151
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Carraro C, Francke A, Sosic A, Kohl F, Helbing T, De Franco M, Fabris D, Göttlich R, Gatto B. Behind the Mirror: Chirality Tunes the Reactivity and Cytotoxicity of Chloropiperidines as Potential Anticancer Agents. ACS Med Chem Lett 2019; 10:552-557. [PMID: 30996795 PMCID: PMC6466835 DOI: 10.1021/acsmedchemlett.8b00580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/13/2019] [Indexed: 12/18/2022] Open
Abstract
![]()
The
pressing demand for sustainable antitumor drugs prompted us
to investigate 3-chloropiperidines as potential mustard-based anticancer
agents. In this study, an explorative set of variously decorated monofunctional
3-chloropiperidines (M-CePs) was efficiently synthesized through a
fast and affordable route providing high yields of pure racemates
and enantiomers. Consistently with their reactivity, M-CePs were demonstrated
to alkylate DNA in vitro. On a panel of carcinoma
cell lines, M-CePs exhibited low nanomolar cytotoxicity indexes, which
showed their remarkable activity against pancreatic cancer cells and
in all cases performed strikingly better than the chlorambucil control.
Very interestingly, stereochemistry modulated the activity of M-CePs
in unexpected ways, pointing to additional molecular mechanisms of
action beyond the direct damage of genomic DNA. This encouraging combination
of efficacy and sustainability suggests they are valid candidates
for anticancer agent development.
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Affiliation(s)
- Caterina Carraro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy
| | - Alexander Francke
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy
| | - Franziska Kohl
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy
| | - Tim Helbing
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy
| | - Daniele Fabris
- Departments of Chemistry and Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Richard Göttlich
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy
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152
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Nayak AK, Rath SK, Subudhi U. Preparation of Stable Branched DNA Nanostructures: Process of Cooperative Self-Assembly. J Phys Chem B 2019; 123:3591-3597. [DOI: 10.1021/acs.jpcb.9b00353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ashok Kumar Nayak
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India
- Department of Biotechnology, Ravenshaw University, Cuttack 753 003, India
| | - Sakti Kanta Rath
- Department of Biotechnology, Ravenshaw University, Cuttack 753 003, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India
- Academy of Scientific & Innovative Research (AcSIR), New Delhi 110025, India
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153
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Liu G, He W, Liu C. Sensitive detection of uracil-DNA glycosylase (UDG) activity based on terminal deoxynucleotidyl transferase-assisted formation of fluorescent copper nanoclusters (CuNCs). Talanta 2019; 195:320-326. [DOI: 10.1016/j.talanta.2018.11.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/06/2018] [Accepted: 11/22/2018] [Indexed: 10/27/2022]
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154
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155
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156
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Organochlorinated pesticides expedite the enzymatic degradation of DNA. Commun Biol 2019; 2:81. [PMID: 30820476 PMCID: PMC6391446 DOI: 10.1038/s42003-019-0326-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 01/24/2019] [Indexed: 01/31/2023] Open
Abstract
Extracellular DNA in the environment may play important roles in genetic diversity and biological evolution. However, the influence of environmental persistent organic contaminants such as organochlorinated pesticides (e.g., hexachlorocyclohexanes [HCHs]) on the enzymatic degradation of extracellular DNA has not been elucidated. In this study, we observed expedited enzymatic degradation of extracellular DNA in the presence of α-HCH, β-HCH and γ-HCH. The HCH-expedited DNA degradation was not due to increased deoxyribonuclease I (DNase I) activity. Our spectroscopic and computational results indicate that HCHs bound to DNA bases (most likely guanine) via Van der Waals forces and halogen bonds. This binding increased the helicity and accumulation of DNA base pairs, leading to a more compact DNA structure that exposed more sites susceptible to DNase I and thus expedited DNA degradation. This study provided insight into the genotoxicity and ecotoxicity of pesticides and improved our understanding of DNA persistence in contaminated environments.
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157
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Räz MH, Sandell ES, Patil KM, Gillingham DG, Sturla SJ. High Sensitivity of Human Translesion DNA Synthesis Polymerase κ to Variation in O 6-Carboxymethylguanine Structures. ACS Chem Biol 2019; 14:214-222. [PMID: 30645109 DOI: 10.1021/acschembio.8b00802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Carboxymethylation of DNA, including the formation of the DNA adduct O6-carboxymethylguanine ( O6-CMG), is associated with lifestyle factors, such as diet. It can impede replicative polymerases (Pols) and lead to replication fork stalling, or an alternative means for replication to proceed by translesion DNA synthesis (TLS). TLS requires specialized DNA Pols characterized by open and preformed active sites capable of preferential bypass of alkylated DNA adducts but that have high error rates, leading to mutations. Human TLS Pols can bypass O6-CMG with varying degrees of accuracy, but it is not known how the chemical structure of the O6-CMG adduct influences polymerase proficiency or fidelity. To better understand how adduct structure determines dNTP selection at lesion sites, we prepared DNA templates with a series of O6-CMG structural analogs and compared the primer extension patterns of Y- and X-family Pols in response to these modifications. The results indicate that the structure of the DNA adduct had a striking effect on dNTP selection by Pol κ and that an increased steric size influences the fidelity of Pol η, whereas Pol ι and β function were only marginally affected. To test the hypothesis that specific hydrogen bonding interactions between the templating base and the incoming dNTP are a basis of this selection, we modeled the structural analogs with incoming dNTP in the Pol κ active site. These data indicate that the base pairing geometry and stabilization by a dense hydrogen bonding network are important molecular features for dNTP incorporation, providing a basis for understanding error-free bypass of O6-CMG by Pol κ.
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Affiliation(s)
- Michael H. Räz
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
| | - Emma S. Sandell
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
| | - Kiran M. Patil
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Dennis G. Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Shana J. Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
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158
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Tharmalingam S, Sreetharan S, Brooks AL, Boreham DR. Re-evaluation of the linear no-threshold (LNT) model using new paradigms and modern molecular studies. Chem Biol Interact 2019; 301:54-67. [PMID: 30763548 DOI: 10.1016/j.cbi.2018.11.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/13/2018] [Accepted: 11/22/2018] [Indexed: 02/06/2023]
Abstract
The linear no-threshold (LNT) model is currently used to estimate low dose radiation (LDR) induced health risks. This model lacks safety thresholds and postulates that health risks caused by ionizing radiation is directly proportional to dose. Therefore even the smallest radiation dose has the potential to cause an increase in cancer risk. Advances in LDR biology and cell molecular techniques demonstrate that the LNT model does not appropriately reflect the biology or the health effects at the low dose range. The main pitfall of the LNT model is due to the extrapolation of mutation and DNA damage studies that were conducted at high radiation doses delivered at a high dose-rate. These studies formed the basis of several outdated paradigms that are either incorrect or do not hold for LDR doses. Thus, the goal of this review is to summarize the modern cellular and molecular literature in LDR biology and provide new paradigms that better represent the biological effects in the low dose range. We demonstrate that LDR activates a variety of cellular defense mechanisms including DNA repair systems, programmed cell death (apoptosis), cell cycle arrest, senescence, adaptive memory, bystander effects, epigenetics, immune stimulation, and tumor suppression. The evidence presented in this review reveals that there are minimal health risks (cancer) with LDR exposure, and that a dose higher than some threshold value is necessary to achieve the harmful effects classically observed with high doses of radiation. Knowledge gained from this review can help the radiation protection community in making informed decisions regarding radiation policy and limits.
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Affiliation(s)
- Sujeenthar Tharmalingam
- Northern Ontario School of Medicine, Laurentian University, 935 Ramsey Lake Rd, Sudbury, ON, P3E 2C6, Canada.
| | - Shayenthiran Sreetharan
- Department of Medical Physics and Applied Radiation Sciences, McMaster University, 1280 Main Street W, Hamilton ON, L8S 4K1, Canada
| | - Antone L Brooks
- Environmental Science, Washington State University, Richland, WA, USA
| | - Douglas R Boreham
- Northern Ontario School of Medicine, Laurentian University, 935 Ramsey Lake Rd, Sudbury, ON, P3E 2C6, Canada; Bruce Power, Tiverton, ON(3), UK.
