- Catalytic Space Engineering as a Strategy to Activate C-H Oxidation on 5-Methylcytosine in Mammalian Genome
-
Conditional remodeling of enzyme catalysis is a formidable challenge in protein engineering. Herein, we have undertaken a unique active site engineering tactic to command catalytic outcomes. With ten-eleven translocation (TET) enzyme as a paradigm, we show that variants with an expanded active site significantly enhance multistep C-H oxidation in 5-methylcytosine (5mC), whereas a crowded cavity leads to a single-step catalytic apparatus. We further identify an evolutionarily conserved residue in the TET family with a remarkable catalysis-directing ability. The activating variant demonstrated its prowess to oxidize 5mC in chromosomal DNA for potentiating expression of genes including tumor suppressors.
- Dey, Debasis,Islam, Kabirul,Sappa, Sushma,Sudhamalla, Babu
-
supporting information
p. 11891 - 11896
(2021/08/20)
-
- RETRACTED ARTICLE: Divergent synthesis of 5-substituted pyrimidine 2′-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases
-
Recent studies have indicated that 5-methylcytosine (5mC) residues in DNA can be oxidized and potentially deaminated to the corresponding thymine analogs. Some of these oxidative DNA damages have been implicated as new epigenetic markers that could have profound influences on chromatin function as well as disease pathology. In response to oxidative damage, the cells have a complex network of repair systems that recognize, remove and rebuild the lesions. However, how the modified nucleobases are detected and repaired remains elusive, largely due to the limited availability of synthetic oligodeoxynucleotides (ODNs) containing these novel DNA modifications. A concise and divergent synthetic strategy to 5mC derivatives has been developed. These derivatives were further elaborated to the corresponding phosphoramidites to enable the site-specific incorporation of modified nucleobases into ODNs using standard solid-phase DNA synthesis. The synthetic methodology, along with the panel of ODNs, is of great value to investigate the biological functions of epigenetically important nucleobases, and to elucidate the diversity in chemical lesion repair.
- Tran, Ai,Zheng, Song,White, Dawanna S.,Curry, Alyson M.,Cen, Yana
-
p. 11818 - 11826
(2020/11/18)
-
- Fluorescent Wittig reagent as a novel ratiometric probe for the quantification of 5-formyluracil and its application in cell imaging
-
The chemically selective detection of natural nucleobase modifications has been regarded as the key step in understanding their important roles in epigenetics. Herein, for the first time, we introduce a Wittig reaction into the design of reaction-based fluorescent probes for ratiometrically detecting 5fU, selectively labelling 5fU-modified DNA and imaging intracellular 5fU produced by γ-irradiation.
- Zhou, Qian,Li, Kun,Liu, Yan-Hong,Li, Ling-Ling,Yu, Kang-Kang,Zhang, Hong,Yu, Xiao-Qi
-
p. 13722 - 13725
(2019/01/03)
-
- Sonochemical transformation of thymidine: A mass spectrometric study
-
Abstract Ultrasound is extensively used in medical field for a number of applications including targeted killing of cancer cells. DNA is one of the most susceptible entities in any kind of free radical induced reactions in living systems. In the present work, the transformation of thymidine (dT) induced by ultrasound (US) was investigated using high resolution mass spectrometry (LC-Q-ToF-MS). dT was subjected to sonolysis under four different frequencies (200, 350, 620 and 1000 kHz) and at three power densities (10.5, 24.5 and 42 W/mL) in aerated as well as argon saturated conditions. A total of twenty modified nucleosides including non-fully characterized dT dimeric compounds were detected by LC-Q-ToF-MS. Out of these products, seven were obtained only in the argon atmosphere and two only in the aerated conditions. Among the identified products, there were base modified products and sugar modified products. The products were formed by the reaction of hydroxyl radical and hydrogen atom. Under aerated conditions, the reactions proceed via the formation of hydroperoxides, while in argon atmosphere disproportionation and radical recombinations predominate. The study provides a complete picture of sonochemical transformation pathways of dT which has relevance in DNA damage under ultrasound exposure.
