Methylation of thymine and uracil with free methyl cations formed due to beta-decay of tritiated methane: possible implication in mutagenesis and carcinogenesis

Exposure of solid thymine and uracil at room temperature to free methyl cations, produced due to beta-decay of tritiated methane, resulted in formation of their 1-, O2-, 3-, O4-, and 6-methyl derivatives. In addition, uracil formed a 5-methyl derivative (thymine); tritium-containing thymine and uracil were also detected. Both thymine and uracil formed predominantly unidentified products which resulted presumably from their oligomerization. Incubation at -195 degrees C did not markedly change the pattern of reaction products. Aqueous-ammonia solutions of these pyrimidines formed methylated derivatives and considerable amounts of methanol and tritiated water. The possible implication of these reactions in mutagenic and carcinogenic effects of tritium-substituted hydrocarbons is discussed.     

Interfacial behavior of uracil derivatives

The adsorption of a number of methylated uracil derivatives and of 5-fluorouracil has been studied by surface electrochemical methods at a mercury electrode. All derivatives exhibit an initial or dilute adsorption region where they are adsorbed flat on the electrode surface and are bound by pi-electron overlap with the electrode. Uracil, thymine, 1,5-dimethyl-uracil, 5,6-dimethyluracil, 1,5,6-trimethyluracil and 5-fluorouracil undergo a surface reorientation from the initial flat solution activities for each compound. An unsubstituted N(3)-H group is an absolute requirement for a uracil derivative to be capable of adopting the perpendicular surface stance. In the perpendicular orientation the uracil derivative appears to be bound to the electrode primarily via a N(3)-H--(-) electrode bond although a similar but weaker hydrogen bond can be formed via the N(1)-H group for certain compounds.     

Reaction of Bromotrichloromethane Derived Free Radicals with Uracil in a Model System. Structures of Products Formed

Free radicals generated by benzoyl peroxide-mediated catalytic decomposition of bromotrichloromethane (eg. trichloromethyl) were allowed to react under nitrogen or under air with uracil. Under nitrogen two reaction products were formed, one was identified as 5-chlorouracil and the other as a 5-bromouracil. Under air, besides the above two products other nine were also formed: 5,6-dihydrouracil; 5-hydroxyuracil; a chlorohydroxy adduct of uracil; a bromohydroxy derivative of uracil having the 5,6 bond in the saturated form; other bromohydroxy derivative of uracil having the double bond intact; 5,6-dihydroxyuracil; two dihalogenated hydroxylated uracil derivatives and one peak we were not able to descipher its structure. No single reaction product formed had carbon centered radicals (eg. trichloromethyl) added from CBrCl₃ and consequently would be missed in 'in vivo' covalent binding studies where ^l4C haloalkane (CBrCl₃ or carbon tetrachloride) were employed. If similar reaction products resulted during interaction of CBrCl₃ reactive metabolites with uracil in RNAs, significant deleterious effects in their function would be expected. That possibility, however, remains to be established.     

E.s.r. of free radicals in aqueous solutions of substituted pyrimidines.

Reactions of OH radicals with methyl and ethyl derivatives of uracil, cytosine and thymine in aqueous solutions have been investigated. Photolysis of H2O2 was used to generate OH radicals and the radicals on the base derivatives were spin-trapped using t-nitrosobutane and identified with the help of e.s.r. spectroscopy. Addition of OH radicals was found to take place predominantly to the C(5)--C(6) double bond of the bases. H-abstraction from the methyl group occurred in the N(1) methyl derivatives of uracil, cytosine and thymine. Radicals formed by H-abstraction from the methyl group were also detected for 3-methyluracil, thymine, 1-methylthymine and 1-ethylthymine. Introduction of a methyl or ethyl group at the N(1) position of uracil, cytosine and thymine causes an increase in the C(6) proton coupling and a decrease in the N(1) splitting for radicals formed by OH addition at the C(5) position.     

