern Alberta Genome Sciences Center (SAGSC), University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
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5
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Paul D, Mu H, Tavakoli A, Dai Q, Chakraborty S, He C, Ansari A, Broyde S, Min JH. Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex. DNA Repair (Amst) 2021; 107:103194. [PMID: 34428697 PMCID: PMC8934541 DOI: 10.1016/j.dnarep.2021.103194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 01/14/2023]
Abstract
Rad4/XPC recognizes diverse DNA lesions to initiate nucleotide excision repair (NER). However, NER propensities among lesions vary widely and repair-resistant lesions are persistent and thus highly mutagenic. Rad4 recognizes repair-proficient lesions by unwinding ('opening') the damaged DNA site. Such 'opening' is also observed on a normal DNA sequence containing consecutive C/G's (CCC/GGG) when tethered to Rad4 to prevent protein diffusion. However, it was unknown if such tethering-facilitated DNA 'opening' could occur on any DNA or if certain structures/sequences would resist being 'opened'. Here, we report that DNA containing alternating C/G's (CGC/GCG) failed to be opened even when tethered; instead, Rad4 bound in a 180°-reversed manner, capping the DNA end. Fluorescence lifetime studies of DNA conformations in solution showed that CCC/GGG exhibits local pre-melting that is absent in CGC/GCG. In MD simulations, CGC/GCG failed to engage Rad4 to promote 'opening' contrary to CCC/GGG. Altogether, our study illustrates how local sequences can impact DNA recognition by Rad4/XPC and how certain DNA sites resist being 'opened' even with Rad4 held at that site indefinitely. The contrast between CCC/GGG and CGC/GCG sequences in Rad4-DNA recognition may help decipher a lesion's mutagenicity in various genomic sequence contexts to explain lesion-determined mutational hot and cold spots.
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Affiliation(s)
- Debamita Paul
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Hong Mu
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Amirrasoul Tavakoli
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Sagnik Chakraborty
- Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA; Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Suse Broyde
- Department of Biology, New York University, New York, NY, 10003, USA.
| | - Jung-Hyun Min
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA.
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6
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Baiken Y, Kanayeva D, Taipakova S, Groisman R, Ishchenko AA, Begimbetova D, Matkarimov B, Saparbaev M. Role of Base Excision Repair Pathway in the Processing of Complex DNA Damage Generated by Oxidative Stress and Anticancer Drugs. Front Cell Dev Biol 2021; 8:617884. [PMID: 33553154 PMCID: PMC7862338 DOI: 10.3389/fcell.2020.617884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/17/2020] [Indexed: 01/22/2023] Open
Abstract
Chemical alterations in DNA induced by genotoxic factors can have a complex nature such as bulky DNA adducts, interstrand DNA cross-links (ICLs), and clustered DNA lesions (including double-strand breaks, DSB). Complex DNA damage (CDD) has a complex character/structure as compared to singular lesions like randomly distributed abasic sites, deaminated, alkylated, and oxidized DNA bases. CDD is thought to be critical since they are more challenging to repair than singular lesions. Although CDD naturally constitutes a relatively minor fraction of the overall DNA damage induced by free radicals, DNA cross-linking agents, and ionizing radiation, if left unrepaired, these lesions cause a number of serious consequences, such as gross chromosomal rearrangements and genome instability. If not tightly controlled, the repair of ICLs and clustered bi-stranded oxidized bases via DNA excision repair will either inhibit initial steps of repair or produce persistent chromosomal breaks and consequently be lethal for the cells. Biochemical and genetic evidences indicate that the removal of CDD requires concurrent involvement of a number of distinct DNA repair pathways including poly(ADP-ribose) polymerase (PARP)-mediated DNA strand break repair, base excision repair (BER), nucleotide incision repair (NIR), global genome and transcription coupled nucleotide excision repair (GG-NER and TC-NER, respectively), mismatch repair (MMR), homologous recombination (HR), non-homologous end joining (NHEJ), and translesion DNA synthesis (TLS) pathways. In this review, we describe the role of DNA glycosylase-mediated BER pathway in the removal of complex DNA lesions.
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Affiliation(s)
- Yeldar Baiken
- School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan.,National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Damira Kanayeva
- School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Regina Groisman
- Groupe ≪Mechanisms of DNA Repair and Carcinogenesis≫, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
| | - Alexander A Ishchenko
- Groupe ≪Mechanisms of DNA Repair and Carcinogenesis≫, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
| | - Dinara Begimbetova
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Bakhyt Matkarimov
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Murat Saparbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan.,Groupe ≪Mechanisms of DNA Repair and Carcinogenesis≫, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
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7
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Chakraborty S, Steinbach PJ, Paul D, Mu H, Broyde S, Min JH, Ansari A. Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex. Nucleic Acids Res 2019; 46:1240-1255. [PMID: 29267981 PMCID: PMC5815138 DOI: 10.1093/nar/gkx1216] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 12/12/2017] [Indexed: 12/15/2022] Open
Abstract
Rad4/XPC recognizes diverse DNA lesions including ultraviolet-photolesions and carcinogen-DNA adducts, initiating nucleotide excision repair. Studies have suggested that Rad4/XPC senses lesion-induced helix-destabilization to flip out nucleotides from damaged DNA sites. However, characterizing how DNA deformability and/or distortions impact recognition has been challenging. Here, using fluorescence lifetime measurements empowered by a maximum entropy algorithm, we mapped the conformational heterogeneities of artificially destabilized mismatched DNA substrates of varying Rad4-binding specificities. The conformational distributions, as probed by FRET between a cytosine-analog pair exquisitely sensitive to DNA twisting/bending, reveal a direct connection between intrinsic DNA deformability and Rad4 recognition. High-specificity CCC/CCC mismatch, free in solution, sampled a strikingly broad range of conformations from B-DNA-like to highly distorted conformations that resembled those observed with Rad4 bound; the extent of these distortions increased with bound Rad4 and with temperature. Conversely, the non-specific TAT/TAT mismatch had a homogeneous, B-DNA-like conformation. Molecular dynamics simulations also revealed a wide distribution of conformations for CCC/CCC, complementing experimental findings. We propose that intrinsic deformability promotes Rad4 damage recognition, perhaps by stalling a diffusing protein and/or facilitating ‘conformational capture’ of pre-distorted damaged sites. Surprisingly, even mismatched DNA specifically bound to Rad4 remains highly dynamic, a feature that may reflect the versatility of Rad4/XPC to recognize many structurally dissimilar lesions.