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159
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Caron C, Duong XNT, Guillot R, Bombard S, Granzhan A. Interaction of Functionalized Naphthalenophanes with Abasic Sites in DNA: DNA Cleavage, DNA Cleavage Inhibition, and Formation of Ligand–DNA Adducts. Chemistry 2019; 25:1949-1962. [DOI: 10.1002/chem.201805555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/30/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Coralie Caron
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Xuan N. T. Duong
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Régis Guillot
- CNRS UMR8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO)Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Sophie Bombard
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
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160
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A theoretical investigation of sugar and phosphate contributions to the activation barriers of guanine methylation by carcinogenic methane diazonium ion. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.10.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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161
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Dorrah MA, Mohamed AA, Shaurub ESH. Immunosuppressive effects of the limonoid azadirachtin, insights on a nongenotoxic stress botanical, in flesh flies. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 153:55-66. [PMID: 30744897 DOI: 10.1016/j.pestbp.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 09/08/2018] [Accepted: 11/03/2018] [Indexed: 06/09/2023]
Abstract
The tetranortriterpenoid azadirachtin (Aza) is a well-known insect growth disruptor of plant origin. Although its actions on insects have been extensively studied; fragmentary reports are available from the immunological point of view. Therefore, in the present study, total (THC) and differential hemocyte counts (DHC), nodulation, phenoloxidase (PO) activity, immune-reactive lysozymes and inducible nitric oxide (NO) were assessed, as measures of immune responses, in Sarcophaga argyrostoma 3rd instars challenged individually with M. luteus or Aza, or in combination with both compared to the control larvae. THC was significantly declined after 12 h and 24 h of treatment with Aza. DHC varied considerably; in particular, plasmatocytes were significantly decreased after 36 h and 48 h of treatment with Aza; whereas granulocytes were significantly increased. Nodulation was significantly increased with the increase of time after all treatments. Challenging with M. luteus significantly increased the activity of PO in hemocytes and plasma; whereas such activity was significantly decreased after treatment with Aza or combined Aza and M. luteus. Treatment with Aza or M. luteus alone or in couple significantly increased lysozyme activity of fat body, hemocytes and plasma. However, challenging with M. luteus significantly increased NO concentration in the same tissues. A hypothetical model of Aza as a potential mutagen is presented. However, no genotoxic effect was observed through tracking apoptosis-associated changes in Aza-treated hemocytes via flow cytometry-based apoptosis detection. Our study suggests that the integration of Aza, as an eco-friendly pesticide, with bacterial biopesticides may be a successful approach for controlling insect pests.
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Affiliation(s)
- Moataza A Dorrah
- Department of Entomology, Faculty of Science, Cairo University, Giza, PO Box 12613, Egypt
| | - Amr A Mohamed
- Department of Entomology, Faculty of Science, Cairo University, Giza, PO Box 12613, Egypt
| | - El-Sayed H Shaurub
- Department of Entomology, Faculty of Science, Cairo University, Giza, PO Box 12613, Egypt.
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162
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Leitão MPS, Herrera F, Petronilho A. N-Heterocyclic Carbenes Derived from Guanosine: Synthesis and Evidences of Their Antiproliferative Activity. ACS OMEGA 2018; 3:15653-15656. [PMID: 30556009 PMCID: PMC6288774 DOI: 10.1021/acsomega.8b02387] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Palladium(II) and platinum(II) complexes bearing N-heterocyclic carbenes derived from guanosine are synthesized via oxidative addition, followed by protonation in the presence of acid. Cytotoxicity of the compounds is evaluated in several cell lines. Compounds 2a, 2b, and 3a are selective for glioblastoma U251 cells and are nontoxic toward healthy human embryonic kidney (HEK293) cells.
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163
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Liu C, Luo X, Chen Y, Wu F, Yang W, Wang Y, Zhang X, Zou G, Zhou X. Selective Labeling Aldehydes in DNA. Anal Chem 2018; 90:14616-14621. [PMID: 30441892 DOI: 10.1021/acs.analchem.8b04822] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A naphthalimide hydroxylamine probe has been designed and synthesized to selectively label the whole natural aldehydes present in DNAs including 5-formylcytosine, 5-formyluracil, and abasic sites. The fluorescence characteristics of the generated nucleosides have been examined in detail, and the reaction activities of hydroxylamine, amine groups toward aldehydes in DNA have been discussed with others, which will be a vital reference for designing chemicals for selective labeling of DNAs.
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Affiliation(s)
- Chaoxing Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Xiaomeng Luo
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Yuqi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Fan Wu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Wei Yang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Yafen Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Xiong Zhang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Guangrong Zou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China
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164
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Bevilacqua PC, Assmann SM. Technique Development for Probing RNA Structure In Vivo and Genome-Wide. Cold Spring Harb Perspect Biol 2018; 10:a032250. [PMID: 30275275 PMCID: PMC6169808 DOI: 10.1101/cshperspect.a032250] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
How organisms perceive and respond to their surroundings is one of the great questions in biology. It is clear that RNA plays key roles in sensing. Cellular and environmental cues that RNA responds to include temperature, ions, metabolites, and biopolymers. Recent advances in next-generation sequencing and in vivo chemical probing have provided unprecedented insights into RNA folding in vivo and genome-wide. Patterns of chemical reactivity have implicated control of gene expression by RNA and aided prediction of RNA structure. Central to these advances has been development of molecular biological and chemical techniques. Key advances are improvements in the quality, cost, and throughput of library preparation; availability of a wider array of chemicals for probing RNA structure in vivo; and robustness and user friendliness of data analysis. Insights from probing transcriptomes and future directions are provided.
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Affiliation(s)
- Philip C Bevilacqua
- Departments of Chemistry and Biochemistry & Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
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165
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Gabr MT, Pigge FC. Platinum(II) Complexes with Sterically Expansive Tetraarylethylene Ligands as Probes for Mismatched DNA. Inorg Chem 2018; 57:12641-12649. [DOI: 10.1021/acs.inorgchem.8b01782] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Moustafa T. Gabr
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - F. Christopher Pigge
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
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166
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Belostotskii AM. Nanosecond-Scale Isomerization of the 4'-Carboxonium Cation Oxidatively Produced in Pyrimidine Units of DNA. J Org Chem 2018; 83:11604-11613. [PMID: 30153025 DOI: 10.1021/acs.joc.8b01580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The long-standing puzzle of the chemistry producing the Stubbe-Kozarich abasic site, which is the minor product in the oxidation of 2'-deoxycytidine units of DNA by Fe(II)-bleomycin, has been computationally solved in this study. Scrupulous DFT-based calculations that included extensive screening of the potential energy surface of model-solvated nucleotides and the elucidation of the chemical structure of the located nucleotide cations via natural bond orbital analysis demonstrated that the 2'-deoxycytidine unit bearing the 2'-deoxyribose ring 2e-oxidized at the 4'-position undergoes carboxonium ion- iminium ion (C═O+-C → C═N+) isomerization. This 1,2-elimination of the carbonyl group 4'-C═O from the carboxonium cation fragment is associated with minimal spatial reorganization of the molecule and appears to be an ultrafast reaction. The calculated barrier Δ G0# of 2.7 kcal mol-1 for this isomerization is lower than that reported for the addition of water to oxocarbenium ions. Thus, this unusual nucleotide transformation is the key chemical reaction that yields the Stubbe-Kozarich product. Such a product cannot be formed for purine nucleotide units in DNA. The isomerization of 4'-dehydro-2'-deoxyribose-4'-carboxonium cations formed in these DNA units is slower because it destroys the purine aromaticity, and the cations are intercepted by water molecules before they isomerize.
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167
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Groehler AS, Najjar D, Pujari SS, Sangaraju D, Tretyakova NY. N 6-(2-Deoxy-d- erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-(2-hydroxy-3-buten-1-yl)-formamidopyrimidine Adducts of 1,3-Butadiene: Synthesis, Structural Identification, and Detection in Human Cells. Chem Res Toxicol 2018; 31:885-897. [PMID: 30016111 DOI: 10.1021/acs.chemrestox.8b00123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
1,3-Butadiene (BD) is an environmental and occupational toxicant classified as a human carcinogen. BD is metabolically activated by cytochrome P450 monooxygenases to 3,4-epoxy-1-butene (EB), which alkylates DNA to form a range of nucleobase adducts. Among these, the most abundant are the hydrolytically labile N7-guanine adducts such as N7-(2-hydroxy-3-buten-1-yl)-guanine (N7-EB-dG). We now report that N7-EB-dG can be converted to the corresponding ring open N6-(2-deoxy-d- erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-(2-hydroxy-3-buten-1-yl)-formamidopyrimidine (EB-Fapy-dG) adducts. EB-Fapy-dG lesions were detected in EB-treated calf thymus DNA and in EB-treated mammalian cells using quantitative isotope dilution nanoLC-ESI+-MS/MS. EB-Fapy-dG adduct formation in EB-treated calf thymus DNA was concentration dependent and was greatly accelerated at an increased pH. EB-FAPy-dG adduct amounts were 2-fold higher in base excision repair-deficient NEIL1-/- mouse embryonic fibroblasts (MEF) as compared to isogenic controls (NEIL1+/+), suggesting that this lesion may be a substrate for NEIL1. Furthermore, NEIL1-/- cells were sensitized to EB treatment as compared to NEIL1+/+ fibroblasts. Overall, our results indicate that ring-opened EB-FAPy-dG adducts form under physiological conditions, prompting future studies to determine their contributions to genotoxicity and mutagenicity of BD.