- Chandran, Jisha,Aravind, Usha K.,Aravindakumar
-
p. 178 - 186
(2015/06/02)
-
- 5-Hydroxymethylcytosine and 5-formylcytosine containing deoxyoligonucleotides: Facile syntheses and melting temperature studies
-
An oxidation-based synthetic approach was developed for facile preparation of 5-formyl-2′-deoxycytidine and 5-hydroxymethyl-2′-deoxycytidine phosphoramidites. Upon introducing organic solvent components and copper catalysts, C5-methyl groups of 5-methyl-2′-deoxycytidine and thymidine were readily oxidized to formyl and hydroxyl functionality, respectively. Standard solid phase DNA synthesis and conventional deprotection methods were applicable to synthesize 5-formyl- or 5-hydroxymethyl-cytosine containing DNA oligonucleotides, which were used to study the effect of epigenetic modifications on DNA thermal dynamic stability.
- Xuan, Shuguang,Wu, Qiong,Cui, Liang,Zhang, Dawei,Shao, Fangwei
-
supporting information
p. 1186 - 1191
(2015/03/14)
-
- One-step to get 5-azidomethyl-2′-deoxyuridine from 5-hydroxymethyl-2′-deoxyuridine and detection of it through click reaction
-
Nowadays a few ways to synthesize 5-azidomethyl-2′-deoxyuridine from 5-hydroxymethyl-2′-deoxyuridine have been reported. But none of them was one-step. And many of them need to protect the hydroxyl group on the pentose ring. The detection of 5-hydroxymethyl-2′-deoxyuridine is also very important in many biological processes. However few fluorescence detection strategies have been tried to do this. Herein, we reported a one-step protocol to synthesize 5-azidomethyl-2′-deoxyuridine, which was then used for detecting 5-hydroxymethyl-2′-deoxyuridine through a click reaction.
- Xu, Xiaowei,Yan, Shengyong,Hu, Jianlin,Guo, Pu,Wei, Lai,Weng, Xiaocheng,Zhou, Xiang
-
p. 9870 - 9874
(2013/10/22)
-
- Deamination, oxidation, and C-C bond cleavage reactivity of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine
-
Three new cytosine derived DNA modifications, 5-hydroxymethyl-2′- deoxycytidine (hmdC), 5-formyl-2′-deoxycytidine (fdC) and 5-carboxy-2′-deoxycytidine (cadC) were recently discovered in mammalian DNA, particularly in stem cell DNA. Their function is currently not clear, but it is assumed that in stem cells they might be intermediates of an active demethylation process. This process may involve base excision repair, C-C bond cleaving reactions or deamination of hmdC to 5-hydroxymethyl-2′- deoxyuridine (hmdU). Here we report chemical studies that enlighten the chemical reactivity of the new cytosine nucleobases. We investigated their sensitivity toward oxidation and deamination and we studied the C-C bond cleaving reactivity of hmdC, fdC, and cadC in the absence and presence of thiols as biologically relevant (organo)catalysts. We show that hmdC is in comparison to mdC rapidly oxidized to fdC already in the presence of air. In contrast, deamination reactions were found to occur only to a minor extent. The C-C bond cleavage reactions require the presence of high concentration of thiols and are acid catalyzed. While hmdC dehydroxymethylates very slowly, fdC and especially cadC react considerably faster to dC. Thiols are active site residues in many DNA modifiying enzymes indicating that such enzymes could play a role in an alternative active DNA demethylation mechanism via deformylation of fdC or decarboxylation of cadC. Quantum-chemical calculations support the catalytic influence of a thiol on the C-C bond cleavage.
- Schiesser, Stefan,Pfaffeneder, Toni,Sadeghian, Keyarash,Hackner, Benjamin,Steigenberger, Barbara,Schroeder, Arne S.,Steinbacher, Jessica,Kashiwazaki, Gengo,Hoefner, Georg,Wanner, Klaus T.,Ochsenfeld, Christian,Carell, Thomas
-
p. 14593 - 14599
(2013/10/22)
-
- One-pot approach to functional nucleosides possessing a fluorescent group using nucleobase-exchange reaction by thymidine phosphorylase
-
Herein, we describe β-selective coupling between a modified uracil and a deoxyribose to produce functionalized nucleosides catalyzed by thymidine phosphorylase derived from Escherichia coli. This enzyme mediates nucleobase-exchange reactions to convert unnatural nucleosides possessing a large functional group such as a fluorescent molecule, coumarin or pyrene, linked via an alkyl chain at the C5 position of uracil. 5-(Coumarin-7-oxyhex-5- yn)uracil (C4U) displayed 57.2% conversion at 40% DMSO concentration in 1.0 mM phosphate buffer pH 6.8 to transfer thymidine to an unnatural nucleoside with C4U as the base. In the case of using 5-(pyren-1-methyloxyhex-5-yn)uracil (P4U) as the substrate, TP also could catalyse the reaction to generate a product with a very large functional group at 50% DMSO concentration (21.6% conversion). We carried out docking simulations using MF myPrest for the modified uracil bound to the active site of TP. The uracil moiety of the substrate binds to the active site of TP, with the fluorescent moiety linked to the C5 position of the nucleobase located outside the surface of the enzyme. As a consequence, the bulky fluorescent moiety binding to uracil has little influence on the coupling reaction.