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Affiliation(s)
- Sagnik Chakraborty
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Peter J Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Debamita Paul
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Hong Mu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Suse Broyde
- Department of Biology, New York University, New York, NY 10003, USA
| | - Jung-Hyun Min
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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8
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Dolgova EV, Evdokimov AN, Proskurina AS, Efremov YR, Bayborodin SI, Potter EA, Popov AA, Petruseva IO, Lavrik OI, Bogachev SS. Double-Stranded DNA Fragments Bearing Unrepairable Lesions and Their Internalization into Mouse Krebs-2 Carcinoma Cells. Nucleic Acid Ther 2019; 29:278-290. [PMID: 31194620 DOI: 10.1089/nat.2019.0786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Murine Krebs-2 tumor-initiating stem cells are known to natively internalize extracellular double-stranded DNA fragments. Being internalized, these fragments interfere in the repair of chemically induced interstrand cross-links. In the current investigation, 756 bp polymerase chain reaction (PCR) product containing bulky photoreactive dC adduct was used as extracellular DNA. This adduct was shown to inhibit the cellular system of nucleotide excision repair while being resistant to excision by this DNA repair system. The basic parameters for this DNA probe internalization by the murine Krebs-2 tumor cells were characterized. Being incubated under regular conditions (60 min, 24°C, 500 μL of the incubation medium, in the dark), 0.35% ± 0.18% of the Krebs-2 ascites cells were shown to natively internalize modified DNA. The saturating amount of the modified DNA was detected to be 0.37 μg per 106 cells. For the similar unmodified DNA fragments, this ratio is 0.73 μg per 106 cells. Krebs-2 tumor cells were shown to be saturated internalizing either (190 ± 40) × 103 molecules of modified DNA or (1,000 ± 100) × 103 molecules of native DNA. On internalization, the fragments of DNA undergo partial and nonuniform hydrolysis of 3' ends followed by circularization. The degree of hydrolysis, assessed by sequencing of several clones with the insertion of specific PCR product, was 30-60 nucleotides.
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Affiliation(s)
- Evgeniya V Dolgova
- Laboratory of Induced Cell Processes, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey N Evdokimov
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasia S Proskurina
- Laboratory of Induced Cell Processes, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yaroslav R Efremov
- Laboratory of Induced Cell Processes, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Natural Sciences Department, Novosibirsk State University, Novosibirsk, Russia
| | - Sergey I Bayborodin
- Laboratory of Induced Cell Processes, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Ekaterina A Potter
- Laboratory of Induced Cell Processes, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey A Popov
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Irina O Petruseva
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga I Lavrik
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Natural Sciences Department, Novosibirsk State University, Novosibirsk, Russia.,Department of Physical Chemistry and Biotechnology, Altai State University, Barnaul, Russia
| | - Sergey S Bogachev
- Laboratory of Induced Cell Processes, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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9
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Mu H, Zhang Y, Geacintov NE, Broyde S. Lesion Sensing during Initial Binding by Yeast XPC/Rad4: Toward Predicting Resistance to Nucleotide Excision Repair. Chem Res Toxicol 2018; 31:1260-1268. [PMID: 30284444 PMCID: PMC6247245 DOI: 10.1021/acs.chemrestox.8b00231] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleotide excision repair (NER) excises a variety of environmentally derived DNA lesions. However, NER efficiencies for structurally different DNA lesions can vary by orders of magnitude; yet the origin of this variance is poorly understood. Our goal is to develop computational strategies that predict and identify the most hazardous, repair-resistant lesions from the plethora of such adducts. In the present work, we are focusing on lesion recognition by the xeroderma pigmentosum C protein complex (XPC), the first and required step for the subsequent assembly of factors needed to produce successful NER. We have performed molecular dynamics simulations to characterize the initial binding of Rad4, the yeast orthologue of human XPC, to a library of 10 different lesion-containing DNA duplexes derived from environmental carcinogens. These vary in lesion chemical structures and conformations in duplex DNA and exhibit a wide range of relative NER efficiencies from repair resistant to highly susceptible. We have determined a promising set of structural descriptors that characterize initial binding of Rad4 to lesions that are resistant to NER. Key initial binding requirements for successful recognition are absent in the repair-resistant cases: There is little or no duplex unwinding, very limited interaction between the β-hairpin domain 2 of Rad4 and the minor groove of the lesion-containing duplex, and no conformational capture of a base on the lesion partner strand. By contrast, these key binding features are present to different degrees in NER susceptible lesions and correlate to their relative NER efficiencies. Furthermore, we have gained molecular understanding of Rad4 initial binding as determined by the lesion structures in duplex DNA and how the initial binding relates to the repair efficiencies. The development of a computational strategy for identifying NER-resistant lesions is grounded in this molecular understanding of the lesion recognition mechanism.
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Affiliation(s)
| | - Yingkai Zhang
- NYU-ECNU Center for Computational Chemistry at New York University Shanghai , Shanghai 200062 , China
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10
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Mu H, Geacintov NE, Broyde S, Yeo JE, Schärer OD. Molecular basis for damage recognition and verification by XPC-RAD23B and TFIIH in nucleotide excision repair. DNA Repair (Amst) 2018; 71:33-42. [PMID: 30174301 DOI: 10.1016/j.dnarep.2018.08.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Global genome nucleotide excision repair (GG-NER) is the main pathway for the removal of bulky lesions from DNA and is characterized by an extraordinarily wide substrate specificity. Remarkably, the efficiency of lesion removal varies dramatically and certain lesions escape repair altogether and are therefore associated with high levels of mutagenicity. Central to the multistep mechanism of damage recognition in NER is the sensing of lesion-induced thermodynamic and structural alterations of DNA by the XPC-RAD23B protein and the verification of the damage by the transcription/repair factor TFIIH. Additional factors contribute to the process: UV-DDB, for the recognition of certain UV-induced lesions in particular in the context of chromatin, while the XPA protein is believed to have a role in damage verification and NER complex assembly. Here we consider the molecular mechanisms that determine repair efficiency in GG-NER based on recent structural, computational, biochemical, cellular and single molecule studies of XPC-RAD23B and its yeast ortholog Rad4. We discuss how the actions of XPC-RAD23B are integrated with those of other NER proteins and, based on recent high-resolution structures of TFIIH, present a structural model of how XPC-RAD23B and TFIIH cooperate in damage recognition and verification.
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Affiliation(s)
- Hong Mu
- Department of Biology, New York University, New York, NY 10003, USA
| | | | - Suse Broyde
- Department of Biology, New York University, New York, NY 10003, USA
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea; Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
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11
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Abstract
The eukaryotic global genomic nucleotide excision repair (GG-NER) pathway is the major mechanism that removes most bulky and some nonbulky lesions from cellular DNA. There is growing evidence that certain DNA lesions are repaired slowly or are entirely resistant to repair in cells, tissues, and in cell extract model assay systems. It is well established that the eukaryotic DNA lesion-sensing proteins do not detect the damaged nucleotide, but recognize the distortions/destabilizations in the native DNA structure caused by the damaged nucleotides. In this article, the nature of the structural features of certain bulky DNA lesions that render them resistant to NER, or cause them to be repaired slowly, is compared to that of those that are good-to-excellent NER substrates. Understanding the structural features that distinguish NER-resistant DNA lesions from good NER substrates may be useful for interpreting the biological significance of biomarkers of exposure of human populations to genotoxic environmental chemicals. NER-resistant lesions can survive to replication and cause mutations that can initiate cancer and other diseases. Furthermore, NER diminishes the efficacy of certain chemotherapeutic drugs, and the design of more potent pharmaceuticals that resist repair can be advanced through a better understanding of the structural properties of DNA lesions that engender repair-resistance.