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Affiliation(s)
- Arnold S Groehler
- Department of Medicinal Chemistry and Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Dominic Najjar
- Department of Medicinal Chemistry and Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Suresh S Pujari
- Department of Medicinal Chemistry and Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Dewakar Sangaraju
- Department of Medicinal Chemistry and Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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168
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Khateri S, Balali-Mood M, Blain P, Williams F, Jowsey P, Soroush MR, Behravan E, Sadeghi M. DNA damage and repair proteins in cellular response to sulfur mustard in Iranian veterans more than two decades after exposure. Toxicol Lett 2018; 293:67-72. [DOI: 10.1016/j.toxlet.2017.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/28/2017] [Accepted: 12/03/2017] [Indexed: 01/15/2023]
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169
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Abstract
The base excision repair (BER) pathway removes modified nucleobases that can be deleterious to an organism. BER is initiated by a glycosylase, which finds and removes these modified nucleobases. Most of the characterization of glycosylase activity has been conducted in the context of DNA oligomer substrates. However, DNA within eukaryotic organisms exists in a packaged environment with the basic unit of organization being the nucleosome core particle (NCP). The NCP is a complex substrate for repair in which a variety of factors can influence glycosylase activity. In this Review, we focus on the geometric positioning of modified nucleobases in an NCP and the consequences on glycosylase activity and initiating BER.
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Affiliation(s)
- Erin E Kennedy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, United States
| | - Paul J Caffrey
- Department of Chemistry, Brown University, Providence, RI 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI 02912, United States.
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170
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What happens at the lesion does not stay at the lesion: Transcription-coupled nucleotide excision repair and the effects of DNA damage on transcription in cis and trans. DNA Repair (Amst) 2018; 71:56-68. [PMID: 30195642 DOI: 10.1016/j.dnarep.2018.08.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Unperturbed transcription of eukaryotic genes by RNA polymerase II (Pol II) is crucial for proper cell function and tissue homeostasis. However, the DNA template of Pol II is continuously challenged by damaging agents that can result in transcription impediment. Stalling of Pol II on transcription-blocking lesions triggers a highly orchestrated cellular response to cope with these cytotoxic lesions. One of the first lines of defense is the transcription-coupled nucleotide excision repair (TC-NER) pathway that specifically removes transcription-blocking lesions thereby safeguarding unperturbed gene expression. In this perspective, we outline recent data on how lesion-stalled Pol II initiates TC-NER and we discuss new mechanistic insights in the TC-NER reaction, which have resulted in a better understanding of the causative-linked Cockayne syndrome and UV-sensitive syndrome. In addition to these direct effects on lesion-stalled Pol II (effects in cis), accumulating evidence shows that transcription, and particularly Pol II, is also affected in a genome-wide manner (effects in trans). We will summarize the diverse consequences of DNA damage on transcription, including transcription inhibition, induction of specific transcriptional programs and regulation of alternative splicing. Finally, we will discuss the function of these diverse cellular responses to transcription-blocking lesions and their consequences on the process of transcription restart. This resumption of transcription, which takes place either directly at the lesion or is reinitiated from the transcription start site, is crucial to maintain proper gene expression following removal of the DNA damage.
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171
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Grienke U, Radić Brkanac S, Vujčić V, Urban E, Ivanković S, Stojković R, Rollinger JM, Kralj J, Brozovic A, Radić Stojković M. Biological Activity of Flavonoids and Rare Sesquiterpene Lactones Isolated From Centaurea ragusina L. Front Pharmacol 2018; 9:972. [PMID: 30190676 PMCID: PMC6117149 DOI: 10.3389/fphar.2018.00972] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 08/06/2018] [Indexed: 01/28/2023] Open
Abstract
The endemic Croatian species Centaurea ragusina L., like other species from the genus Centaurea, has been traditionally used in Croatia as an antibacterial agent and for the treatment of gastrointestinal and urogenital disorders. In several chromatographic steps, three flavonoids and three sesquiterpene lactones (STLs) were isolated and identified from the most active fractions of the ethanol extract. Two STLs, one for which we created the trivial name ragusinin, and hemistepsin A are here reported for the first time as constituents of the genus Centaurea. All six compounds were screened for their effect on several tumor and one normal cell lines. Among them, ragusinin showed the best bioactivity and high specificity to affect tumor murine SCCVII, human HeLa and Caco-2 cell lines, but not the viability of normal V79 fibroblasts. Due to these characteristics the action of ragusinin was investigated in more detail. Since DNA is the primary target for many drugs with antibacterial and anticancer activity, we studied its interaction with ragusinin. Rather moderate binding affinity to DNA excluded it as the primary target of ragusinin. Due to the possibility of STL interaction with glutathione (GSH), the ubiquitous peptide that traps reactive compounds and other xenobiotics to prevent damage to vital proteins and nucleic acids, its role in deactivation of ragusinin was evaluated. Addition of the GSH precursor N-acetyl-cysteine potentiated the viability of HeLa cells, while the addition of GSH inhibitor L-buthionine sulfoximine decreased it. Moreover, pre-treatment of HeLa cells with the inhibitor of glutathione-S-transferase decreased their viability indicating the detoxifying role of GSH in ragusinin treated cells. Cell death, derived by an accumulation of cells in a G2 phase of the cell cylce, was shown to be independent of poly (ADP-ribose) polymerase and caspase-3 cleavage pointing toward an alternative cell death pathway.
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Affiliation(s)
- Ulrike Grienke
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Sandra Radić Brkanac
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Valerija Vujčić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ernst Urban
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Siniša Ivanković
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ranko Stojković
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Juran Kralj
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Anamaria Brozovic
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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172
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Huang J, Alnajjar KS, Mahmoud MM, Eckenroth B, Doublié S, Sweasy JB. The nature of the DNA substrate influences pre-catalytic conformational changes of DNA polymerase β. J Biol Chem 2018; 293:15084-15094. [PMID: 30068550 DOI: 10.1074/jbc.ra118.004564] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/29/2018] [Indexed: 11/06/2022] Open
Abstract
DNA polymerase β (Pol β) is essential for maintaining genomic integrity. During short-patch base excision repair (BER), Pol β incorporates a nucleotide into a single-gapped DNA substrate. Pol β may also function in long-patch BER, where the DNA substrate consists of larger gap sizes or 5'-modified downstream DNA. We have recently shown that Pol β fills small gaps in DNA during microhomology-mediated end-joining as part of a process that increases genomic diversity. Our previous results with single-nucleotide gapped DNA show that Pol β undergoes two pre-catalytic conformational changes upon binding to the correct nucleotide substrate. Here we use FRET to investigate nucleotide incorporation of Pol β with various DNA substrates. The results show that increasing the gap size influences the fingers closing step by increasing its reverse rate. However, the 5'-phosphate group has a more significant effect. The absence of the 5'-phosphate decreases the DNA binding affinity of Pol β and results in a conformationally more open binary complex. Moreover, upon addition of the correct nucleotide in the absence of 5'-phosphate, a slow fingers closing step is observed. Interestingly, either increasing the gap size or removing the 5'-phosphate group results in loss of the noncovalent step. Together, these results suggest that the character of the DNA substrate impacts the nature and rates of pre-catalytic conformational changes of Pol β. Our results also indicate that conformational changes are important for the fidelity of DNA synthesis by Pol β.
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Affiliation(s)
- Ji Huang
- From the Departments of Therapeutic Radiology and
| | | | | | - Brian Eckenroth
- the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405
| | - Sylvie Doublié
- the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405
| | - Joann B Sweasy
- From the Departments of Therapeutic Radiology and .,Genetics, Yale University School of Medicine, New Haven, Connecticut 06520 and
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173
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Malla S, Kadimisetty K, Jiang D, Choudhary D, Rusling JF. Pathways of Metabolite-Related Damage to a Synthetic p53 Gene Exon 7 Oligonucleotide Using Magnetic Enzyme Bioreactor Beads and LC-MS/MS Sequencing. Biochemistry 2018; 57:3883-3893. [PMID: 29750510 DOI: 10.1021/acs.biochem.8b00271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Reactive metabolites of environmental chemicals and drugs can cause site specific damage to the p53 tumor suppressor gene in a major pathway for genotoxicity. We report here a high-throughput, cell-free, 96-well plate magnetic bead-enzyme system interfaced with LC-MS/MS sequencing for bioactivating test chemicals and identifying resulting adduction sites on genes. Bioactivated aflatoxin B1 was reacted with a 32 bp exon 7 fragment of the p53 gene using eight microsomal cytochrome (cyt) P450 enzymes from different organs coated on magnetic beads. All cyt P450s converted aflatoxin B1 to aflatoxin B1-8,9-epoxide that adducts guanine (G) in codon 249, with subsequent depurination to give abasic sites and then strand breaks. This is the first demonstration in a cell-free medium that the aflatoxin B1 metabolite selectively causes abasic site formation and strand breaks at codon 249 of the p53 probe, corresponding to the chemical pathway and mutations of p53 in human liver cells and tumors. Molecular modeling supports the view that binding of aflatoxin B1-8,9-epoxide to G in codon 249 precedes the SN2 adduction reaction. Among a range of metabolic enzymes characteristic of different organs, human liver microsomes and cyt P450 3A5 supersomes showed the highest bioactivation rate for p53 exon 7 damage. This method of identifying metabolite-related gene damage sites may facilitate predictions of organ specific cancers for test chemicals via correlations with mutation sites.