- Hatano, Akihiko,Kurosu, Masayuki,Yonaha, Susumu,Okada, Munehiro,Uehara, Sanae
-
p. 6900 - 6905
(2013/10/08)
-
- Deconvoluting the reactivity of two intermediates formed from modified pyrimidines
-
Generation of the 5-(2′-deoxyuridinyl)methyl radical (6) was reexamined. Trapping by 4-hydroxy-2,2,6,6-tetramethylpiperidin-1-oxyl confirms that 6 is generated. However, trapping by methoxyamine reveals that the respective carbocation (10) is also produce
- Weng, Liwei,Horvat, Sonia M.,Schiesser, Carl H.,Greenberg, Marc M.
-
supporting information
p. 3618 - 3621
(2013/08/23)
-
- Oxidation and reduction of the 5-(2-Deoxyuridinyl)methyl radical
-
Sleeping beauty: The 5-(2-Deoxyuridinyl)methyl radical 1 is a key intermediate in the thymine oxidative reaction mediated by reactive oxygen species. Evidence is presented that 1 is prone to both oxidation and reduction reactions at the absence of O2. These results question the current paradigm and suggest that the redox chemistry of 1, which has been largely overlooked in the past, may play a major role in determining the fate of 1. Copyright
- Lin, Gengjie,Li, Lei
-
p. 5594 - 5598
(2013/06/27)
-
- Hypoxia-selective DNA interstrand cross-link formation by two modified nucleosides
-
The clean crossed code: Two nitroimidazole-modified thymidines 1 a and 1 b were synthesized and incorporated into DNA oligomers. The 350 nm photolysis of 1 a and 1 b generated a 5-(2'-deoxyuridinyl)methyl radical that induced DNA interstrand cross-links (ICL; see scheme). A higher ICL yield was observed under hypoxic conditions than under aerobic conditions. Copyright
- Kuang, Yunyan,Sun, Huabing,Blain, J. Craig,Peng, Xiaohua
-
supporting information
p. 12609 - 12613
(2012/11/14)
-
- Syntheses of two 5-hydroxymethyl-2′-deoxycytidine phosphoramidites with TBDMS as the 5-hydroxymethyl protecting group and their incorporation into DNA
-
5-Hydroxymethylcytosine (5-hmC) is a newly discovered DNA base modification in mammalian genomic DNA that is proposed to be a major epigenetic mark. We report here the syntheses of two new versions of phosphoramidites III and IV from 5-iodo-2′-deoxyuridine in 18% and 32% overall yields, respectively, with TBDMS as the 5-hydroxyl protecting group. Phosphoramidites III and IV allow efficient incorporation of 5-hmC into DNA and a "one-step" deprotection procedure to cleanly remove all the protecting groups. A "two-step" deprotection strategy is compatible with ultramild DNA synthesis, which enables the synthesis of 5hmC-containing DNA with additional modifications.
- Dai, Qing,Song, Chun-Xiao,Pan, Tao,He, Chuan
-
scheme or table
p. 4182 - 4188
(2011/07/31)
-
- Methyltransferase-directed derivatization of 5-hydroxymethylcytosine in DNA
-
Sequence-specific derivatization: Enzymatic methylation of cytosine in DNA is part of an epigenetic regulatory network in vertebrates. In the absence of the methylation cofactor S-adenosyl-L-methionine, bacterial cytosine-5 methyltransferases can catalyze the condensation of aliphatic thiols and selenols with 5-hydroxymethylcytosine, a recently discovered nucleobase in mammalian DNA, to yield 5-chalcogenomethyl derivatives (see scheme).