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Affiliation(s)
- Nicholas E. Geacintov
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
| | - Suse Broyde
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
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12
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Talhaoui I, Matkarimov BT, Tchenio T, Zharkov DO, Saparbaev MK. Aberrant base excision repair pathway of oxidatively damaged DNA: Implications for degenerative diseases. Free Radic Biol Med 2017; 107:266-277. [PMID: 27890638 DOI: 10.1016/j.freeradbiomed.2016.11.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 02/06/2023]
Abstract
In cellular organisms composition of DNA is constrained to only four nucleobases A, G, T and C, except for minor DNA base modifications such as methylation which serves for defence against foreign DNA or gene expression regulation. Interestingly, this severe evolutionary constraint among other things demands DNA repair systems to discriminate between regular and modified bases. DNA glycosylases specifically recognize and excise damaged bases among vast majority of regular bases in the base excision repair (BER) pathway. However, the mismatched base pairs in DNA can occur from a spontaneous conversion of 5-methylcytosine to thymine and DNA polymerase errors during replication. To counteract these mutagenic threats to genome stability, cells evolved special DNA repair systems that target the non-damaged DNA strand in a duplex to remove mismatched regular DNA bases. Mismatch-specific adenine- and thymine-DNA glycosylases (MutY/MUTYH and TDG/MBD4, respectively) initiated BER and mismatch repair (MMR) pathways can recognize and remove normal DNA bases in mismatched DNA duplexes. Importantly, in DNA repair deficient cells bacterial MutY, human TDG and mammalian MMR can act in the aberrant manner: MutY and TDG removes adenine and thymine opposite misincorporated 8-oxoguanine and damaged adenine, respectively, whereas MMR removes thymine opposite to O6-methylguanine. These unusual activities lead either to mutations or futile DNA repair, thus indicating that the DNA repair pathways which target non-damaged DNA strand can act in aberrant manner and introduce genome instability in the presence of unrepaired DNA lesions. Evidences accumulated showing that in addition to the accumulation of oxidatively damaged DNA in cells, the aberrant DNA repair can also contribute to cancer, brain disorders and premature senescence. For example, the aberrant BER and MMR pathways for oxidized guanine residues can lead to trinucleotide expansion that underlies Huntington's disease, a severe hereditary neurodegenerative syndrome. This review summarises the present knowledge about the aberrant DNA repair pathways for oxidized base modifications and their possible role in age-related diseases.
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Affiliation(s)
- Ibtissam Talhaoui
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Bakhyt T Matkarimov
- National laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Thierry Tchenio
- LBPA, UMR8113 ENSC - CNRS, Ecole Normale Supérieure de Cachan, Cachan, France
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Murat K Saparbaev
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France.
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13
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Matkarimov BT, Saparbaev MK. Aberrant DNA glycosylase-initiated repair pathway of free radicals in-duced DNA damage: implications for age-related diseases and natural aging. ACTA ACUST UNITED AC 2017. [DOI: 10.7124/bc.000943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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14
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Otto C, Spivak G, Aloisi CMN, Menigatti M, Naegeli H, Hanawalt PC, Tanasova M, Sturla SJ. Modulation of Cytotoxicity by Transcription-Coupled Nucleotide Excision Repair Is Independent of the Requirement for Bioactivation of Acylfulvene. Chem Res Toxicol 2017; 30:769-776. [PMID: 28076683 DOI: 10.1021/acs.chemrestox.6b00240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioactivation as well as DNA repair affects the susceptibility of cancer cells to the action of DNA-alkylating chemotherapeutic drugs. However, information is limited with regard to the relative contributions of these processes to the biological outcome of metabolically activated DNA alkylating agents. We evaluated the influence of cellular bioactivation capacity and DNA repair on cytotoxicity of the DNA alkylating agent acylfulvene (AF). We compared the cytotoxicity and RNA synthesis inhibition by AF and its synthetic activated analogue iso-M0 in a panel of fibroblast cell lines with deficiencies in transcription-coupled (TC-NER) or global genome nucleotide excision repair (GG-NER). We related these data to the inherent bioactivation capacity of each cell type on the basis of mRNA levels. We demonstrated that specific inactivation of TC-NER by siRNA had the largest positive impact on AF activity in a cancer cell line. These findings establish that transcription-coupled DNA repair reduces cellular sensitivity to AF, independent of the requirement for bioactivation.
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Affiliation(s)
- Claudia Otto
- Department of Health Sciences and Technology, ETH Zurich , 8092 Zurich, Switzerland
| | - Graciela Spivak
- Department of Biology, Stanford University , Stanford, California 94305, United States
| | - Claudia M N Aloisi
- Department of Health Sciences and Technology, ETH Zurich , 8092 Zurich, Switzerland
| | - Mirco Menigatti
- Institute of Molecular Cancer Research, University of Zurich , 8057 Zurich, Switzerland
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse , 8057 Zurich, Switzerland
| | - Philip C Hanawalt
- Department of Biology, Stanford University , Stanford, California 94305, United States
| | - Marina Tanasova
- Department of Health Sciences and Technology, ETH Zurich , 8092 Zurich, Switzerland.,Department of Chemistry, Michigan Technological University , Houghton, Michigan 49932, United States
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich , 8092 Zurich, Switzerland
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15
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El-Bayoumy K, Chen KM, Zhang SM, Sun YW, Amin S, Stoner G, Guttenplan JB. Carcinogenesis of the Oral Cavity: Environmental Causes and Potential Prevention by Black Raspberry. Chem Res Toxicol 2016; 30:126-144. [DOI: 10.1021/acs.chemrestox.6b00306] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | | | - Shang-Min Zhang
- Department
of Pathology, Yale University, Yale School of Medicine, New Haven, Connecticut 06510, United States
| | | | | | - Gary Stoner
- Department
of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Joseph B. Guttenplan
- Department
of Basic Science, and Department of Environmental Medicine, New York University College of Dentistry and New York University School of Medicine, New York, New York 10010, United States
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16
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Wang X, Yang P, Li J, Ihsan A, Liu Q, Cheng G, Tao Y, Liu Z, Yuan Z. Genotoxic risk of quinocetone and its possible mechanism in in vitro studies. Toxicol Res (Camb) 2016; 5:446-460. [PMID: 30090359 PMCID: PMC6062406 DOI: 10.1039/c5tx00341e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/18/2015] [Indexed: 12/14/2022] Open
Abstract
Quinoxalines possessing the quinoxaline-1,4-dioxide (QdNOs) basic structure are used for their antibacterial action, although their mechanism of genotoxicity is not clear. After comparing the sensitivity of V79 cells and HepG2 cells to quinocetone (QCT) and other QdNOs, it was found that HepG2 cells are more sensitive. The results show that QCT induces the generation of O2˙- and OH˙ during metabolism. Free radicals could then attack guanine and induce 8-hydroxy-deoxyguanine (8-OHdG) generation, causing DNA strand breakage, the inhibition of topoisomerase II (topo II) activity, and alter PCNA, Gadd45 and topo II gene expression. QCT also caused mutations in the mtDNA genes COX1, COX3 and ATP6, which might affect the function of the mitochondrial respiratory chain and increase the production of reactive oxygen species (ROS). Nuclear extracts from HepG2 cells treated with QCT had markedly reduced topo II activity, as judged by the inability to convert pBR322 DNA from the catenated to the decatenated form by producing stable DNA-topo II complexes. This study suggests that QCT electrostatically bound to DNA in a groove, affecting the dissociation of topo II from DNA and impacting DNA replication. Taken together, these data reveal that DNA damage induced by QCT resulted from O2˙- and OH˙ generated in the metabolism process. This data throws new light onto the genotoxicity of quinoxalines.