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Affiliation(s)
- Spundana Malla
- Department of Chemistry , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Karteek Kadimisetty
- Department of Chemistry , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Di Jiang
- Department of Chemistry , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Dharamainder Choudhary
- Department of Surgery and Neag Cancer Center , UConn Health , Farmington , Connecticut 06032 , United States
| | - James F Rusling
- Department of Chemistry , University of Connecticut , Storrs , Connecticut 06269 , United States.,Department of Surgery and Neag Cancer Center , UConn Health , Farmington , Connecticut 06032 , United States.,Institute of Material Science , University of Connecticut , Storrs , Connecticut 06269 , United States.,School of Chemistry , National University of Ireland at Galway , Galway , Ireland
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174
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Zheng L, Greenberg MM. Traceless Tandem Lesion Formation in DNA from a Nitrogen-Centered Purine Radical. J Am Chem Soc 2018; 140:6400-6407. [PMID: 29738242 DOI: 10.1021/jacs.8b02828] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nitrogen-centered nucleoside radicals are commonly produced reactive intermediates in DNA exposed to γ-radiolysis and oxidants, but their reactivity is not well understood. Examination of the reactivity of independently generated 2'-deoxyadenosin- N6-yl radical (dA•) reveals that it is an initiator of tandem lesions, an important form of DNA damage that is a hallmark of γ-radiolysis. dA• yields O2-dependent tandem lesions by abstracting a hydrogen atom from the C5-methyl group of a 5'-adjacent thymidine to form 5-(2'-deoxyuridinyl)methyl radical (T•). The subsequently formed thymidine peroxyl radical adds to the 5'-adjacent dG, ultimately producing a 5'-OxodGuo-fdU tandem lesion. Importantly, the initial hydrogen abstraction repairs dA• to form dA. Thus, the involvement of dA• in tandem lesion formation is traceless by product analysis. The tandem lesion structure, as well as the proposed mechanism, are supported by LC-MS/MS, isotopic labeling, chemical reactivity experiments, and independent generation of T•. Tandem lesion formation efficiency is dependent on the ease of ionization of the 5'-flanking sequence, and the yields are >27% in the 5'-d(GGGT) flanking sequence. The traceless involvement of dA• in tandem lesion formation may be general for nitrogen-centered radicals in nucleic acids, and presents a new pathway for forming a deleterious form of DNA damage.
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Affiliation(s)
- Liwei Zheng
- 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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175
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Tan KX, Lau SY, Danquah MK. Process evaluation and in vitro selectivity analysis of aptamer-drug polymeric formulation for targeted pharmaceutical delivery. Biomed Pharmacother 2018; 101:996-1002. [PMID: 29635910 DOI: 10.1016/j.biopha.2018.03.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/05/2018] [Accepted: 03/09/2018] [Indexed: 11/29/2022] Open
Abstract
Targeted drug delivery is a promising strategy to promote effective delivery of conventional and emerging pharmaceuticals. The emergence of aptamers as superior targeting ligands to direct active drug molecules specifically to desired malignant cells has created new opportunities to enhance disease therapies. The application of biodegradable polymers as delivery carriers to develop aptamer-navigated drug delivery system is a promising approach to effectively deliver desired drug dosages to target cells. This study reports the development of a layer-by-layer aptamer-mediated drug delivery system (DPAP) via a w/o/w double emulsion technique homogenized by ultrasonication or magnetic stirring. Experimental results showed no significant differences in the biophysical characteristics of DPAP nanoparticles generated using the two homogenization techniques. The DPAP formulation demonstrated a strong targeting performance and selectivity towards its target receptor molecules in the presence of non-targets. The DPAP formulation demonstrated a controlled and sustained drug release profile under the conditions of pH 7 and temperature 37 °C. Also, the drug release rate of DPAP formulation was successfully accelerated under an endosomal acidic condition of ∼pH 5.5, indicating the potential to enhance drug delivery within the endosomal micro-environment. The findings from this work are useful to understanding polymer-aptamer-drug relationship and their impact on developing effective targeted delivery systems.
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Affiliation(s)
- Kei X Tan
- Department of Chemical Engineering, Curtin University, Sarawak 98009, Malaysia; Curtin Sarawak Research Institute, Curtin University, Sarawak 98009, Malaysia
| | - Sie Yon Lau
- Department of Chemical Engineering, Curtin University, Sarawak 98009, Malaysia; Curtin Sarawak Research Institute, Curtin University, Sarawak 98009, Malaysia
| | - Michael K Danquah
- Department of Chemical Engineering, Curtin University, Sarawak 98009, Malaysia; Curtin Sarawak Research Institute, Curtin University, Sarawak 98009, Malaysia.
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176
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Yañuk JG, Denofrio MP, Rasse-Suriani FAO, Villarruel FD, Fassetta F, García Einschlag FS, Erra-Balsells R, Epe B, Cabrerizo FM. DNA damage photo-induced by chloroharmine isomers: hydrolysis versus oxidation of nucleobases. Org Biomol Chem 2018. [PMID: 29528081 DOI: 10.1039/c8ob00162f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Photodynamic therapy (PDT) is an emerging clinical treatment currently being used against a wide range of both cancerous and noncancerous diseases. The search for new active photosensitizers as well as the development of novel selective delivery systems are the major challenges faced in the application of PDT. We investigated herein three chloroharmine derivatives (6-, 8- and 6,8-dichloroharmines) with quite promising intrinsic photochemical tunable properties and their ability to photoinduce DNA damage in order to elucidate the underlying photochemical mechanisms. Data revealed that the three compounds are quite efficient photosensitizers. The overall extent of photo-oxidative DNA damage induced by both 8-chloro-substituted β-carbolines is higher than that induced by 6-chloro-harmine. The predominant type of lesion generated also depends on the position of the chlorine atom in the β-carboline ring. Both 8-chloro-substituted β-carbolines mostly oxidize purines via type I mechanism, whereas 6-chloro-harmine mainly behaves as a "clean" artificial photonuclease inducing single-strand breaks and site of base loss via proton transfer and concerted (HO--mediated) hydrolytic attack. The latter finding represents an exception to the general photosensitizing reactions and, to the best of our knowledge, this is the first time that this process is well documented. The controlled and selective production of different oxygen-independent lesions could be fine-tuned by simply changing the substituent groups in the β-carboline ring. This could be a promising tool for the design and development of novel photo-therapeutic agents aimed to tackle hypoxic conditions shown in certain types of tumours.
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Affiliation(s)
- Juan G Yañuk
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Intendente Marino Km 8.2, CC 164 (B7130IWA), Chascomús, Argentina.
| | - M Paula Denofrio
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Intendente Marino Km 8.2, CC 164 (B7130IWA), Chascomús, Argentina.
| | - Federico A O Rasse-Suriani
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Intendente Marino Km 8.2, CC 164 (B7130IWA), Chascomús, Argentina. and INIFTA - CONICET, Universidad Nacional de La Plata, Diag. 113 y 64, 1900 La Plata, Argentina
| | - Fernando D Villarruel
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Intendente Marino Km 8.2, CC 164 (B7130IWA), Chascomús, Argentina. and INIFTA - CONICET, Universidad Nacional de La Plata, Diag. 113 y 64, 1900 La Plata, Argentina
| | - Federico Fassetta
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Intendente Marino Km 8.2, CC 164 (B7130IWA), Chascomús, Argentina.
| | | | - Rosa Erra-Balsells
- CIHIDECAR - CONICET, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, 3p, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Bernd Epe
- Institute of Pharmacy and Biochemistry, University of Mainz, Staudingerweg 5, Mainz, Germany
| | - Franco M Cabrerizo
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Intendente Marino Km 8.2, CC 164 (B7130IWA), Chascomús, Argentina.
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177
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Zeng T, Fleming AM, Ding Y, Ren H, White HS, Burrows CJ. Nanopore Analysis of the 5-Guanidinohydantoin to Iminoallantoin Isomerization in Duplex DNA. J Org Chem 2018; 83:3973-3978. [PMID: 29490132 DOI: 10.1021/acs.joc.8b00317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In DNA, guanine oxidation yields diastereomers of 5-guanidinohydantoin (Gh) as one of the major products. In nucleosides and single-stranded DNA, Gh is in a pH-dependent equilibrium with its constitutional isomer iminoallantoin (Ia). Herein, the isomerization reaction between Gh and Ia was monitored in duplex DNA using a protein nanopore by measuring the ionic current when duplex DNA interacts with the pore under an electrophoretic force. Monitoring current levels in this single-molecule method proved to be superior for analysis of population distributions in an equilibrating mixture of four isomers in duplex DNA as a function of pH. The results identified Gh as a major isomer observed when base paired with A, C, or G at pH 6.4-8.4, and Ia was a minor isomer of the reaction mixture that was only observed when the pH was >7.4 in the duplex DNA context. The present results suggest that Gh will be the dominant isomer in duplex DNA under physiological conditions regardless of the base-pairing partner in the duplex.