- Liutkeviaciute, Zita,Kriukiene, Edita,Grigaityte, Indre,Masevieius, Viktoras,Klimasauskas, Saulius
-
supporting information; experimental part
p. 2090 - 2093
(2011/04/23)
-
- Improved synthesis of 5-hydroxymethyl-2′-deoxycytidine phosphoramidite using a 2′-deoxyuridine to 2′-deoxycytidine conversion without temporary protecting groups
-
5-Hydroxymethylcytosine has recently been characterized as the 'sixth base' in human DNA. To enable research on this DNA modification, we report an improved method for the synthesis of 5-hydroxymethyl-2′-deoxycytidine (5-HOMedC) phosphoramidite for site-specific incorporation into oligonucleotides. To minimize manipulations we employed a temporary protecting group-free 2′-deoxyuridine to 2′-deoxycytidine conversion procedure that utilizes phase transfer catalysis. The desired 5-HOMedC phosphoramidite is obtained in six steps and 24% overall yield from 2′-deoxyuridine.
- Hansen, Anders S.,Thalhammer, Armin,El-Sagheer, Afaf H.,Brown, Tom,Schofield, Christopher J.
-
supporting information; experimental part
p. 1181 - 1184
(2011/04/16)
-
- Hydroxylation of methylated CpG dinucleotides reverses stabilisation of DNA duplexes by cytosine 5-methylation
-
Cytosine-5-methylation stabilises DNA duplexes and is associated with transcriptional repression; 5-methylcytosine undergoes hydroxylation to 5-hydroxymethylcytosine, a modification of unknown biological function. Spectroscopic and calorimetric analyses show that 5-hydroxymethylcytosine introduction reverses the stabilising effect of 5-methylcytosine, suggesting that in some contexts, 5-methylcytosine hydroxylation may, along with other factors, contribute to the alleviation of transcriptional repression.
- Thalhammer, Armin,Hansen, Anders S.,El-Sagheer, Afaf H.,Brown, Tom,Schofield, Christopher J.
-
supporting information; scheme or table
p. 5325 - 5327
(2011/06/21)
-
- Potent radiosensitizing agents: 5-Methylselenyl- and 5-phenylselenyl- methyl-2′-deoxyuridine
-
This Letter describes the novel radiosensitizing agents based on nucleoside base modification. In addition to the known 5-phenylselenide derivative, 5-methylselenide modified thymidine, which has a van der Waals radius smaller than the phenyl group, was newly synthesized. The similar monomer activity of 5-methylselenide derivative under oxidation condition was confirmed by NMR experiments. The cytotoxicity tests and radiosensitizing experiments of both compounds were carried out using the H460 lung cancer cell line. Both the 5-phenylselenide and the 5-methylselenide derivatives showed a relatively low toxicity to the cells. However, in combination with γ-radiolysis, both exerted good radiosensitizing effects to the lung cancer cell lines in vitro. This result confirms that 5-methylselenide modified thymidine could be a useful candidate as a potential radiosensitizing agent in vivo.
- Rode, Ambadas B.,Kim, Byeong Mo,Park, Seon Hwa,Hong, In Seok,Hong, Sung Hee
-
p. 1151 - 1154
(2011/04/16)
-
- 5-Modified-2'-dU and 2'-dC as mutagenic Anti HIV-1 proliferation agents: Synthesis and activity
-
With the goal of limiting HIV-I proliferation by increasing the mutation rate of the viral genome, we synthesized a series of pyrrolidine nucleoside analogues modified in position 5 of the aglycone moiety but unmodified on the sugar part. The synthetic strategies allow us to prepare the targeted compounds directly from commercially available nucleosides. All compounds were tested for their ability to reduce HIV-I. proliferation in cell culture. Two of them (5-hydroxymethyl-2'-dU (1c) and 5-hydroxymethyl-2'-dC (2c)) displayed a moderate antiviral activity in single passage experiments. The same two compounds plus two additional ones (5-carbamoyl-2'-dU (la) and 5-carbamoylmethyl-2'-dU (1b)) were potent, inhibitors of HIV-1 RT activity in serial passage assays, in which they induced a progressive loss of HIV-1 replication. In addition, viruses collected after seven passages in the presence of 1c and 2c replicated very poorly after withdrawal of these compounds, consistent with the accumulation of deleterious mutations in the HIV-1. genome.