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Affiliation(s)
- Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues , Wuhan , Hubei 430070 , China . ; ; Tel: +86-27-87287186
| | - Panpan Yang
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products , Huazhong Agricultural University , Wuhan , Hubei 430070 , China
| | - Juan Li
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products , Huazhong Agricultural University , Wuhan , Hubei 430070 , China
| | - Awais Ihsan
- Department of Biosciences , COMSATS Institute of Information Technology , Sahiwal , Pakistan
| | - Qianying Liu
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products , Huazhong Agricultural University , Wuhan , Hubei 430070 , China
| | - Guyue Cheng
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products , Huazhong Agricultural University , Wuhan , Hubei 430070 , China
| | - Yanfei Tao
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety , Wuhan , Hubei , China
| | - Zhengli Liu
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety , Wuhan , Hubei , China
| | - Zonghui Yuan
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues , Wuhan , Hubei 430070 , China . ; ; Tel: +86-27-87287186
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products , Huazhong Agricultural University , Wuhan , Hubei 430070 , China
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety , Wuhan , Hubei , China
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17
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Kathuria P, Sharma P, Wetmore SD. Effect of base sequence context on the conformational heterogeneity of aristolactam-I adducted DNA: structural and energetic insights into sequence-dependent repair and mutagenicity. Toxicol Res (Camb) 2016; 5:197-209. [PMID: 30090337 PMCID: PMC6061885 DOI: 10.1039/c5tx00302d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/19/2015] [Indexed: 11/21/2022] Open
Abstract
Aristolochic acids (AAs) are nephrotoxic and potentially carcinogenic plant mutagens that form bulky DNA adducts at the exocyclic amino groups of the purines. The present work utilizes classical molecular dynamics simulations and free energy calculations to investigate the role of lesion site sequence context in dictating the conformational outcomes of DNA containing ALI-N6-dA, the most persistent and mutagenic adduct arising from the AAs. Our calculations reveal that the anti base-displaced intercalated conformer is the lowest energy conformer of damaged DNA in all sequence contexts considered (CXC, CXG, GXC and GXG). However, the experimentally-observed greater mutagenicity of the adduct in the CXG sequence context does not correlate with the relative thermodynamic stability of the adduct in different sequences. Instead, AL-N6-dA adducted DNA is least distorted in the CXG sequence context, which points toward a possible differential repair propensity of the lesion in different sequences. Nevertheless, the structural deviations between adducted DNA with different lesion site sequences are small, and therefore other factors (such as interactions between the adducted DNA and lesion-bypass polymerases during replication) are likely more important for dictating the observed sequence-dependent mutagenicity of ALI-N6-dA.
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Affiliation(s)
- Preetleen Kathuria
- Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta , Canada T1K 3M4 . ; ; Tel: +1 403-329-2323
| | - Purshotam Sharma
- Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta , Canada T1K 3M4 . ; ; Tel: +1 403-329-2323
- Centre for Computational Sciences , Central University of Punjab , Bathinda , Punjab , India 151001
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta , Canada T1K 3M4 . ; ; Tel: +1 403-329-2323
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18
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Toxicology of DNA Adducts Formed Upon Human Exposure to Carcinogens. ADVANCES IN MOLECULAR TOXICOLOGY 2016. [DOI: 10.1016/b978-0-12-804700-2.00007-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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19
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Kathuria P, Sharma P, Wetmore SD. Adenine versus guanine DNA adducts of aristolochic acids: role of the carcinogen-purine linkage in the differential global genomic repair propensity. Nucleic Acids Res 2015; 43:7388-97. [PMID: 26175048 PMCID: PMC4551933 DOI: 10.1093/nar/gkv701] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/29/2015] [Indexed: 12/29/2022] Open
Abstract
Computational modeling is employed to provide a plausible structural explanation for the experimentally-observed differential global genome repair (GGR) propensity of the ALII-N(2)-dG and ALII-N(6)-dA DNA adducts of aristolochic acid II. Our modeling studies suggest that an intrinsic twist at the carcinogen-purine linkage of ALII-N(2)-dG induces lesion site structural perturbations and conformational heterogeneity of damaged DNA. These structural characteristics correlate with the relative repair propensities of AA-adducts, where GGR recognition occurs for ALII-N(2)-dG, but is evaded for intrinsically planar ALII-N(6)-dA that minimally distorts DNA and restricts the conformational flexibility of the damaged duplex. The present analysis on the ALII adduct model systems will inspire future experimental studies on these adducts, and thereby may extend the list of structural factors that directly correlate with the propensity for GGR recognition.
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Affiliation(s)
- Preetleen Kathuria
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada
| | - Purshotam Sharma
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada
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20
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Stavros KM, Hawkins EK, Rizzo CJ, Stone MP. Base-Displaced Intercalated Conformation of the 2-Amino-3-methylimidazo[4,5-f]quinoline N(2)-dG DNA Adduct Positioned at the Nonreiterated G(1) in the NarI Restriction Site. Chem Res Toxicol 2015; 28:1455-68. [PMID: 26083477 PMCID: PMC4511292 DOI: 10.1021/acs.chemrestox.5b00140] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
The
conformation of an N2-dG adduct
arising from the heterocyclic amine 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), a potent food mutagen, was determined
in 5′-d(C1T2C3X4G5C6G7C8C9A10T11C12)-3′:5′-d(G13A14T15G16G17C18G19C20C21G22A23G24)-3′; X = N2-dG-IQ, in which the modified nucleotide X4 corresponds to G1 in the 5′-d(G1G2CG3CC)-3′ NarI restriction endonuclease site. Circular dichroism (CD) revealed
blue shifts relative to the unmodified duplex, consistent with adduct-induced
twisting, and a hypochromic effect for the IQ absorbance in the near
UV region. NMR revealed that the N2-dG-IQ
adduct adopted a base-displaced intercalated conformation in which
the modified guanine remained in the anti conformation
about the glycosidic bond, the IQ moiety intercalated into the duplex,
and the complementary base C21 was displaced into the major
groove. The processing of the N2-dG-IQ
lesion by hpol η is sequence-dependent; when placed at the reiterated
G3 position, but not at the G1 position, this
lesion exhibits a propensity for frameshift replication [Choi, J.
Y., et al. (2006) J. Biol. Chem., 281, 25297–25306]. The structure of the N2-dG-IQ adduct at the nonreiterated G1 position
was compared to that of the same adduct placed at the G3 position [Stavros, K. M., et al. (2014) Nucleic Acids Res., 42, 3450–3463]. CD indicted minimal spectral
differences between the G1 vs G3N2-dG-IQ adducts. NMR indicated that the N2-dG-IQ adduct exhibited similar base-displaced intercalated
conformations at both the G1 and G3 positions.
This result differed as compared to the corresponding C8-dG-IQ adducts
placed at the same positions. The C8-dG-IQ adduct adopted a minor
groove conformation when placed at position G1 but a base-displaced
intercalated conformation when placed at position G3 in
the NarI sequence. The present studies suggest that
differences in lesion bypass by hpol η may be mediated by differences
in the 3′-flanking sequences, perhaps modulating the ability
to accommodate transient strand slippage intermediates.