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Affiliation(s)
- Tao Zeng
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Yun Ding
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Hang Ren
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
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178
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Cartwright JF, Anderson K, Longworth J, Lobb P, James DC. Highly sensitive detection of mutations in CHO cell recombinant DNA using multi-parallel single molecule real-time DNA sequencing. Biotechnol Bioeng 2018; 115:1485-1498. [DOI: 10.1002/bit.26561] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/01/2017] [Accepted: 02/04/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Joseph F. Cartwright
- Department of Chemical and Biological Engineering; University of Sheffield; Sheffield UK
| | - Karin Anderson
- Cell Line Development; BioTherapeutic Pharmaceutical Sciences; Pfizer Inc; Andover Massachusetts
| | - Joseph Longworth
- Department of Chemical and Biological Engineering; University of Sheffield; Sheffield UK
| | | | - David C. James
- Department of Chemical and Biological Engineering; University of Sheffield; Sheffield UK
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179
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Kumari P, Kumar S, Gupta S, Mishra A, Kumar A. Efficacious and Selective Oxidation of Atrazine with Hydrogen Peroxide Catalyzed by Magnetite Nanoparticles: Influence of Reaction Media. ChemistrySelect 2018. [DOI: 10.1002/slct.201703117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Pratibha Kumari
- Department of Chemistry, Deshbandhu College; University of Delhi; New Delhi India
| | - Sanjay Kumar
- Department of Chemistry, Deshbandhu College; University of Delhi; New Delhi India
| | - Shilpi Gupta
- Department of Chemistry, Deshbandhu College; University of Delhi; New Delhi India
| | - Avinash Mishra
- Department of Chemistry, Deshbandhu College; University of Delhi; New Delhi India
| | - Arun Kumar
- Department of physics; Himachal Pradesh University; Summer Hill Shilma India
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180
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Wang L, He X, Zhang W, Liu Y, Banks CE, Zhang Y. Investigating structure-property relationships of biomineralized calcium phosphate compounds as fluorescent quenching-recovery platform. ROYAL SOCIETY OPEN SCIENCE 2018; 5:170877. [PMID: 29515827 PMCID: PMC5830716 DOI: 10.1098/rsos.170877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 12/15/2017] [Indexed: 03/14/2024]
Abstract
The structure-property relationship between biomineralized calcium phosphate compounds upon a fluorescent quenching-recovery platform and their distinct crystalline structure and surficial functional groups are investigated. A fluorescence-based sensing platform is shown to be viable for the sensing of 8-hydroxy-2-deoxy-guanosine in simulated systems.
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Affiliation(s)
- Liuzheng Wang
- College of Science, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Xiang He
- Research Institute of Powder Metallurgy, Central South University, Changsha 410083, People's Republic of China
| | - Wei Zhang
- Wuhan Institute of Marine electric Propulsion, Wuhan 430064, People's Republic of China
| | - Yong Liu
- Research Institute of Powder Metallurgy, Central South University, Changsha 410083, People's Republic of China
| | - Craig E. Banks
- Faculty of Science and Engineering, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Ying Zhang
- College of Science, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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181
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Salam T, Premila Devi S, Duncan Lyngdoh RH. Molecular criteria for mutagenesis by DNA methylation: Some computational elucidations. Mutat Res 2018; 807:10-20. [PMID: 29220701 DOI: 10.1016/j.mrfmmm.2017.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/05/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
Alkylating agents and N-nitroso compounds are well-known mutagens and carcinogens which act by alkylating DNA at the nucleobase moieties. Criteria for mutagenicity through DNA alkylation include (a) absence of the Watson-Crick (N1-guanine and N3-thymine) protons, (b) rotation of the alkyl group away from the H-bonding zone, (c) configuration of the alkylated base pair close to the Watson-Crick type. This computational study brings together these three molecular criteria for the first time. Three methylated DNA bases-N7-methylguanine, O6-methylguanine and O4-methylthymine-are studied using computational chemical methods. Watson-Crick proton loss is predicted more feasible for the mutagenic O6-methylguanine and O4-methylthymine than for the non-mutagenic N7-methylguanine in agreement with the observed trend for pKa values. Attainment of a conformer conducive to mutagenesis is more feasible for O6-methylguanine than for O4-methylthymine, though the latter is more mutagenic. These methylated bases yield 9 H-bonded pairs with normal DNA bases. At biological pH, O6-methylguanine and O4-methylthymine would yield stable mutagenic pairs having Watson-Crick type configuration by H-bonded pairing with thymine and guanine respectively, while N7-methylguanine would yield a non-mutagenic pair with cytosine. The three criteria thus well differentiate the non-mutagenic N7-methylguanine from the mutagenic O6-methylguanine and O4-methylthymine in good accord with experimental observations.
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Affiliation(s)
- Tejeshwori Salam
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - S Premila Devi
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - R H Duncan Lyngdoh
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India.
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182
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Syro LV, Rotondo F, Camargo M, Ortiz LD, Serna CA, Kovacs K. Temozolomide and Pituitary Tumors: Current Understanding, Unresolved Issues, and Future Directions. Front Endocrinol (Lausanne) 2018; 9:318. [PMID: 29963012 PMCID: PMC6013558 DOI: 10.3389/fendo.2018.00318] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/28/2018] [Indexed: 01/26/2023] Open
Abstract
Temozolomide, an alkylating agent, initially used in the treatment of gliomas was expanded to include pituitary tumors in 2006. After 12 years of use, temozolomide has shown a notable advancement in pituitary tumor treatment with a remarkable improvement rate in the 5-year overall survival and 5-year progression-free survival in both aggressive pituitary adenomas and pituitary carcinomas. In this paper, we review the mechanism of action of temozolomide as alkylating agent, its interaction with deoxyribonucleic acid repair systems, therapeutic effects in pituitary tumors, unresolved issues, and future directions relating to new possibilities of targeted therapy.
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Affiliation(s)
- Luis V. Syro
- Department of Neurosurgery, Hospital Pablo Tobon Uribe and Clinica Medellin, Medellin, Colombia
- *Correspondence: Luis V. Syro,
| | - Fabio Rotondo
- Department of Laboratory Medicine, Division of Pathology, St. Michael’s Hospital, University of Toronto, Toronto, ON, Canada
| | - Mauricio Camargo
- Genetics, Regeneration and Cancer Laboratory, Universidad de Antioquia, Medellin, Colombia
| | - Leon D. Ortiz
- Division of Neuro-oncology, Instituto de Cancerología, Clinica Las Americas, Pharmacogenomics, Universidad CES, Medellin, Colombia
| | - Carlos A. Serna
- Laboratorio de Patologia y Citologia Rodrigo Restrepo, Department of Pathology, Clinica Las Américas, Universidad CES, Medellin, Colombia
| | - Kalman Kovacs
- Department of Laboratory Medicine, Division of Pathology, St. Michael’s Hospital, University of Toronto, Toronto, ON, Canada
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183
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Harada K, Imai T, Kizu J, Mochizuki M, Inami K. DNA interaction of bromomethyl-substituted acridines. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2030-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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184
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Zheng L, Lin L, Qu K, Adhikary A, Sevilla MD, Greenberg MM. Independent Photochemical Generation and Reactivity of Nitrogen-Centered Purine Nucleoside Radicals from Hydrazines. Org Lett 2017; 19:6444-6447. [PMID: 29125775 DOI: 10.1021/acs.orglett.7b03368] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Photochemical precursors that produce dA• and dG(N2-H)• are needed to investigate their reactivity. The synthesis of two 1,1-diphenylhydrazines (1, 2) and their use as photochemical sources of dA• and dG(N2-H)• is presented. Trapping studies indicate production of these radicals with good fidelity, and 1 was incorporated into an oligonucleotide via solid-phase synthesis. Cyclic voltammetric studies show that reduction potentials of 1 and 2 are lower than those of widely used "hole sinks", e.g., 8-oxodGuo and 7-deazadGuo, to investigate DNA-hole transfer processes. These molecules could be useful (a) as sources of dA• and dG(N2-H)• at specific sites in oligonucleotides and (b) as "hole sinks" for the study of DNA-hole transfer processes.
