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Semyonov DA, Eltsov IV, Nechipurenko YD. A New Bias Site for Epigenetic Modifications: How Non-Canonical GC Base Pairs Favor Mechanochemical Cleavage of DNA. Bioessays 2020; 42:e2000051. [PMID: 32830350 DOI: 10.1002/bies.202000051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/23/2020] [Indexed: 11/11/2022]
Abstract
Properties of non-canonical GC base pairs and their relations with mechanochemical cleavage of DNA are analyzed. A hypothesis of the involvement of the transient GC wobble base pairs both in the mechanisms of the mechanochemical cleavage of DNA and epigenetic mechanisms involving of 5-methylcytosine, is proposed. The hypothesis explains the increase in the frequency of the breaks of the sugar-phosphate backbone of DNA after cytosines, the asymmetric character of these breaks, and an increase in break frequency in CpG after cytosine methylation. As an alternative hypothesis, probable implication of GC+ Hoogsteen base pairs is considered, which now exemplify the best-studied non-canonical GC base pairs in the DNA double helix. Also see the video abstract here https://youtu.be/EUunVWL0ptw.
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Affiliation(s)
- Denis A Semyonov
- Institute of Biophysics, Institute of Biophysics, Siberian Branch of Russian Academy of Science., Akademgorodok 50, Krasnoyarsk, 660036, Russia
| | | | - Yury D Nechipurenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Kou Y, Koag MC, Lee S. Promutagenicity of 8-Chloroguanine, A Major Inflammation-Induced Halogenated DNA Lesion. Molecules 2019; 24:molecules24193507. [PMID: 31569643 PMCID: PMC6804246 DOI: 10.3390/molecules24193507] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 12/18/2022] Open
Abstract
Chronic inflammation is closely associated with cancer development. One possible mechanism for inflammation-induced carcinogenesis is DNA damage caused by reactive halogen species, such as hypochlorous acid, which is released by myeloperoxidase to kill pathogens. Hypochlorous acid can attack genomic DNA to produce 8-chloro-2′-deoxyguanosine (ClG) as a major lesion. It has been postulated that ClG promotes mutagenic replication using its syn conformer; yet, the structural basis for ClG-induced mutagenesis is unknown. We obtained crystal structures and kinetics data for nucleotide incorporation past a templating ClG using human DNA polymerase β (polβ) as a model enzyme for high-fidelity DNA polymerases. The structures showed that ClG formed base pairs with incoming dCTP and dGTP using its anti and syn conformers, respectively. Kinetic studies showed that polβ incorporated dGTP only 15-fold less efficiently than dCTP, suggesting that replication across ClG is promutagenic. Two hydrogen bonds between syn-ClG and anti-dGTP and a water-mediated hydrogen bond appeared to facilitate mutagenic replication opposite the major halogenated guanine lesion. These results suggest that ClG in DNA promotes G to C transversion mutations by forming Hoogsteen base pairing between syn-ClG and anti-G during DNA synthesis.
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Affiliation(s)
- Yi Kou
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, Austin, TX 78712, USA.
| | - Myong-Chul Koag
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, Austin, TX 78712, USA.
| | - Seongmin Lee
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, Austin, TX 78712, USA.
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Jana K, Ganguly B. In silico studies with substituted adenines to achieve a remarkable stability of mispairs with thymine nucleobase. NEW J CHEM 2016. [DOI: 10.1039/c5nj02311d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The modified adenine and thymine mispair achieves a remarkable stability, which can presumably help the DNA lesions to be less cytotoxic.