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Affiliation(s)
- Kallie M Stavros
- †Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235-1822, United States
| | | | - Carmelo J Rizzo
- †Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235-1822, United States
| | - Michael P Stone
- †Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235-1822, United States
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21
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Siddens LK, Bunde KL, Harper TA, McQuistan TJ, Löhr CV, Bramer LM, Waters KM, Tilton SC, Krueger SK, Williams DE, Baird WM. Cytochrome P450 1b1 in polycyclic aromatic hydrocarbon (PAH)-induced skin carcinogenesis: Tumorigenicity of individual PAHs and coal-tar extract, DNA adduction and expression of select genes in the Cyp1b1 knockout mouse. Toxicol Appl Pharmacol 2015; 287:149-160. [PMID: 26049101 DOI: 10.1016/j.taap.2015.05.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 05/12/2015] [Accepted: 05/29/2015] [Indexed: 01/05/2023]
Abstract
FVB/N mice wild-type, heterozygous or null for Cyp 1b1 were used in a two-stage skin tumor study comparing PAH, benzo[a]pyrene (BaP), dibenzo[def,p]chrysene (DBC), and coal tar extract (CTE, SRM 1597a). Following 20 weeks of promotion with TPA the Cyp 1b1 null mice, initiated with DBC, exhibited reductions in incidence, multiplicity, and progression. None of these effects were observed with BaP or CTE. The mechanism of Cyp 1b1-dependent alteration of DBC skin carcinogenesis was further investigated by determining expression of select genes in skin from DBC-treated mice 2, 4 and 8h post-initiation. A significant reduction in levels of Cyp 1a1, Nqo1 at 8h and Akr 1c14 mRNA was observed in Cyp 1b1 null (but not wt or het) mice, whereas no impact was observed in Gst a1, Nqo 1 at 2 and 4h or Akr 1c19 at any time point. Cyp 1b1 mRNA was not elevated by DBC. The major covalent DNA adducts, dibenzo[def,p]chrysene-(±)-11,12-dihydrodiol-cis and trans-13,14-epoxide-deoxyadenosine (DBCDE-dA) were quantified by UHPLC-MS/MS 8h post-initiation. Loss of Cyp1 b1 expression reduced DBCDE-dA adducts in the skin but not to a statistically significant degree. The ratio of cis- to trans-DBCDE-dA adducts was higher in the skin than other target tissues such as the spleen, lung and liver (oral dosing). These results document that Cyp 1b1 plays a significant role in bioactivation and carcinogenesis of DBC in a two-stage mouse skin tumor model and that loss of Cyp 1b1 has little impact on tumor response with BaP or CTE as initiators.
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Affiliation(s)
- Lisbeth K Siddens
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA; Superfund Research Center, Oregon State University, Corvallis, OR 97331, USA
| | - Kristi L Bunde
- College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA
| | - Tod A Harper
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA; Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA; Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, USA
| | - Tammie J McQuistan
- Superfund Research Center, Oregon State University, Corvallis, OR 97331, USA; Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
| | - Christiane V Löhr
- Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, USA; College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA
| | - Lisa M Bramer
- Applied Statistics and Computational Modeling, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Katrina M Waters
- Superfund Research Center, Oregon State University, Corvallis, OR 97331, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Susan C Tilton
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA; Superfund Research Center, Oregon State University, Corvallis, OR 97331, USA
| | - Sharon K Krueger
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA; Superfund Research Center, Oregon State University, Corvallis, OR 97331, USA; Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
| | - David E Williams
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA; Superfund Research Center, Oregon State University, Corvallis, OR 97331, USA; Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA; Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, USA.
| | - William M Baird
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA; Superfund Research Center, Oregon State University, Corvallis, OR 97331, USA; Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, USA
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22
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Kathuria P, Sharma P, Abendong MN, Wetmore SD. Conformational Preferences of DNA following Damage by Aristolochic Acids: Structural and Energetic Insights into the Different Mutagenic Potential of the ALI and ALII-N6-dA Adducts. Biochemistry 2015; 54:2414-28. [PMID: 25761009 DOI: 10.1021/bi501484m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Preetleen Kathuria
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Purshotam Sharma
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Minette N. Abendong
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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23
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Harper TA, Morré J, Lauer FT, McQuistan TJ, Hummel JM, Burchiel SW, Williams DE. Analysis of dibenzo[def,p]chrysene-deoxyadenosine adducts in wild-type and cytochrome P450 1b1 knockout mice using stable-isotope dilution UHPLC-MS/MS. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 782:51-6. [PMID: 25868132 DOI: 10.1016/j.mrgentox.2015.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 12/31/2022]
Abstract
The polycyclic aromatic hydrocarbon (PAH), dibenzo[def,p]chrysene (DBC; also known as dibenzo[a,l]pyrene), is a potent carcinogen in animal models and a class 2A human carcinogen. Recent investigations into DBC-mediated toxicity identified DBC as a potent immunosuppressive agent similar to the well-studied immunotoxicant 7,12-dimethylbenz[a]anthracene (DMBA). DBC, like DMBA, is bioactivated by cytochrome P450 (CYP) 1B1 and forms the reactive metabolite DBC-11,12-diol-13,14-epoxide (DBCDE). DBCDE is largely responsible for the genotoxicity associated with DBC exposure. The immunosuppressive properties of several PAHs are also linked to genotoxic mechanisms. Therefore, this study was designed to identify DBCDE-DNA adduct formation in the spleen and thymus of wild-type and cytochrome P450 1b1 (Cyp1b1) knockout (KO) mice using a highly sensitive stable-isotope dilution UHPLC-MS/MS method. Stable-isotope dilution UHPLC-MS/MS identified the major DBC adducts (±)-anti-cis-DBCDE-dA and (±)-anti-trans-DBCDE-dA in the lung, liver, and spleen of both WT and Cyp1b1 KO mice. However, adduct formation in the thymus was below the level of quantitation for our method. Additionally, adduct formation in Cyp1b1 KO mice was significantly reduced compared to wild-type (WT) mice receiving DBC via oral gavage. In conclusion, the current study identifies for the first time DBCDE-dA adducts in the spleen of mice supporting the link between genotoxicity and immunosuppression, in addition to supporting previous studies identifying Cyp1b1 as the primary CYP involved in DBC bioactivation to DBCDE. The high levels of DBC-DNA adducts identified in the spleen, along with the known high levels of Cyp1b1 expression in this organ, supports further investigation into DBC-mediated immunotoxicity.
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Affiliation(s)
- Tod A Harper
- Superfund Research Program, Oregon State University, 1011 ALS, Corvallis, OR 97331, USA; Environmental and Molecular Toxicology Department, Oregon State University, 1007 ALS, Corvallis, OR 97331, USA; Linus Pauling Institute, Oregon State University, 307 LPSC, Corvallis, OR 97331, USA.
| | - Jeff Morré
- Department of Chemistry, Oregon State University, 153A Gilbert Hall, Corvallis, OR 97331, USA; Environmental Health Science Center, Oregon State University, 1011 ALS, Corvallis, OR 97331, USA.
| | - Fredine T Lauer
- Department of Pharmaceutical Sciences, University of New Mexico, 2502 Marble NE, Albuquerque NM 87131, USA.
| | - Tammie J McQuistan
- Superfund Research Program, Oregon State University, 1011 ALS, Corvallis, OR 97331, USA; Linus Pauling Institute, Oregon State University, 307 LPSC, Corvallis, OR 97331, USA.
| | - Jessica M Hummel
- Linus Pauling Institute, Oregon State University, 307 LPSC, Corvallis, OR 97331, USA.
| | - Scott W Burchiel
- Department of Pharmaceutical Sciences, University of New Mexico, 2502 Marble NE, Albuquerque NM 87131, USA.
| | - David E Williams
- Superfund Research Program, Oregon State University, 1011 ALS, Corvallis, OR 97331, USA; Environmental and Molecular Toxicology Department, Oregon State University, 1007 ALS, Corvallis, OR 97331, USA; Linus Pauling Institute, Oregon State University, 307 LPSC, Corvallis, OR 97331, USA; Environmental Health Science Center, Oregon State University, 1011 ALS, Corvallis, OR 97331, USA.