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Affiliation(s)
- Liwei Zheng
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Lu Lin
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Ke Qu
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Amitava Adhikary
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Michael D Sevilla
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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185
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Hansen MLRW, Ramsussen MA, Skov T, Clausen A, Risbo J. The possible causal relationship between fragmentation of genomic DNA and formation of viable, but non-culturable probiotic bacteria upon storage in dry state. Biotechnol Prog 2017; 34:231-242. [PMID: 29063712 DOI: 10.1002/btpr.2573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/24/2017] [Indexed: 11/10/2022]
Abstract
In this study, the aim was to establish if loss of DNA integrity is a cause of loss of culturability for probiotic bacteria during storage in dry state. The number of colony forming units (CFU), number of metabolically active cells, and DNA integrity during dry storage of probiotic strains, B. animalis subsp. lactis BB-12 and L. acidophilus LA-5, were investigated. The probiotic strains were freeze-dried and stored at 20°C, with and without oxygen present, and at water activity levels 0.22 or 0.32. Dry storage resulted in a decrease in CFU during the entire storage period. The number of metabolically active cells was unchanged during storage of B. animalis subsp. lactis BB-12, but did decrease during the first week of storage of L. acidophilus LA-5. Loss of DNA integrity was evident for both strains during storage and correlated well with the loss of CFU. Both loss of CFU and loss of DNA integrity were significantly greater for both strains when oxygen was present and when aw was increased. Statistical analysis indicates a possible causal relationship between DNA degradation and loss of culturability and this idea is consistent with the function of DNA at cell division. The study contributes with new knowledge of the cause for loss of CFU during dry storage of probiotic bacteria, which possibly can aid in the improvement of preservation techniques. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:231-242, 2018.
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Affiliation(s)
| | - Morten Arendt Ramsussen
- Dept. of Food Science, University of Copenhagen, Denmark.,Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health and Medical Sciences, University of Copenhagen & Danish Pediatric Asthma Center, Gentofte Hospital, University of Copenhagen, Denmark
| | - Thomas Skov
- Dept. of Food Science, University of Copenhagen, Denmark
| | | | - Jens Risbo
- Dept. of Food Science, University of Copenhagen, Denmark
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186
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Kashida H, Kurihara A, Kawai H, Asanuma H. Orientation-dependent FRET system reveals differences in structures and flexibilities of nicked and gapped DNA duplexes. Nucleic Acids Res 2017; 45:e105. [PMID: 28369626 PMCID: PMC5499647 DOI: 10.1093/nar/gkx200] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/17/2017] [Indexed: 12/18/2022] Open
Abstract
Differences in structures and flexibilities of DNA duplexes play important roles on recognition by DNA-binding proteins. We herein describe a novel method for structural analyses of DNA duplexes by using orientation dependence of Förster resonance energy transfer (FRET). We first analyzed canonical B-form duplex and correct structural parameters were obtained. The experimental FRET efficiencies were in excellent agreement with values theoretically calculated by using determined parameters. We then investigated DNA duplexes with nick and gaps, which are key intermediates in DNA repair systems. Effects of gap size on structures and flexibilities were successfully revealed. Since our method is facile and sensitive, it could be widely used to analyze DNA structures containing damages and non-natural molecules.
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Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ayako Kurihara
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hayato Kawai
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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187
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Yang Z, Price NE, Johnson KM, Wang Y, Gates KS. Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA. Nucleic Acids Res 2017; 45:6275-6283. [PMID: 28531327 PMCID: PMC5499897 DOI: 10.1093/nar/gkx394] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/02/2017] [Indexed: 01/04/2023] Open
Abstract
Interstrand cross-links are exceptionally bioactive DNA lesions. Endogenous generation of interstrand cross-links in genomic DNA may contribute to aging, neurodegeneration, and cancer. Abasic (Ap) sites are common lesions in genomic DNA that readily undergo spontaneous and amine-catalyzed strand cleavage reactions that generate a 2,3-didehydro-2,3-dideoxyribose sugar remnant (3’ddR5p) at the 3’-terminus of the strand break. Interestingly, this strand scission process leaves an electrophilic α,β-unsaturated aldehyde residue embedded within the resulting nicked duplex. Here we present evidence that 3’ddR5p derivatives generated by spermine-catalyzed strand cleavage at Ap sites in duplex DNA can react with adenine residues on the opposing strand to generate a complex lesion consisting of an interstrand cross-link adjacent to a strand break. The cross-link blocks DNA replication by ϕ29 DNA polymerase, a highly processive polymerase enzyme that couples synthesis with strand displacement. This suggests that 3’ddR5p-derived cross-links have the potential to block critical cellular DNA transactions that require strand separation. LC-MS/MS methods developed herein provide powerful tools for studying the occurrence and properties of these cross-links in biochemical and biological systems.
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Affiliation(s)
- Zhiyu Yang
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA
| | - Nathan E Price
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Kevin M Johnson
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Kent S Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA.,Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA
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188
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El Zahar NM, Magdy N, El-Kosasy AM, Bartlett MG. Chromatographic approaches for the characterization and quality control of therapeutic oligonucleotide impurities. Biomed Chromatogr 2017; 32. [PMID: 28869310 DOI: 10.1002/bmc.4088] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/13/2017] [Accepted: 08/28/2017] [Indexed: 12/16/2022]
Abstract
Phosphorothioate (PS) oligonucleotides are a rapidly rising class of drugs with significant therapeutic applications. However, owing to their complex structure and multistep synthesis and purification processes, generation of low-level impurities and degradation products are common. Therefore, they require significant investment in quality control and impurity identification. This requires the development of advanced methods for analysis, characterization and quantitation. In addition, the presence of the PS linkage leads to the formation of chiral centers which can affect their biological properties and therapeutic efficiency. In this review, the different types of oligonucleotide impurities and degradation products, with an emphasis on their origin, mechanism of formation and methods to reduce, prevent or even eliminate their production, will be extensively discussed. This review will focus mainly on the application of chromatographic techniques to determine these impurities but will also discuss other approaches such as mass spectrometry, capillary electrophoresis and nuclear magnetic resonance spectroscopy. Finally, the chirality and formation of diastereomer mixtures of PS oligonucleotides will be covered as well as approaches used for their characterization and the application for the development of stereochemically-controlled PS oligonucleotides.
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Affiliation(s)
- N M El Zahar
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.,Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, USA
| | - N Magdy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - A M El-Kosasy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, USA
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189
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Liu M, Xu J, Yang F, Gu Y, Chen H, Wang Y, Li F. Sensitive electrochemical detection of DNA damage based on in situ double strand growth via hybridization chain reaction. Anal Bioanal Chem 2017; 409:6821-6829. [DOI: 10.1007/s00216-017-0641-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/05/2017] [Accepted: 09/14/2017] [Indexed: 12/12/2022]
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190
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Marangoni LFDB, Marques JA, Duarte GAS, Pereira CM, Calderon EN, Castro CBE, Bianchini A. Copper effects on biomarkers associated with photosynthesis, oxidative status and calcification in the Brazilian coral Mussismilia harttii (Scleractinia, Mussidae). MARINE ENVIRONMENTAL RESEARCH 2017; 130:248-257. [PMID: 28823595 DOI: 10.1016/j.marenvres.2017.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
Seawater contamination with metals, such as copper (Cu), is a notable local impact threatening coral reefs. Cu effects on biomarkers associated with photosynthesis, oxidative status and calcification were evaluated in the Brazilian coral Mussismilia harttii using a marine mesocosm facility. Polyps were kept under control conditions (1.9 μg L-1 Cu) or exposed to dissolved Cu (3.0, 4.8, and 6.7 μg L-1) for 12 days. Photochemical efficiency of the photosystem II of symbiotic algae (zooxanthellae) was measured and polyps were analyzed for antioxidant capacity, lipid peroxidation, DNA damage, and carbonic anhydrase Ca-ATPase, Mg-ATPase and (Ca,Mg)-ATPase activities after 12 days. Results highlighted the effects of Cu exposure, leading corals to an oxidative stress condition [increased total antioxidant capacity (TAC) and DNA damage] and a possible reduced calcification ability [decreased (Ca,Mg)-ATPase activity]. Therefore, biomarkers associated with oxidative status (TAC and DNA damage) and calcification [(Ca, Mg)-ATPase] are indicated as good predictors of corals health.