- El Safadi, Yazan,Paillarte, Jean-Christophe,Laumond, Géraldine,Aubertin, Anne-Marie,Burger, Alain,Marquet, Roland,Vivet-Boudou, Valérie
-
experimental part
p. 1534 - 1545
(2010/07/09)
-
- Selective one-electron oxidation of duplex DNA oligomers: Reaction at thymines
-
The one-electron oxidation of duplex DNA generates a nucleobase radical cation (electron hole ) that migrates long distances by a hopping mechanism. The radical cation reacts irreversibly with H2O or O 2 to form oxidation products (damaged bases). In normal DNA (containing the four common DNA bases), reaction occurs most frequently at guanine. However, in DNA duplexes that do not contain guanine (i.e., those comprised exclusively of A/T base pairs), we discovered that reaction occurs primarily at thymine and gives products resulting from oxidation of the T-C5 methyl group and from addition to its C5-C6 double bond. This surprising result shows that it is the relative reactivity, not the stability, of a nucleobase radical cation that determines the nature of the products formed from oxidation of DNA. A mechanism for reaction is proposed whereby a thymine radical cation may either lose a proton from its methyl group or H2O/O2 may add across its double bond. In the latter case, addition may initiate a tandem reaction that converts both thymines of a TT step to oxidation products. The Royal Society of Chemistry.
- Ghosh, Avik,Joy, Abraham,Schuster, Gary B.,Douki, Thierry,Cadet, Jean
-
body text
p. 916 - 928
(2008/10/09)
-
- DNA interstrand cross-link formation initiated by reaction between singlet oxygen and a modified nucleotide
-
DNA is the target of many anti-cancer therapies. These agents damage the biopolymer by oxidation or by alkylation. Interstrand DNA cross-links are believed to be the source of cytotoxicity of anti-tumor agents, such as mitomycin C, which alkylate the biopolymer. In contrast, deoxyguanosine oxidation is the result of reaction between DNA and singlet oxygen, which is the damaging species produced in photodynamic therapy. We have shown that, upon oxidation by singlet oxygen, an analogue of thymidine (2) rearranges to a methide, which forms DNA-DNA interstrand cross-links. This novel process suggests that 2 may be a useful adjuvant in photodynamic therapy. Copyright
- Hong, In Seok,Greenberg, Marc M.
-
p. 10510 - 10511
(2007/10/03)
-
- Mild generation of 5-(2′-deoxyuridinyl)methyl radical from a phenyl selenide precursor
-
(Chemical Equation Presented) 5-(2′-Deoxyuridinyl)methyl radical (1) resulting from formal hydrogen atom abstraction from the methyl group of thymidine is produced from the respective phenyl selenide precursor (2) via 350 nm photolysis or mild thermolysis (37°C in the presence of glutathione) under aerobic or anaerobic conditions. The mild thermal generation of a nucleoside radical provides an alternative to previously reported photochemical methods, which are not always compatible with nucleic acids.
- In, Seok Hong,Greenberg, Marc M.
-
p. 5011 - 5013
(2007/10/03)
-
- Formation of a methide derivative upon photolysis of thymidine bromohydrins
-
Reaction of bromine with thymidine in aqueous solution produces, in high yield, the corresponding 5-bromo-6-hydroxy-5,6-dihydroderivative (thymidine bromohydrins). UVC photolysis of thymidine bromohydrins gives rise to a reactive intermediate that is converted into 5-(hydroxymethyl)-2′-deoxyuridine upon incubation in water. When the former compound is left in methanol, ethanol, or propanol, the corresponding 5-alkoxymethyl derivatives are produced. The proposed structure for the primary photolysis product of thymidine bromohydrins is a methide derivative of the thymine ring. This compound could be an interesting intermediate in the synthesis of methyl-substituted thymidine.
- Douki, Thierry,Vadesne-Bauer, Guillaume,Cadet, Jean
-
p. 478 - 482
(2007/10/03)
-
- Synthesis and UV photolysis of oligodeoxynucleotides that contain 5-(phenylthiomethyl)-2'-deoxyuridine: a specific photolabile precursor of 5-(2'-deoxyuridilyl)methyl radical.