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Chen X, Velmurugu Y, Zheng G, Park B, Shim Y, Kim Y, Liu L, Van Houten B, He C, Ansari A, Min JH. Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Nat Commun 2015; 6:5849. [PMID: 25562780 PMCID: PMC4354021 DOI: 10.1038/ncomms6849] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 11/13/2014] [Indexed: 01/24/2023] Open
Abstract
The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites. XPC nucleotide excision repair factor is key to starting the repair of diverse helix-distorting DNA lesions caused by environmental insults. Here, the authors propose a kinetic gating mechanism whereby XPC recognizes DNA lesions by preferentially opening damaged sites while readily diffusing away from undamaged sites.
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Affiliation(s)
- Xuejing Chen
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA
| | - Yogambigai Velmurugu
- Department of Physics, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA
| | - Guanqun Zheng
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Beomseok Park
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA
| | - Yoonjung Shim
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA
| | - Youngchang Kim
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, Illinois 60439, USA
| | - Lili Liu
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Chuan He
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Anjum Ansari
- 1] Department of Physics, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA [2] Department of Bioengineering, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA
| | - Jung-Hyun Min
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA
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Lior-Hoffmann L, Ding S, Geacintov NE, Zhang Y, Broyde S. Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity. Biochemistry 2014; 53:5683-91. [PMID: 25148552 PMCID: PMC4159208 DOI: 10.1021/bi5007964] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
DNA
lesion bypass polymerases process different lesions with varying
fidelities, but the structural, dynamic, and mechanistic origins of
this phenomenon remain poorly understood. Human DNA polymerase κ
(Polκ), a member of the Y family of lesion bypass polymerases,
is specialized to bypass bulky DNA minor groove lesions in a predominantly
error-free manner, by housing them in its unique gap. We have investigated
the role of the unique Polκ gap and N-clasp structural features
in the fidelity of minor groove lesion processing with extensive molecular
modeling and molecular dynamics simulations to pinpoint their functioning
in lesion bypass. Here we consider the N2-dG covalent adduct derived from the carcinogenic aromatic amine,
2-acetylaminofluorene (dG-N2-AAF), that
is produced via the combustion of kerosene and diesel fuel. Our simulations
reveal how the spacious gap directionally accommodates the lesion
aromatic ring system as it transits through the stages of incorporation
of the predominant correct partner dCTP opposite the damaged guanine,
with preservation of local active site organization for nucleotidyl
transfer. Furthermore, flexibility in Polκ’s N-clasp
facilitates the significant misincorporation of dTTP opposite dG-N2-AAF via wobble pairing. Notably, we show that
N-clasp flexibility depends on lesion topology, being markedly reduced
in the case of the benzo[a]pyrene-derived major adduct
to N2-dG, whose bypass by Polκ is
nearly error-free. Thus, our studies reveal how Polκ’s
unique structural and dynamic properties can regulate its bypass fidelity
of polycyclic aromatic lesions and how the fidelity is impacted by
lesion structures.
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Affiliation(s)
- Lee Lior-Hoffmann
- Department of Biology and ‡Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States
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27
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Wilson KA, Wetmore SD. Complex Conformational Heterogeneity of the Highly Flexible O6-Benzyl-guanine DNA Adduct. Chem Res Toxicol 2014; 27:1310-25. [PMID: 24941023 DOI: 10.1021/tx500178x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Katie A. Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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28
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Lee YC, Cai Y, Mu H, Broyde S, Amin S, Chen X, Min JH, Geacintov NE. The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: is there a correlation? DNA Repair (Amst) 2014; 19:55-63. [PMID: 24784728 DOI: 10.1016/j.dnarep.2014.03.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The first eukaryotic NER factor that recognizes NER substrates is the heterodimeric XPC-RAD23B protein. The currently accepted hypothesis is that this protein recognizes the distortions/destabilization caused by DNA lesions rather than the lesions themselves. The resulting XPC-RAD23B-DNA complexes serve as scaffolds for the recruitment of subsequent NER factors that lead to the excision of the oligonucleotide sequences containing the lesions. Based on several well-known examples of DNA lesions like the UV radiation-induced CPD and 6-4 photodimers, as well as cisplatin-derived intrastrand cross-linked lesions, it is generally believed that the differences in excision activities in human cell extracts is correlated with the binding affinities of XPC-RAD23B to these DNA lesions. However, using electrophoretic mobility shift assays, we have found that XPC-RAD23B binding affinities of certain bulky lesions derived from metabolically activated polycyclic aromatic hydrocarbon compounds such as benzo[a]pyrene and dibenzo[a,l]pyrene, are not directly, or necessarily correlated with NER excision activities observed in cell-free extracts. These findings point to features of XPC-RAD23B-bulky DNA adduct complexes that may involve the formation of NER-productive or unproductive forms of binding that depend on the structural and stereochemical properties of the DNA adducts studied. The pronounced differences in NER cleavage efficiencies observed in cell-free extracts may be due to differences in the successful recruitment of subsequent NER factors by the XPC-RAD23B-DNA adduct complexes, and/or in the verification step. These phenomena appear to depend on the structural and conformational properties of the class of bulky DNA adducts studied.
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Affiliation(s)
- Yuan-Cho Lee
- Chemistry Department, New York University, Silver Complex, 100 Washington Square East, New York, NY 10012, USA
| | - Yuqin Cai
- Biology Department, New York University, Silver Complex, 100 Washington Square East, New York, NY 10012, USA
| | - Hong Mu
- Biology Department, New York University, Silver Complex, 100 Washington Square East, New York, NY 10012, USA
| | - Suse Broyde
- Biology Department, New York University, Silver Complex, 100 Washington Square East, New York, NY 10012, USA
| | - Shantu Amin
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Xuejing Chen
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jung-Hyun Min
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Nicholas E Geacintov
- Chemistry Department, New York University, Silver Complex, 100 Washington Square East, New York, NY 10012, USA.
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29
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Jarvis IWH, Dreij K, Mattsson Å, Jernström B, Stenius U. Interactions between polycyclic aromatic hydrocarbons in complex mixtures and implications for cancer risk assessment. Toxicology 2014; 321:27-39. [PMID: 24713297 DOI: 10.1016/j.tox.2014.03.012] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 03/28/2014] [Accepted: 03/30/2014] [Indexed: 01/27/2023]
Abstract
In this review we discuss the effects of exposure to complex PAH mixtures in vitro and in vivo on mechanisms related to carcinogenesis. Of particular concern regarding exposure to complex PAH mixtures is how interactions between different constituents can affect the carcinogenic response and how these might be included in risk assessment. Overall the findings suggest that the responses resulting from exposure to complex PAH mixtures is varied and complicated. More- and less-than additive effects on bioactivation and DNA damage formation have been observed depending on the various mixtures studied, and equally dependent on the different test systems that are used. Furthermore, the findings show that the commonly used biological end-point of DNA damage formation is insufficient for studying mixture effects. At present the assessment of the risk of exposure to complex PAH mixtures involves comparison to individual compounds using either a surrogate or a component-based potency approach. We discuss how future risk assessment strategies for complex PAH mixtures should be based around whole mixture assessment in order to account for interaction effects. Inherent to this is the need to incorporate different experimental approaches using robust and sensitive biological endpoints. Furthermore, the emphasis on future research should be placed on studying real life mixtures that better represent the complex PAH mixtures that humans are exposed to.