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Affiliation(s)
- Laura Fernandes de Barros Marangoni
- Programa de Pós-Graduação em Oceanografia Biológica, Instituto de Oceanografia, Universidade Federal do Rio Grande, Av. Itália, km 8, Rio Grande, RS 96203-900, Brazil.
| | - Joseane Aparecida Marques
- Programa de Pós-Graduação em Oceanografia Biológica, Instituto de Oceanografia, Universidade Federal do Rio Grande, Av. Itália, km 8, Rio Grande, RS 96203-900, Brazil.
| | - Gustavo Adolpho Santos Duarte
- Programa de Pós-graduação em Zoologia, Museu Nacional, Universidade Federal do Rio de Janeiro, Parque Quinta da Boa Vista, São Cristovão, Rio de Janeiro, RJ 20940-040, Brazil.
| | - Cristiano Macedo Pereira
- Programa de Pós-graduação em Zoologia, Museu Nacional, Universidade Federal do Rio de Janeiro, Parque Quinta da Boa Vista, São Cristovão, Rio de Janeiro, RJ 20940-040, Brazil; Instituto Coral Vivo, Rua dos Coqueiros, Parque Yaya, Santa Cruz Cabrália, BA 45.807-000, Brazil.
| | - Emiliano Nicolas Calderon
- Instituto Coral Vivo, Rua dos Coqueiros, Parque Yaya, Santa Cruz Cabrália, BA 45.807-000, Brazil; Museu Nacional, Universidade Federal do Rio de Janeiro, Parque Quinta da Boa Vista, São Cristovão, Rio de Janeiro, RJ 20940-040, Brazil; Programa de Pós-Graduação em Ciências Ambientais e Conservação, Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé, Universidade Federal do Rio de Janeiro (NUPEM/UFRJ), Av. São José do Barreto, 764, 27965-045 Macaé, RJ, Brazil.
| | - Clovis Barreira E Castro
- Instituto Coral Vivo, Rua dos Coqueiros, Parque Yaya, Santa Cruz Cabrália, BA 45.807-000, Brazil; Museu Nacional, Universidade Federal do Rio de Janeiro, Parque Quinta da Boa Vista, São Cristovão, Rio de Janeiro, RJ 20940-040, Brazil.
| | - Adalto Bianchini
- Programa de Pós-Graduação em Oceanografia Biológica, Instituto de Oceanografia, Universidade Federal do Rio Grande, Av. Itália, km 8, Rio Grande, RS 96203-900, Brazil; Instituto Coral Vivo, Rua dos Coqueiros, Parque Yaya, Santa Cruz Cabrália, BA 45.807-000, Brazil; Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Av. Itália, km 8, Rio Grande, RS 96203-900, Brazil.
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191
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Bedi MF, Li W, Gutwald T, Bryant-Friedrich AC. Synthesis of damaged DNA containing the oxidative lesion 3'-oxothymidine. Bioorg Med Chem 2017; 25:5598-5602. [PMID: 28927804 DOI: 10.1016/j.bmc.2017.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 11/16/2022]
Abstract
Oxidative events that take place during regular oxygen metabolism can lead to the formation of organic or inorganic radicals. The interaction of these radicals with macromolecules in the organism and with DNA in particular is suspected to lead to apoptosis, DNA lesions and cell damage. Independent generation of DNA lesions resulting from oxidative damage is used to promote the study of their effects on biological systems. An efficient synthesis of oligodeoxyribonucleotides (ODNs) containing the oxidative damage lesion 3'-oxothymidine has been accomplished via incorporation of C3'-hydroxymethyl thymidine as its corresponding 5'-phosphoramidite. Through oxidative cleavage using sodium periodate in aqueous solution, the lesion of interest is easily generated. Due to its inherent instability it cannot be directly isolated, but must be generated in situ. 3'-Oxothymidine is a demonstrated damage product formed upon generation of the C3'-thymidinyl radical in ODN.
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Affiliation(s)
- Mel F Bedi
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo, 2801 W. Bancroft St., Toledo, OH, United States
| | - Weiye Li
- Department of Medicinal Chemistry and Pharmacognosy, The University of Illinois Chicago, 1601 Parkview Ave. Rm A301, Rockford, IL 61107, United States
| | - Taylor Gutwald
- Chicago College of Pharmacy, Midwestern University, Chicago, 555 31st Street, Downers Grove, IL 60515, United States
| | - Amanda C Bryant-Friedrich
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo, 2801 W. Bancroft St., Toledo, OH, United States.
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192
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Wilson KA, Wetmore SD. Conformational Flexibility of the Benzyl-Guanine Adduct in a Bypass Polymerase Active Site Permits Replication: Insights from Molecular Dynamics Simulations. Chem Res Toxicol 2017; 30:2013-2022. [PMID: 28810119 DOI: 10.1021/acs.chemrestox.7b00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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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193
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Sosic A, Zuravka I, Schmitt NK, Miola A, Göttlich R, Fabris D, Gatto B. Direct and Topoisomerase II Mediated DNA Damage by Bis-3-chloropiperidines: The Importance of Being an Earnest G. ChemMedChem 2017; 12:1471-1479. [PMID: 28724198 DOI: 10.1002/cmdc.201700368] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/19/2017] [Indexed: 01/19/2023]
Abstract
Bis-3-chloropiperidines are a new class of DNA-active compounds capable of alkylating nucleobases and inducing strand cleavage. In this study, we investigated the reactivity of these mustard-based agents with both single- and double-stranded DNA constructs. Polyacrylamide gel electrophoresis (PAGE) and electrospray ionization mass spectrometry (ESI-MS) were used to obtain valuable insight into their mechanism at the molecular level and to investigate their time- and concentration-dependent activity. The results revealed the preferential formation of mono- and bifunctional adducts at nucleophilic guanine sites. In a stepwise fashion, alkylation was followed by depurination and subsequent strand scission at the ensuing apurinic site. We demonstrated that the covalent modifications introduced by this new class of compounds can inhibit the activity of essential DNA-processing proteins, such as topoisomerase IIα, thereby suggesting that bis-3-chloropiperidines may have excellent anticancer potential.
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Affiliation(s)
- Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131, Padova, Italy
| | - Ivonne Zuravka
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131, Padova, Italy.,Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Nina-Katharina Schmitt
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131, Padova, Italy
| | - Angelica Miola
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131, Padova, Italy
| | - Richard Göttlich
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Dan Fabris
- Departments of Chemistry and Biological Sciences, University at Albany - SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131, Padova, Italy
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194
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Meyer S, Schröter MA, Hahn MB, Solomun T, Sturm H, Kunte HJ. Ectoine can enhance structural changes in DNA in vitro. Sci Rep 2017; 7:7170. [PMID: 28775267 PMCID: PMC5543045 DOI: 10.1038/s41598-017-07441-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/26/2017] [Indexed: 11/20/2022] Open
Abstract
Strand breaks and conformational changes of DNA have consequences for the physiological role of DNA. The natural protecting molecule ectoine is beneficial to entire bacterial cells and biomolecules such as proteins by mitigating detrimental effects of environmental stresses. It was postulated that ectoine-like molecules bind to negatively charged spheres that mimic DNA surfaces. We investigated the effect of ectoine on DNA and whether ectoine is able to protect DNA from damages caused by ultraviolet radiation (UV-A). In order to determine different isoforms of DNA, agarose gel electrophoresis and atomic force microscopy experiments were carried out with plasmid pUC19 DNA. Our quantitative results revealed that a prolonged incubation of DNA with ectoine leads to an increase in transitions from supercoiled (undamaged) to open circular (single-strand break) conformation at pH 6.6. The effect is pH dependent and no significant changes were observed at physiological pH of 7.5. After UV-A irradiation in ectoine solution, changes in DNA conformation were even more pronounced and this effect was pH dependent. We hypothesize that ectoine is attracted to the negatively charge surface of DNA at lower pH and therefore fails to act as a stabilizing agent for DNA in our in vitro experiments.
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Affiliation(s)
- S Meyer
- Federal Institute for Materials Research and Testing, D-12205, Berlin, Germany. .,Institute of Biochemistry and Biology, University of Potsdam, D-14476, Potsdam, Germany.
| | - M-A Schröter
- Federal Institute for Materials Research and Testing, D-12205, Berlin, Germany
| | - M B Hahn
- Federal Institute for Materials Research and Testing, D-12205, Berlin, Germany.,Institute of Experimental Physics, Free University Berlin, Department of Physics, D-14195, Berlin, Germany
| | - T Solomun
- Federal Institute for Materials Research and Testing, D-12205, Berlin, Germany
| | - H Sturm
- Federal Institute for Materials Research and Testing, D-12205, Berlin, Germany.,Technical University Berlin, D-10587, Berlin, Germany
| | - H J Kunte
- Federal Institute for Materials Research and Testing, D-12205, Berlin, Germany
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195
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Tan KX, Danquah MK, Sidhu A, Lau SY, Ongkudon CM. Biophysical characterization of layer-by-layer synthesis of aptamer-drug microparticles for enhanced cell targeting. Biotechnol Prog 2017; 34:249-261. [PMID: 28699244 DOI: 10.1002/btpr.2524] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 05/04/2017] [Indexed: 11/12/2022]
Abstract
Targeted delivery of drug molecules to specific cells in mammalian systems demonstrates a great potential to enhance the efficacy of current pharmaceutical therapies. Conventional strategies for pharmaceutical delivery are often associated with poor therapeutic indices and high systemic cytotoxicity, and this result in poor disease suppression, low surviving rates, and potential contraindication of drug formulation. The emergence of aptamers has elicited new research interests into enhanced targeted drug delivery due to their unique characteristics as targeting elements. Aptamers can be engineered to bind to their cognate cellular targets with high affinity and specificity, and this is important to navigate active drug molecules and deliver sufficient dosage to targeted malignant cells. However, the targeting performance of aptamers can be impacted by several factors including endonuclease-mediated degradation, rapid renal filtration, biochemical complexation, and cell membrane electrostatic repulsion. This has subsequently led to the development of smart aptamer-immobilized biopolymer systems as delivery vehicles for controlled and sustained drug release to specific cells at effective therapeutic dosage and minimal systemic cytotoxicity. This article reports the synthesis and in vitro characterization of a novel multi-layer co-polymeric targeted drug delivery system based on drug-loaded PLGA-Aptamer-PEI (DPAP) formulation with a stage-wise delivery mechanism. A thrombin-specific DNA aptamer was used to develop the DPAP system while Bovine Serum Albumin (BSA) was used as a biopharmaceutical drug in the synthesis process by ultrasonication. Biophysical characterization of the DPAP system showed a spherical shaped particulate formulation with a unimodal particle size distribution of average size ∼0.685 µm and a zeta potential of +0.82 mV. The DPAP formulation showed a high encapsulation efficiency of 89.4 ± 3.6%, a loading capacity of 17.89 ± 0.72 mg BSA protein/100 mg PLGA polymeric particles, low cytotoxicity and a controlled drug release characteristics in 43 days. The results demonstrate a great promise in the development of DPAP formulation for enhanced in vivo cell targeting. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:249-261, 2018.