-
[formula: see text] The title exocyclic radical (2) is generated via photochemical cleavage of 5-(phenylthiomethyl)-2'-deoxyuridine (8). The latter thionucleoside (8) was successfully incorporated into DNA oligomers by automated DNA synthesis using phosphoramidite chemistry. UV exposure of 8 containing oligonucleotides under (an)aerobic conditions gives rise to specific base lesions. The photoproducts have been isolated and further characterized on the basis of detailed NMR and mass spectrometric analyses.
- Romieu,Bellon,Gasparutto,Cadet
-
p. 1085 - 1088
(2007/10/03)
-
- Synthesis of oligodeoxynucleotides containing 5-(β-D- glucopyranosyloxymethyl)-2'-deoxyuridine, a modified nucleoside in the DNA of Trypanosoma brucei
-
The synthesis of the recently discovered modified DNA base 5-(β-D- glucopyranosyloxymethyl)-2'-deoxyuridine (β-dJ, 1) is described. TMSOTf mediated β-glucosylation of 5-hydroxymethyl-2'-deoxyuridine (5-HMdU) derivative 10 (obtained in 20% from 2'-deoxyuridine) with trichloroacetimidate 12 gave dimer 13 in 47% yield. On the other hand, condensation of 12 with N3-POM-protected derivative 20, readily available from thymidine in 48%, afforded the fully protected nucleoside 22 in 96% yield. The latter compound was converted into phosphoramidite 3 which was applied in the automated solid phase synthesis of several biological interesting β-dJ containing DNA fragments.
- De Kort, Martin,Ebrahimi, Edwin,Wijsman, Eric R.,Van Der Marel, Gijs A.,Van Boom, Jacques H.
-
p. 2337 - 2344
(2007/10/03)
-
- Synthesis and characterization of isotopically enriched pyrimidine deoxynucleoside oxidation damage products
-
Oxidative damage to DNA is an established source of genomic instability. In this paper, we describe the synthesis and characterization of several pyrimidine deoxynucleoside oxidation damage products, enriched with stable isotopes. These products include the 2'-deoxynucleoside derivatives of 5- (hydroxymethyl)uracil, 5-formyluracil, 5-hydroxyuracil, 5-(hydroxymethyl)- cytosine, 5-formylcytosine, and 5-hydroxycytosine. The common precursor is 2'-deoxy-2''-deutero[1,3-15N]uridine. Additional stable isotopes are added during functional group conversions. Characterization of these derivatives includes mass spectrometry and 1H and 15N NMR spectroscopy. Proton and nitrogen NMR studies reported here allow an examination of the influence of the modification on sugar conformation and tautomeric equilibrium, properties likely to be important in understanding the biological consequences of these DNA damage products.
- LaFrancois, Christopher J.,Fujimoto, June,Sowers, Lawrence C.
-
-
- Novel modification of 5-formyluracil by cysteine derivatives in aqueous solution
-
Reactivities of 5-formyl-2'-deoxyuridine (fdU) and its 5'-monophosphate (fdUMP) to amino acids, amines and thiol compounds in neutral aqueous solution have been studied to elucidate the postmodification of the 5- formyluracil (fU) moiety in cells. fdU and fdUMP specifically reacted with cysteine and its analogs to form thiazolidine derivatives. The reaction involved condensation of the formyl group of fU with both α-NH2(or NH2 at the equivalent position) and SH groups of cysteine derivatives.
- Terato, Hiroaki,Morita, Hajime,Ohyama, Yoshihiko,Ide, Hiroshi
-
p. 131 - 141
(2007/10/03)
-
- Peroxy radical oxidation of thymidine
-
The peroxy radical (ROO·) is unique among reactive oxygen species implicated in the production of DNA damage in that it possesses an extremely long half-life (order of seconds) and is predicted to have a relatively greater chemical selectivity in its reactions relative to other radical intermediates. Yet no product studies of the reactions of ROO· with bases, nucleosides, or DNA have appeared, and thus no meaningful predictions can be made regarding its potential involvement in the production of DNA base damage and the mutagenic process. We report here on the reaction products formed by peroxy radical with thymidine, a major target of oxidative base damage. ROO· reacts with thymine to yield predominantly 5-Me oxidation products. The highly mutagenic 5-(hydroperoxymethyl)-2'-deoxyuridine, 5-formyl-2'- deoxyuridine, and 5-(hydroxymethyl)-2'-deoxyuridine are produced by peroxy radical oxidation. In contrast, 5-Me oxidation products are minor products of thymidine oxidation by ·OH, which yields predominantly saturated derivatives via addition to the 5,6 double bond. A plausible mechanistic scheme for the formation of the base oxidation products of thymidine by peroxy radicals is presented. Attack at the deoxyribose moiety resulting in oxidative depyrimidination is also found to occur, as indicated by free base release. Phosphodiester backbone cleavage resulting in single and double strand breaks is also catalyzed by peroxy radical, as demonstrated using a plasmid nicking assay.