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Affiliation(s)
- Ian W H Jarvis
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, SE-171 77 Stockholm, Sweden.
| | - Kristian Dreij
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, SE-171 77 Stockholm, Sweden
| | - Åse Mattsson
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, SE-171 77 Stockholm, Sweden
| | - Bengt Jernström
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, SE-171 77 Stockholm, Sweden
| | - Ulla Stenius
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, SE-171 77 Stockholm, Sweden
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30
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Kim KT, Kim HW, Moon D, Rhee YM, Kim BH. (DNS)C: a fluorescent, environmentally sensitive cytidine derivative for the direct detection of GGG triad sequences. Org Biomol Chem 2014; 11:5605-14. [PMID: 23846401 DOI: 10.1039/c3ob41222a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With the goal of developing a fluorescent nucleoside sensitive to its environment, in this study we synthesized (DNS)C, a novel modified 2'-deoxycytidine bearing a 5-(dimethylamino)naphthalene-1-sulfonyl (dansyl) moiety at the N4 position, and tested its properties in monomeric and oligomeric states. (DNS)C undergoes intramolecular photoinduced electron transfer between its dansyl and cytosine units, resulting in remarkable changes in fluorescence that depend on the choice of solvent. In addition, the fluorescence behavior and thermal stability of oligonucleotides containing (DNS)C are dependent on the nature of the flanking and neighboring bases. Notably, (DNS)C exhibits fluorescence enhancement only in fully matched duplex DNA containing a GGG triad sequence. The environmental sensitivity of (DNS)C can be exploited as a fluorescence tool for monitoring the interactions of DNA with other biomolecules, including DNA, RNA, and proteins.
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Affiliation(s)
- Ki Tae Kim
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
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31
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Rodríguez FA, Liu Z, Lin CH, Ding S, Cai Y, Kolbanovskiy A, Kolbanovskiy M, Amin S, Broyde S, Geacintov NE. Nuclear magnetic resonance studies of an N2-guanine adduct derived from the tumorigen dibenzo[a,l]pyrene in DNA: impact of adduct stereochemistry, size, and local DNA sequence on solution conformations. Biochemistry 2014; 53:1827-41. [PMID: 24617538 PMCID: PMC3985812 DOI: 10.1021/bi4017044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
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The
dimensions and arrangements of aromatic rings (topology) in
adducts derived from the reactions of polycyclic aromatic hydrocarbon
(PAH) diol epoxide metabolites with DNA influence the distortions
and stabilities of double-stranded DNA, and hence their recognition
and processing by the human nucleotide excision repair (NER) system.
Dibenzo[a,l]pyrene (DB[a,l]P) is a highly tumorigenic six-ring PAH, which
contains a nonplanar and aromatic fjord region that is absent in the
structurally related bay region five-ring PAH benzo[a]pyrene (B[a]P). The PAH diol epoxide–DNA
adducts formed include the stereoisomeric 14S and
14Rtrans-anti-DB[a,l]P-N2-dG
and the stereochemically analogous 10S- and 10R-B[a]P-N2-dG
(B[a]P-dG) guanine adducts. However, nuclear magnetic
resonance (NMR) solution studies of the 14S-DB[a,l]P-N2-dG
adduct in DNA have not yet been presented. Here we have investigated
the 14S-DB[a,l]P-N2-dG adduct in two different sequence contexts
using NMR methods with distance-restrained molecular dynamics simulations.
In duplexes with dC opposite the adduct deleted, a well-resolved base-displaced
intercalative adduct conformation can be observed. In full duplexes,
in contrast to the intercalated 14R stereoisomeric
adduct, the bulky DB[a,l]P residue
in the 14S adduct is positioned in a greatly widened
and distorted minor groove, with significant disruptions and distortions
of base pairing at the lesion site and two 5′-side adjacent
base pairs. These unique structural features are significantly different
from those of the stereochemically analogous but smaller B[a]P-dG adduct. The greater size and different topology of
the DB[a,l]P aromatic ring system
lead to greater structurally destabilizing DNA distortions that are
partially compensated by stabilizing DB[a,l]P-DNA van der Waals interactions, whose combined effects
impact the NER response to the adduct. These structural results broaden
our understanding of the structure–function relationship in
NER.
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Affiliation(s)
- Fabián A Rodríguez
- Department of Chemistry, New York University , New York, New York 10003, United States
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32
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Kropachev K, Ding S, Terzidis MA, Masi A, Liu Z, Cai Y, Kolbanovskiy M, Chatgilialoglu C, Broyde S, Geacintov NE, Shafirovich V. Structural basis for the recognition of diastereomeric 5',8-cyclo-2'-deoxypurine lesions by the human nucleotide excision repair system. Nucleic Acids Res 2014; 42:5020-32. [PMID: 24615810 PMCID: PMC4041128 DOI: 10.1093/nar/gku162] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The hydroxyl radical is a powerful oxidant that generates DNA lesions including the
stereoisomeric R and S
5′,8-cyclo-2′-deoxyadenosine (cdA) and
5′,8-cyclo-2′-deoxyguanosine (cdG) pairs that have been detected in cellular
DNA. Unlike some other oxidatively generated DNA lesions, cdG and cdA are repaired by the
human nucleotide excision repair (NER) apparatus. The relative NER efficiencies of all
four cyclopurines were measured and compared in identical human HeLa cell extracts for the
first time under identical conditions, using identical sequence contexts. The cdA and cdG
lesions were excised with similar efficiencies, but the efficiencies for both
5′R cyclopurines were greater by a factor of ∼2 than for the
5′S lesions. Molecular modeling and dynamics simulations have
revealed structural and energetic origins of this difference in NER-incision efficiencies.
These lesions cause greater DNA backbone distortions and dynamics relative to unmodified
DNA in 5′R than in 5′S stereoisomers,
producing greater impairment in van der Waals stacking interaction energies in the
5′R cases. The locally impaired stacking interaction energies
correlate with relative NER incision efficiencies, and explain these results on a
structural basis in terms of differences in dynamic perturbations of the DNA backbone
imposed by the R and S covalent 5′,8 bonds.
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Affiliation(s)
- Konstantin Kropachev
- Department of Chemistry New York University, 100 Washington Square East, New York, NY 10003, USA, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA and Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
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33
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Zhang X, Rahman M, Neff D, Norton ML. DNA origami deposition on native and passivated molybdenum disulfide substrates. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2014; 5:501-506. [PMID: 33708460 PMCID: PMC7879407 DOI: 10.3762/bjnano.5.58] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 04/03/2014] [Indexed: 05/14/2023]
Abstract
Maintaining the structural fidelity of DNA origami structures on substrates is a prerequisite for the successful fabrication of hybrid DNA origami/semiconductor-based biomedical sensor devices. Molybdenum disulfide (MoS2) is an ideal substrate for such future sensors due to its exceptional electrical, mechanical and structural properties. In this work, we performed the first investigations into the interaction of DNA origami with the MoS2 surface. In contrast to the structure-preserving interaction of DNA origami with mica, another atomically flat surface, it was observed that DNA origami structures rapidly lose their structural integrity upon interaction with MoS2. In a further series of studies, pyrene and 1-pyrenemethylamine, were evaluated as surface modifications which might mitigate this effect. While both species were found to form adsorption layers on MoS2 via physisorption, 1-pyrenemethylamine serves as a better protective agent and preserves the structures for significantly longer times. These findings will be beneficial for the fabrication of future DNA origami/MoS2 hybrid electronic structures.