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Affiliation(s)
- Kei X Tan
- Dept. of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Michael K Danquah
- Dept. of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Amandeep Sidhu
- Curtin Sarawak Research Institute, Curtin University, Sarawak, 98009, Malaysia.,Faculty of Health Sciences, Curtin University, Perth, 6102, Australia
| | - Sie Yon Lau
- Dept. of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Clarence M Ongkudon
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia
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196
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Pfeifer CM, Gass A, Klein-Unseld R, Wiegand P. DNA persistence of bite marks on food and its relevance for STR typing. Int J Legal Med 2017; 131:1221-1228. [PMID: 28653154 DOI: 10.1007/s00414-017-1627-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/13/2017] [Indexed: 01/20/2023]
Abstract
In forensic DNA analysis, salivary traces at crime scenes are a promising way to identify a person. However, crime scenes are oftentimes investigated a while after the crime and recovered samples might have been degraded leading to poor PCR amplification. Probably due to decomposition and negative visual impression of spoiled food, bite mark samples make up only a small part of our casework routine. In this study, bite marks on apples and chocolate bars as well as on an inert surface (microscope slide) were stored up to 3 weeks indoors and outdoors during different seasons and analyzed for amylase activity and DNA quantity and quality. The results underlined the stability of human nuclear DNA not only on inert but also on biological surfaces and their forensic usefulness even when bite marks are stored 21 days under adverse but realistic conditions at a crime scene. Overall, amylase activity as well as DNA quantity decreased over time depending on storage environment with a certain inter- and intrapersonal variation. But amylase activity testing was not found to be an appropriate screening tool for further analysis. Apple bite marks resulted in generally higher DNA amounts than chocolate bars and microscope slides. Although mold reduced the DNA quantity, complete STR profiles could be analyzed. High air humidity and cold temperatures were found to act preservative on raw food with high water content but caused loss of information over time for smooth inert surfaces and hygroscopic foods like sweets. Many factors are involved in the stability of DNA in bite marks and its resulting quality and quantity available for an STR analysis. However, since there was a substantial proportion of informative STR profiles even from bite marks stored for 21 days, the results encourage the analysis of those even if their visual appearance seems unfavorable.
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Affiliation(s)
- Céline M Pfeifer
- Institute of Legal Medicine, Albert-Einstein-Allee 23, 89081, Ulm, Germany.
| | - Anja Gass
- Institute of Legal Medicine, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | | | - Peter Wiegand
- Institute of Legal Medicine, Albert-Einstein-Allee 23, 89081, Ulm, Germany
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197
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Grüber R, Aranda J, Bellili A, Tuñón I, Dumont E. Free energy profiles for two ubiquitous damaging agents: methylation and hydroxylation of guanine in B-DNA. Phys Chem Chem Phys 2017; 19:14695-14701. [PMID: 28537602 DOI: 10.1039/c6cp07966k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methylation and hydroxylation are two ubiquitous reactions in DNA damage induction, yet insights are scarce concerning the free energy of activation within B-DNA. We resort to multiscale simulations to investigate the attack of a hydroxyl radical and of the primary diazonium onto a guanine embedded in a solvated dodecamer. Reaction free energy profiles characterize two strongly exergonic processes, yet allow unprecedented quantification of the barrier towards this damage reaction, not higher than 6 kcal mol-1 and sometimes inexistent, and of the exergonicities. In the case of the [G(C8)-OH]˙ intermediate, we challenge the functional dependence of such simulations: recently-proposed functionals, such as M06-2X and LC-BLYP, agree on a ∼4 kcal mol-1 barrier, whereas the hybrid GGA B3LYP functional predicts a barrier-less pathway. In the long term, multiscale approaches can help build up a unified panorama of DNA lesion induction. These results stress the importance of DFT/MM-MD simulations involving new functionals towards the sound modelling of biomolecule damage even in the ground state.
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Affiliation(s)
- R Grüber
- Univ. Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France.
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198
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Alternative sampling strategies for the assessment of biomarkers of exposure. CURRENT OPINION IN TOXICOLOGY 2017. [DOI: 10.1016/j.cotox.2017.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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199
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Fleming AM, Burrows CJ. Formation and processing of DNA damage substrates for the hNEIL enzymes. Free Radic Biol Med 2017; 107:35-52. [PMID: 27880870 PMCID: PMC5438787 DOI: 10.1016/j.freeradbiomed.2016.11.030] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/13/2016] [Accepted: 11/16/2016] [Indexed: 12/13/2022]
Abstract
Reactive oxygen species (ROS) are harnessed by the cell for signaling at the same time as being detrimental to cellular components such as DNA. The genome and transcriptome contain instructions that can alter cellular processes when oxidized. The guanine (G) heterocycle in the nucleotide pool, DNA, or RNA is the base most prone to oxidation. The oxidatively-derived products of G consistently observed in high yields from hydroxyl radical, carbonate radical, or singlet oxygen oxidations under conditions modeling the cellular reducing environment are discussed. The major G base oxidation products are 8-oxo-7,8-dihydroguanine (OG), 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), spiroiminodihydantoin (Sp), and 5-guanidinohydantoin (Gh). The yields of these products show dependency on the oxidant and the reaction context that includes nucleoside, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and G-quadruplex DNA (G4-DNA) structures. Upon formation of these products in cells, they are recognized by the DNA glycosylases in the base excision repair (BER) pathway. This review focuses on initiation of BER by the mammalian Nei-like1-3 (NEIL1-3) glycosylases for removal of 2Ih, Sp, and Gh. The unique ability of the human NEILs to initiate removal of the hydantoins in ssDNA, bulge-DNA, bubble-DNA, dsDNA, and G4-DNA is outlined. Additionally, when Gh exists in a G4 DNA found in a gene promoter, NEIL-mediated repair is modulated by the plasticity of the G4-DNA structure provided by additional G-runs flanking the sequence. On the basis of these observations and cellular studies from the literature, the interplay between DNA oxidation and BER to alter gene expression is discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850, United States.
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200
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Abbotts R, Wilson DM. Coordination of DNA single strand break repair. Free Radic Biol Med 2017; 107:228-244. [PMID: 27890643 PMCID: PMC5443707 DOI: 10.1016/j.freeradbiomed.2016.11.039] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 12/28/2022]
Abstract
The genetic material of all organisms is susceptible to modification. In some instances, these changes are programmed, such as the formation of DNA double strand breaks during meiotic recombination to generate gamete variety or class switch recombination to create antibody diversity. However, in most cases, genomic damage is potentially harmful to the health of the organism, contributing to disease and aging by promoting deleterious cellular outcomes. A proportion of DNA modifications are caused by exogenous agents, both physical (namely ultraviolet sunlight and ionizing radiation) and chemical (such as benzopyrene, alkylating agents, platinum compounds and psoralens), which can produce numerous forms of DNA damage, including a range of "simple" and helix-distorting base lesions, abasic sites, crosslinks and various types of phosphodiester strand breaks. More significant in terms of frequency are endogenous mechanisms of modification, which include hydrolytic disintegration of DNA chemical bonds, attack by reactive oxygen species and other byproducts of normal cellular metabolism, or incomplete or necessary enzymatic reactions (such as topoisomerases or repair nucleases). Both exogenous and endogenous mechanisms are associated with a high risk of single strand breakage, either produced directly or generated as intermediates of DNA repair. This review will focus upon the creation, consequences and resolution of single strand breaks, with a particular focus on two major coordinating repair proteins: poly(ADP-ribose) polymerase 1 (PARP1) and X-ray repair cross-complementing protein 1 (XRCC1).
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Affiliation(s)
- Rachel Abbotts
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
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