The synthesis of [([beta-D-ribofuranosyloxy)methyl]nucleosides

The coupling reaction of acetoxymethoxy ribofuranoside 4 with nucleic acid bases 5a-f to synthesize novel (ribofuranosyloxy)methyl uracil, thymine, cytosine, adenine, guanine derivatives 6a-g respectively in preference to the expected formation of natural nucleosides 2',3',5'-tri-O-benzoyl uridine, methyluridine, cytidine, adenosine and guanosine 7a-g is described. Detailed study of these reactions catalysed by Lewis acids TMSOTf and SnCl4 is described. TMSOTf exhibited selectivity for the formation of ribofuranosyloxy methyl derivatives 6a-g rather than 7a-g. Reason for formation of 6a-g is explained by HSAB principle.     

Potential and structure controlled interfacial behavior of uracil derivatives

The adsorption and related interfacial behavior of uracil, various methylated uracil derivatives, uridine, uridine-5'-monophosphate and uridine-3'5'-cyclic monophosphate has been studied by surface electrochemical measurements at a mercury electrode. All uracil derivatives exhibit an initial "dilute" adsorption region where the virtually flat uracil residue is absorbed flat on the electrode surface. In the case of uracil and its methylated derivatives the area occupied by one molecule is about 60-70 A2. Uracil, thymine and 1,5-dimethyluracil exhibit a second adsorption region where they rearrange on the surface and adopt a perpendicular orientation and occupy about 40 A2 per molecule. In this perpendicular orientation the uracils are bound to the electrode through the N(3)-H or perhaps N(1)-H functions in a manner similar to their Watson-Crick bonding in nucleic acids. When in the perpendicular orientation the adsorbed molecules undergo extensive stacking (association) interactions, again similar to those observed between adjacent bases in nucleic acids. The ability of a uracil derivative to undergo a surface reorientation is critically dependent on electrode potential, bulk-solution concentration and molecular structure.     

Differences in substrate specificity of C(5)-substituted or C(5)-unsubstituted pyrimidine nucleotides by DNA polymerases from thermophilic bacteria, archaea, and phages

The pyrimidine bases of RNA are uracil (U) and cytosine (C), while thymine (T) and C are used for DNA. The C(5) position of C and U is unsubstituted, whereas the C(5) of T is substituted with a Me group. Miller et al. hypothesized that various C(5)-substituted uracil derivatives were formed during chemical evolution, and that C(5)-substituted U derivatives may have played important roles in the transition from an 'RNA world' to a 'DNA-RNA-protein world'. Hyperthermophilic bacteria and archaea are considered to be primitive organisms that are evolutionarily close to the universal ancestor of all life on earth. Thus, we examined the substrate specificity of several C(5)-substituted or C(5)-unsubstituted dUTP and dCTP analogs for several DNA polymerases from hyperthermophilic bacteria, hyperthermophilic archaea, and viruses during PCR or primer extension reaction. The substrate specificity of the C(5)-substituted or C(5)-unsubstituted pyrimidine nucleotides varied greatly depending on the type of DNA polymerase. The significance of this difference in substrate specificity in terms of the origin and evolution of the DNA replication system is discussed briefly.     

Unique misinsertion specificity of poliota may decrease the mutagenic potential of deaminated cytosines

DNA polymerase iota (poliota) is a distributive error-prone enzyme that can incorporate nucleotides opposite a variety of DNA lesions. Further elongation is, however, either substantially inhibited or completely abolished. Here, we provide evidence that poliota can facilitate the efficient bypass of uracil and its derivatives as well as oxidized cytosine and guanine residues. The fidelity of translesion replication depends upon the lesion encountered. Correct nucleotides were inserted preferentially opposite 7,8-dihydro-8-oxoguanine (8-oxoG) and 5-hydroxycytosine (5-OHC). However, when bypassing uracil, 5-hydroxyuracil (5-OHU) or 5,6-dihydrouracil (5,6-DHU), poliota inserted T and G with a 4- to 26-fold preference over the Watson-Crick base, A. While the T:U, T:5-OHU and T:5,6-DHU mispairs were extended poorly, the G:U, G:5-OHU and G:5,6-DHU mispairs were extended with equal or greater efficiency than the correctly paired primer termini. Thus, poliota-dependent misinsertion of G opposite uracil and its derivatives may actually provide a mechanism whereby mammalian cells can decrease the mutagenic potential of lesions formed via the deamination of cytosine.     