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Affiliation(s)
- Xiaoning Zhang
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, West Virginia 25755, United States
| | - Masudur Rahman
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, West Virginia 25755, United States
| | - David Neff
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, West Virginia 25755, United States
| | - Michael Louis Norton
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, West Virginia 25755, United States
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Krzeminski J, Kropachev K, Reeves D, Kolbanovskiy A, Kolbanovskiy M, Chen KM, Sharma AK, Geacintov N, Amin S, El-Bayoumy K. Adenine-DNA adduct derived from the nitroreduction of 6-nitrochrysene is more resistant to nucleotide excision repair than guanine-DNA adducts. Chem Res Toxicol 2013; 26:1746-54. [PMID: 24112095 DOI: 10.1021/tx400296x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Previous studies in rats, mice, and in vitro systems showed that 6-NC can be metabolically activated by two major pathways: (1) the formation of N-hydroxy-6-aminochrysene by nitroreduction to yield three major adducts, N-(dG-8-yl)-6-AC, 5-(dG-N(2)-yl)-6-AC, and N-(dA-8-yl)-6-AC, and (2) the formation of trans-1,2-dihydroxy-1,2-dihydro-6-hydroxylaminochrysene (1,2-DHD-6-NHOH-C) by a combination of nitroreduction and ring oxidation pathways to yield N-(dG-8-yl)-1,2-DHD-6-AC, 5-(dG-N(2)-yl)-1,2-DHD-6-AC and N-(dA-8-yl)-1,2-DHD-6-AC. These DNA lesions are likely to cause mutations if they are not removed by cellular defense mechanisms before DNA replication occurs. Here, we compared for the first time, in HeLa cell extracts in vitro, the relative nucleotide excision repair (NER) efficiencies of DNA lesions derived from simple nitroreduction and from a combination of nitroreduction and ring oxidation pathways. We show that the N-(dG-8-yl)-1,2-DHD-6-AC adduct is more resistant to NER than the N-(dG-8-yl)-6-AC adduct by a factor of ∼2. Furthermore, the N-(dA-8-yl)-6-AC is much more resistant to repair since its NER efficiency is ∼8-fold lower than that of the N-(dG-8-yl)-6-AC adduct. On the basis of our previous study and the present investigation, lesions derived from 6-NC and benzo[a]pyrene can be ranked from the most to the least resistant lesion as follows: N-(dA-8-yl)-6-AC > N-(dG-8-yl)-1,2-DHD-6-AC > 5-(dG-N(2)-yl)-6-AC ≃ N-(dG-8-yl)-6-AC ≃ (+)-7R,8S,9S,10S-benzo[a]pyrene diol epoxide-derived trans-anti-benzo[a]pyrene-N(2)-dG adduct. The slow repair of the various lesions derived from 6-NC and thus their potential persistence in mammalian tissue could in part account for the powerful carcinogenicity of 6-NC as compared to B[a]P in the rat mammary gland.
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Affiliation(s)
- Jacek Krzeminski
- Department of Biochemistry and Molecular Biology, and ‡Department of Pharmacology, College of Medicine, Pennsylvania State University , Hershey, Pennsylvania 17033, United States
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35
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Mu H, Kropachev K, Chen Y, Zhang H, Cai Y, Geacintov NE, Broyde S. Role of structural and energetic factors in regulating repair of a bulky DNA lesion with different opposite partner bases. Biochemistry 2013; 52:5517-21. [PMID: 23902560 DOI: 10.1021/bi4009177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Extensive molecular modeling with molecular dynamics simulations and van der Waals energy analyses were used to elucidate the striking finding that a mutagenic benzo[a]pyrene-derived DNA lesion, the base-displaced intercalated 10R-(+)-cis-anti-B[a]P-N(2)-dG (G*), manifests large differences in nucleotide excision repair (NER) efficiencies in DNA duplexes, which depend on the identities of the partner base opposite G*. The nature of the partner base causes marked differences in the extent of its major groove extrusion and dynamics, as well as energetic stability of the intercalation pocket that parallels the relative NER efficiencies.
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Affiliation(s)
- Hong Mu
- Department of Biology, New York University, New York, NY 10003, USA
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36
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Cai Y, Zheng H, Ding S, Kropachev K, Schwaid AG, Tang Y, Mu H, Wang S, Geacintov NE, Zhang Y, Broyde S. Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: energetic and structural relationships to nucleotide excision repair susceptibility. Chem Res Toxicol 2013; 26:1115-25. [PMID: 23758590 DOI: 10.1021/tx400156a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The crystal structure of Rad4/Rad23, the yeast homolog of the human nucleotide excision repair (NER) lesion recognition factor XPC-RAD23B ( Min , J. H. and Pavletich , N. P. ( 2007 ) Nature 449 , 570 - 575 ) reveals that the lesion-partner base is flipped out of the helix and binds to amino acids of the protein. This suggests the hypothesis that the flipping of this partner base must overcome a free energy barrier, which constitutes one element contributing to changes in the thermodynamic properties induced by the DNA damage and sensed by the recognition protein. We explored this hypothesis by computing complete flipping free energy profiles for two lesions derived from the procarcinogenic polycyclic aromatic hydrocarbons (PAHs), dibenzo[a,l]pyrene (DB[a,l]P) and benzo[a]pyrene (B[a]P), R-trans-anti-DB[a,l]P-N(6)-dA (R-DB[a,l]P-dA) and R-trans-anti-B[a]P-N(6)-dA (R-B[a]P-dA), and the corresponding unmodified duplex. The DB[a,l]P and B[a]P adducts differ in number and organization of their aromatic rings. We integrate these results with prior profiles for the R-trans-anti-DB[a,l]P-dG adduct ( Zheng , H. et al. ( 2010 ) Chem. Res. Toxicol. 23 , 1868 - 1870 ). All adopt conformational themes involving intercalation of the PAH aromatic ring system into the DNA duplex; however, R-DB[a,l]P-dA and R-B[a]P-dA intercalate from the major groove, while R-DB[a,l]P-dG intercalates from the minor groove. These structural differences produce different computed van der Waals stacking interaction energies between the flipping partner base with the lesion aromatic ring system and adjacent bases; we find that the better the stacking, the higher the relative flipping free energy barrier and hence lower flipping probability. The better relative NER susceptibilities correlate with greater ease of flipping in these three differently intercalated lesions. In addition to partner base flipping, the Rad4/Rad23 crystal structure shows that a protein-β-hairpin, BHD3, intrudes from the major groove side between the DNA strands at the lesion site. We present a molecular modeling study for the R-DB[a,l]P-dG lesion in Rad4/Rad23 showing BHD3 β-hairpin intrusion with lesion eviction, and we hypothesize that lesion steric effects play a role in the recognition of intercalated adducts.
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Affiliation(s)
- Yuqin Cai
- Department of Biology, New York University , New York, New York 10003, United States
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