- Martini, Michela,Termini, John
-
p. 234 - 241
(2007/10/03)
-
- Oxidation of nucleic acid related compounds by the peroxodisulfate ion
-
The treatment of nucleic acid bases, nucleosides, and nucleotides with peroxodisulfate ion in a phosphate buffer solution at pH 7.0 or water at 70-75°C was investigated. The reaction of thymine and 5-methylcytosine nucleosides and nucleotides resulted in the oxidation of the 5-methyl groups. The oxidation products from 1,3-dimethyluracils and the time-course of the reaction of uracils led to two plausible reaction mechanisms for the oxidation of uracils.
- Itahara,Yoshitake,Koga,Nishino
-
p. 2257 - 2264
(2007/10/02)
-
- Reactions des radicaux 6-hydroxy-5,6-dihydrothymid-5-yles en solution aqueuse
-
The main reactions of 6-hydroxy-5,6-dihydrothymid-5-yl radicals, specifically obtained by electron capture dissociation of the trans diastereomers of 5-bromo-6-hydroxy-5,6-dihydrothymidine, were determined in aqueous solutions on the basis of final product analysis.In oxygen-free aqueous solutions a complex mixture of both monomeric and dimeric decomposition products was produced.It is worth mentioning the radiation-induced formation of modified nucleosides which involves the transient generation of 5-(2'-deoxyuridyl)methyl radical.This may be explained in terms of initial formation of 6-hydroxy-5,6-dihydrothymid-5-yl radicals, followed by dehydration and subsequent deprotonation.
- Berger, M.,Sarrazin, F.,Cadet, J.
-
p. 853 - 862
(2007/10/02)
-
- Oxidation of Thymidine by Peroxymono- and Peroxodisulfate Ions
-
Oxidation of thymidine by KHSO5 gave thymidine glycols, while a similar treatment with Na2S2O8 gave 5-hydroxymethyl-2'-deoxyuridine.
- Itahara, Toshio,Koga, Sunao
-
-
- Identification of the Products resulting from the Direct effects of γ-Radiation on Thymidine
-
The products formed upon γ-irradiation of thymidine in frozen aqueous solution have been identified.These products may all be explained in terms of the fates of now well documented primary charged radical species, and our results complement well those of previous e.s.r. studies on those primary and secondary radicals.In order to probe the mechanisms of formation of the major products, we have carried out experiments using heavy isotopes, including deuterium oxide and (18)O2.The radical cation undergoes both hydration, yielding the four isomers of 6-hydroxy-5,6-dihydrothymidine, and deprotonation at the methyl group to yield 5-hydroxymethyl-2'-deoxyuridine.As expected, the radical anion reacts primarily by protonation at C-6 to yield the (5R)- and (5S)-diastereoisomers of 5,6-dihydrothymidine and 5-hydroxy-5,6-dihydrothymidine.Excitation processes were shown to occur by the observation of the thymidine cyclobutane dimers.The release of significant amounts of thymine and 2-deoxy-D-ribono-1,4-lactone indicates the formation of radicals centred within the sugar moiety.The proposed role of the initial charged radicals in the formation of certain products has been supported by quantitative experiments carried out using compounds expected to be electron scavengers and electron donors with respect to thymidine.Finally, subsequent to our earlier paper on the e.s.r. identification of the radicals formed upon irradiation of thymidine bromohydrin in frozen aqueous solution, we have isolated the products formed on annealing and identified them as thymidine and 5-hydroxymethyl-2'-deoxyuridine.We discuss their mechanisms of formation.
- Shaw, Anthony A.,Voituriez, Lucienne,Cadet, Jean,Gregoli, Silvano,Symons, Martyn C.