Synthesis of 1-(2-hydroxy-3-methoxypropyl)uracils and their activity against L1210 and macrophage raw 264.7 cells

The title compounds were obtained from appropriate 5-substituted uracil derivatives and 1,2-oxy-3-methoxypropane in the presence of sodium hydride. Under similar conditions 5-iodouracil gave 2-methoxymethyl-2,3-dihydro-oxazolo[3,2-c]pyrimidine-5,7-dione as a result of intramolecular cine type nucleophilic substitution. Cytotoxicity of 1-(2-hydroxy-3-methoxypropyl)-5-substituted uracil derivatives against L1210 and macrophage RAW 264.7 cells in vitro was examined.     

Novel activities of human uracil DNA N-glycosylase for cytosine-derived products of oxidative DNA damage.

Uracil DNA N-glycosylase is a repair enzyme that releases uracil from DNA. A major function of this enzyme is presumably to protect the genome from pre-mutagenic uracil resulting from deamination of cytosine in DNA. Here, we report that human uracil DNA N-glycosylase also recognizes three uracil derivatives that are generated as major products of cytosine in DNA by hydroxyl radical attack or other oxidative processes. DNA substrates were prepared by gamma-irradiation of DNA in aerated aqueous solution and incubated with human uracil DNA N-glycosylase, heat-inactivated enzyme or buffer. Ethanol-precipitated DNA and supernatant fractions were then separated. Supernatant fractions after derivatization, and pellets after hydrolysis and derivatization were analyzed by gas chromatography/isotope-dilution mass spectrometry. The results demonstrated that human uracil DNA N-glycosylase excised isodialuric acid, 5-hydroxyuracil and alloxan from DNA with apparent K(m) values of approximately 530, 450 and 660 nM, respectively. The excision of these uracil analogues is consistent with the recently described mechanism for recognition of uracil by human uracil DNA N-glycosylase [Mol,C.D., Arval,A.S., Slupphaug,G., Kavil,B., Alseth,I., Krokan,H.E. and Tainer,J.A. (1995) Cell, 80, 869-878]. Nine other pyrimidine- and purine-derived products that were identified in DNA samples were not substrates for the enzyme. The results indicate that human uracil DNA N-glycosylase may have a function in the repair of oxidative DNA damage.     

Microbiological assay of purines

A sensitive microbiological assay for purine bases and derivatives is described which depends on purine-limited incorporation of [³H]uracil into E. coli double auxotrophs for uracil and specific bases.     

E.s.r. of spin-trapped radicals in gamma-irradiated aqueous solutions of nucleic acids and their constituents.

The gamma-radiolysis of de-aerated neutral aqueous solutions of uracil, thymine, cytosine and of the corresponding nucleosides and nucleotides and of calf-thymus DNA was investigated. For uracil and thymine, the U.V. photolysis of aqueous solutions containing H2O2 was also studied. The short-lived radicals were spin-trapped by tert-nitrosobutane and identified by electron-spin-resonance spectroscopy. For all compounds two or more radicals were observed, and these could be distinguished by following the thermal decay of the spin adducts. Radicals formed by the addition of H or OH at the C(5) or C(6) positions of the pyrimidine derivatives were observed in all cases. Sodium formate was used as a scavenger for H and OH to identify the radicals formed by eaq-. Spin-trapped radicals in gamma-irradiated aqueous solutions of polynucleotides exhibited broad e.s.r. lines. For DNA gel, additional narrow lines due to scission products were also found.     

The dehalogenation of halouracils by hydroxylamine buffers.