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Affiliation(s)
- Kalyanashis Jana
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR – Central Salt and Marine Chemicals Research Institute
- Bhavnagar – 364002
- India
- Academy of Scientific and Innovative Research
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR – Central Salt and Marine Chemicals Research Institute
- Bhavnagar – 364002
- India
- Academy of Scientific and Innovative Research
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Jana K, Ganguly B. In Silico Studies to Explore the Mutagenic Ability of 5-Halo/Oxy/Li-Oxy-Uracil Bases with Guanine of DNA Base Pairs. J Phys Chem A 2014; 118:9753-61. [DOI: 10.1021/jp507471z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kalyanashis Jana
- Computation
and
Simulation Unit (Analytical Discipline and Centralized Instrument
Facility), CSIR−Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
- Academy of Scientific
and Innovative Research, CSIR−CSMCRI, Bhavnagar, Gujarat 364002, India
| | - Bishwajit Ganguly
- Computation
and
Simulation Unit (Analytical Discipline and Centralized Instrument
Facility), CSIR−Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
- Academy of Scientific
and Innovative Research, CSIR−CSMCRI, Bhavnagar, Gujarat 364002, India
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Theruvathu JA, Yin YW, Pettitt BM, Sowers LC. Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence. Biochemistry 2013; 52:8590-8. [PMID: 24147911 DOI: 10.1021/bi400980c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Inflammation-mediated reactive molecules can result in an array of oxidized and halogenated DNA-damage products, including 5-chlorocytosine ((Cl)C). Previous studies have shown that (Cl)C can mimic 5-methylcytosine ((m)C) and act as a fraudulent epigenetic signal, promoting the methylation of previously unmethylated DNA sequences. Although the 5-halouracils are good substrates for base-excision repair, no repair activity has yet been identified for (Cl)C. Because of the apparent biochemical similarities of (m)C and (Cl)C, we have investigated the effects of (m)C and (Cl)C substitution on oligonucleotide structure and dynamics. In this study, we have constructed oligonucleotide duplexes containing C, (Cl)C, and (m)C within a CpG dinucleotide. The thermal and thermodynamic stability of these duplexes were found to be experimentally indistinguishable. Crystallographic structures of duplex oligonucleotides containing (m)C or (Cl)C were determined to 1.2 and 1.9 Å resolution, respectively. Both duplexes are B-form and are superimposable on a previously determined structure of a cytosine-containing duplex with a rmsd of approximately 0.25 Å. NMR solution studies indicate that all duplexes containing cytosine or the cytosine analogues are normal B-form and that no structural perturbations are observed surrounding the site of each substitution. The magnitude of the base-stacking-induced upfield shifts for nonexchangeable base proton resonances are similar for each of the duplexes examined, indicating that neither (m)C nor (Cl)C significantly alter base-stacking interactions. The (Cl)C analogue is paired with G in an apparently normal geometry; however, the G-imino proton of the (Cl)C-G base pair resonates to higher field relative to (m)C-G or C-G, indicating a weaker imino hydrogen bond. Using selective ¹⁵N-enrichment and isotope-edited NMR, we observe that the amino group of (Cl)C rotates at roughly half of the rate of the corresponding amino groups of the C-G and (m)C-G base pairs. The altered chemical shifts of hydrogen-bonding proton resonances for the (Cl)C-G base pair as well as the slower rotation of the (Cl)C amino group can be attributed to the electron-withdrawing inductive property of the 5-chloro substituent. The apparent similarity of duplexes containing (m)C and (Cl)C demonstrated here is in accord with results of previous biochemical studies and further suggests that (Cl)C is likely to be an unusually persistent form of DNA damage.
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Affiliation(s)
- Jacob A Theruvathu
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch , 3.330 Basic Science Building, 301 University Boulevard, Galveston, Texas 77555, United States
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Bar-Shir A, Liu G, Liang Y, Yadav NN, McMahon MT, Walczak P, Nimmagadda S, Pomper MG, Tallman KA, Greenberg MM, van Zijl PCM, Bulte JWM, Gilad AA. Transforming thymidine into a magnetic resonance imaging probe for monitoring gene expression. J Am Chem Soc 2013; 135:1617-24. [PMID: 23289583 DOI: 10.1021/ja312353e] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Synthetic chemistry has revolutionized the understanding of many biological systems. Small compounds that act as agonists and antagonists of proteins, and occasionally as imaging probes, have contributed tremendously to the elucidation of many biological pathways. Nevertheless, the function of thousands of proteins is still elusive, and designing new imaging probes remains a challenge. Through screening and characterization, we identified a thymidine analogue as a probe for imaging the expression of herpes simplex virus type-1 thymidine kinase (HSV1-TK). To detect the probe, we used chemical exchange saturation transfer magnetic resonance imaging (CEST-MRI), in which a dynamic exchange process between an exchangeable proton and the surrounding water protons is used to amplify the desired contrast. Initially, five pyrimidine-based molecules were recognized as putative imaging agents, since their exchangeable imino protons resonate at 5-6 ppm from the water proton frequency and their detection is therefore less affected by endogenous CEST contrast or confounded by direct water saturation. Increasing the pK(a) value of the imino proton by reduction of its 5,6-double bond results in a significant reduction of the exchange rate (k(ex)) between this proton and the water protons. This reduced k(ex) of the dihydropyrimidine nucleosides fulfills the "slow to intermediate regime" condition for generating high CEST-MRI contrast. Consequently, we identified 5-methyl-5,6-dihydrothymidine as the optimal probe and demonstrated its feasibility for in vivo imaging of HSV1-TK. In light of these findings, this new approach can be generalized for designing specific probes for the in vivo imaging of a variety of proteins and enzymes.