-
p. 1303 - 1308
(2007/10/02)
-
- SYNTHESIS OF 6,5'-cyclo-2',5'-DIDEOXYPYRIMIDINE NUCLEOSIDES ( NUCLEOSIDES AND NUCLEOTIDES. LXXII )
-
6,5'-cyclo-2',5'-dideoxyuridine and 6,5'-cyclo-5'-deoxythymidine, pyrimidine deoxynucleosides fixed in the anti conformation were synthesized.The key intermediate, 3'-O-acetyl-5-chloro-2',5'-dideoxy-5'-iodouridine ( 12 ), prepared from 2'-deoxyuridine, was cyclized by treatment with tributyltin hydride to the 6,5'-cyclo derivative ( 13 ), then dehydrochlorinated to furnish, after de-O-acetylation, 6,5'-cyclo-2',5'dideoxyuridine ( 14 ).For the synthesis of 6,5'-cyclothymidine, 3'-O-acetyl-2',5'-dideoxy-5'-iodo-5-phenylthiomethyluridine ( 22 ) was prepared from 2'-deoxyuridine and this compound was cyclized by treatment with tributyltin hydride to yield, after de-O-acetylation 6,5'-cyclo-5'-deoxythymidine ( 24 ).Keywords - cyclonucleoside; C-cyclouridine; 6,5'-cyclo-2',5'-dideoxyuridine; 6,5'-cyclo-5'deoxythymidine; 5-bromo-6,5'-cyclo-2',5'-dideoxyuridine; radical cyclization; tributyltin hydride; NMR; CD
- Suzuki, Yukari,Matsuda, Akira,Ueda, Tohru
-
p. 1085 - 1092
(2007/10/02)
-
- Radiation-Induced Degradation of Purine and Pyrimidine 2'-Deoxyribonucleosides in Aqueous KBr Solutions
-
Steady-state γ-radiolysis of 5E-4 M pyrimidine and purine 2'-deoxyribonucleosides in aqueous solutions saturated with N2, N2O and O2, respectively, have been carried out in the presence of 0.1 M KBr.The main final degradation products have been isolated and characterised by various spectroscopic measurements including 1H and 13C NMR, UV, C.D. and mass spectrometry.The radiation-induced decomposition of thymidine is mostly accounted for by an ionic mechanism involving Br2, the decay product of Br2, as the reactive oxidising specie.On the other hand the degradation of the purine ring of 2'-deoxyadenosine and 2'-deoxyguanosine may be accounted for by the action of Br2 or Br3. - Keywords: 2'-Deoxyribonucleosides, Inorganic Radical, γ-Irradiation, Radical Reactions, Thymidine Oxidation
- Cadet, J.,Voituriez, L.,Berger, M.,Myers, L. S., (Jr.)
-
p. 1643 - 1651
(2007/10/02)
-
- Synthesis and Biological Activities of 5-(Hydroxymethyl, azidomethyl, or aminomethyl)-2'-deoxyuridine and Related 5'-Substituted Analogues
-
The synthesis of 5-(azidomethyl)-2'-deoxyuridine (10) has been accomplished by two independent methods.The first involved tosylation of 5-(hydroxymethyl)-2'-deoxyuridine (1) to furnish a mixture of two mono- and a ditosyl nucleosides which were converted into the corresponding 5-(azidomethyl) (10), 5-(azidomethyl)-5'-azido (14), and 5-(hydroxymethyl)-5'-azido (15) derivatives of 2'-deoxyuridine.The second method was more selective and required the formation of the intermediate 5-(bromomethyl)-3',5'-di-O-acetyl-2'-deoxyuridine (8), followed by displacement of the bromo group by lithium azide and deacetylation.Catalytic hydrogenation of the azides 9, 10, 14, and 15 gave the corresponding amines 16, 2, 6, and 7, repectively.Compounds 1, 2, 10, and 16 inhibited the growth of murine Sarcoma 180 and L1210 in culture, and the activity of 2 was prevented by 2'-deoxypyrimidine nucleosides by not by purine nucleosides.The replication of herpes simplex virus type 1 (HSV-1) was strongly inhibited only by 1 and 10.Studies on the binding of the various thymidine analogues to HSV-1 encoded pyrimidine deoxyribonucleoside kinase indicate that 1 and 10 have good affinity for the enzyme.
- Shiau, George T.,Schinazi, Raymond F.,Chen, Ming S.,Prusoff, William H.
-
p. 127 - 133
(2007/10/02)
-