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Affiliation(s)
- Amnon Bar-Shir
- Division of MR Research, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Patra A, Harp J, Pallan PS, Zhao L, Abramov M, Herdewijn P, Egli M. Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs. Nucleic Acids Res 2012; 41:2689-97. [PMID: 23275540 PMCID: PMC3575798 DOI: 10.1093/nar/gks1316] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli strain relies on the four building blocks 5-chloro-2'-deoxyuridine (ClU), A, C and G instead of the standard T, A, C, G alphabet [Marlière,P., Patrouix,J., Döring,V., Herdewijn,P., Tricot,S., Cruveiller,S., Bouzon,M. and Mutzel,R. (2011) Chemical evolution of a bacterium's genome. Angew. Chem. Int. Ed., 50, 7109-7114]. The residual fraction of T in the DNA of adapted bacteria was <2% and the switch from T to ClU was accompanied by a massive number of mutations, including >1500 A to G or G to A transitions in a culture. The former is most likely due to wobble base pairing between ClU and G, which may be more common for ClU than T. To identify potential changes in the geometries of base pairs and duplexes as a result of replacement of T by ClU, we determined four crystal structures of a B-form DNA dodecamer duplex containing ClU:A or ClU:G base pairs. The structures reveal nearly identical geometries of these pairs compared with T:A or T:G, respectively, and no consequences for stability and cleavage by an endonuclease (EcoRI). The lack of significant changes in the geometry of ClU:A and ClU:G base pairs relative to the corresponding native pairs is consistent with the sustained unlimited self-reproduction of E. coli strains with virtually complete T→ClU genome substitution.
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Affiliation(s)
- Amritraj Patra
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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Nishikawa T, Miyahara E, Horiuchi M, Izumo K, Okamoto Y, Kawai Y, Kawano Y, Takeuchi T. Benzene metabolite 1,2,4-benzenetriol induces halogenated DNA and tyrosines representing halogenative stress in the HL-60 human myeloid cell line. ENVIRONMENTAL HEALTH PERSPECTIVES 2012; 120:62-67. [PMID: 21859636 PMCID: PMC3261936 DOI: 10.1289/ehp.1103437] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 08/22/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND Although benzene is known to be myelotoxic and to cause myeloid leukemia in humans, the mechanism has not been elucidated. OBJECTIVES We focused on 1,2,4-benzenetriol (BT), a benzene metabolite that generates reactive oxygen species (ROS) by autoxidation, to investigate the toxicity of benzene leading to leukemogenesis. METHODS After exposing HL-60 human myeloid cells to BT, we investigated the cellular effects, including apoptosis, ROS generation, DNA damage, and protein damage. We also investigated how the cellular effects of BT were modified by hydrogen peroxide (H2O2) scavenger catalase, hypochlorous acid (HOCl) scavenger methionine, and 4-aminobenzoic acid hydrazide (ABAH), a myeloperoxidase (MPO)-specific inhibitor. RESULTS BT increased the levels of apoptosis and ROS, including superoxide (O2•-), H2O2, HOCl, and the hydroxyl radical (•OH). Catalase, ABAH, and methionine each inhibited the increased apoptosis caused by BT, and catalase and ABAH inhibited increases in HOCl and •OH. Although BT exposure increased halogenated DNA, this increase was inhibited by catalase, methionine, and ABAH. BT exposure also increased the amount of halogenated tyrosines; however, it did not increase 8-oxo-deoxyguanosine. CONCLUSIONS We suggest that BT increases H2O2 intracellularly; this H2O2 is metabolized to HOCl by MPO, and this HOCl results in possibly cytotoxic binding of chlorine to DNA. Because myeloid cells copiously express MPO and because halogenated DNA may induce both genetic and epigenetic changes that contribute to carcinogenesis, halogenative stress may account for benzene-induced bone marrow disorders and myeloid leukemia.
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Affiliation(s)
- Takuro Nishikawa
- Department of Environmental Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuraga-oka, Kagoshima, Japan.
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Kim CH, Darwanto A, Theruvathu JA, Herring JL, Sowers LC. Polymerase incorporation and miscoding properties of 5-chlorouracil. Chem Res Toxicol 2010; 23:740-8. [PMID: 20104909 DOI: 10.1021/tx900302j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inflammation-mediated hypochlorous acid (HOCl) can damage DNA, DNA precursors, and other biological molecules, thereby producing an array of damage products such as 5-chlorouracil (ClU). In this study, we prepared and studied 5-chloro-2'-deoxyuridine (CldU) and ClU-containing oligonucleotide templates. We demonstrate that human K-562 cells grown in culture with 10 muM CldU incorporate substantial amounts of CldU without significant toxicity. When in the template, ClU residues pair with dATP but also with dGTP, in a pH-dependent manner with incorporation by human polymerase beta, avian myeloblastosis virus reverse transcriptase (AMV-RT), and Escherichia coli Klenow fragment (exo(-)) polymerase. The enhanced miscoding of ClU is attributed to the electron-withdrawing 5-chlorine substituent that promotes the formation of an ionized ClU-G mispair. When mispaired with G, ClU is targeted for removal by human glycosylases. The formation, incorporation, and repair of ClU could promote transition mutations and other forms of heritable DNA damage.
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Affiliation(s)
- Cherine H Kim
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA
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