At room temperature, hydroxylamine dehalogenates 5-Br-and 5-I-uracil. 5-Cl-uracil reacts to a much less extent. Reaction with 5-F-uracil yields the 6-hydroxyamino-adduct as a product. Kinetics monitored spectrally indicate that dehalogenation involves the formation of a 5-halo-6-hydroxyamino-5, 6-dihydrouracil intermediate which then slowly dehalogenates. 5-Bromo-6-methoxy-5,6-dihydrothymine, a model for the above intermediate, also dehalogenates yielding thymine as a product.Hydroxylamine (NH₂OH), a mutagenic agent (1,2) reacts with pyrimidine rings promoting such reactions as the formation of 5,6-dihydro-N⁴-hydroxy-6-hydroxyaminocytosine from cytosine (3,4) and both urea and isoxazoles from uracil derivatives (2,5,6). It is believed to be unreactive toward 5-substituted uracil derivatives (2,5,6) but has been reported to cause the dehalogenation of 5-bromouracil derivatives yielding Br^? and uracil as products (2,7,8). The object of this report is to demonstrate the generality of NH₂OH addition to the 5-halouracils with the subsequent dehalogenation of both 5-Br-and 5-I-uracil; reactions which appear to proceed via pathways similar to bisulfite buffer mediated halouracil dehalogenation (9–13). A preliminary report of this work has appeared (14).     

SYNTHESIS OF 1-(2-HYDROXY-3-METHOXYPROPYL)URACILS AND THEIR ACTIVITY AGAINST L1210 AND MACROPHAGE RAW 264.7 CELLS

ABSTRACT

The title compounds were obtained from appropriate 5-substituted uracil derivatives and 1,2-oxy-3-methoxypropane in the presence of sodium hydride. Under similar conditions 5-iodouracil gave 2-methoxymethyl-2,3-dihydro-oxazolo[3,2-c]pyrimidine-5,7-dione as a result of intramolecular cine type nucleophilic substitution. Cytotoxicity of 1-(2-hydroxy-3-methoxypropyl)-5-substituted uracil derivatives against L1210 and macrophage RAW 264.7 cells in vitro was examined.     

Synthesis and antiproliferative activity of some 4'-C-hydroxymethyl-alpha- and -beta-D-arabino-pentofuranosyl pyrimidine nucleosides

A suitably protected 4-C-hydroxymethyl-arabino-pentofuranose was prepared and condensed with the following nucleobases: uracil, 5-fluorouracil and thymine. The corresponding cytosine and 5-fluorocytosine derivatives have also been obtained respectively from the uracil and 5-fluorouracil nucleosides. Separation of the anomeric mixtures followed by deprotection afforded the target compounds that were found to be non-cytotoxic to CCRF-CEM leukemia cells.     

SYNTHESIS AND ANTIPROLIFERATIVE ACTIVITY OF SOME 4′-C-HYDROXYMETHYL-α- AND -β-D-ARABINO-PENTOFURANOSYL PYRIMIDINE NUCLEOSIDES

A suitably protected 4-C-hydroxymethyl-arabino-pentofuranose was prepared and condensed with the following nucleobases: uracil, 5-fluorouracil and thymine. The corresponding cytosine and 5-fluorocytosine derivatives have also been obtained respectively from the uracil and 5-fluorouracil nucleosides. Separation of the anomeric mixtures followed by deprotection afforded the target compounds that were found to be non-cytotoxic to CCRF-CEM leukemia cells.     

Synthesis of 5-Arylthiouridines via Electrophilic Substitution of 5-Bromouridines with Diaryl Disulfides

Abstract

Novel synthetic method of 5-arylthiouridine derivatives is described. Treatment of 5-bromo-2′,3′-O-isopropylideneuridine (1a) with diaryl disulfides in the presence of sodium hydride at ambient temperature gave the 5-arylthiouridines (2) in moderate yields. The present method is devised by virtue of a combination of efficient participation of the 5′-hydroxy group onto the uracil ring and the electrophilic nature of diaryl disulfide, which was applied to the synthesis of 5-arylthio-1-β-D-arabinofuranosyl-uracils (8).     

Synthesis, conformation and enzymatic properties of 1-(beta-D-allofuranosyl)uracil and some derivatives.

A new route for the synthesis of 1-(beta-D-allofuranosyl)uracil ("allo-uridine") and the corresponding 6'-deoxy-derivative ("6'-deoxy-allo-uridine") as well as for 1-(beta-D-altrofuranosyl) uracil ("altro-uridine") is described. NMR studies of allo-uridine revealed a preferred conformation with the base in anti-position, C-2'-endo-pucker of the sugar moiety, the 5'-OH-group above the furanose ring and the 5'-CH2OH-group in a gt position with the OH-group in the plane of the furanose ring. The same conformation is found for the 5'- and 6'-phosphate, indicated by the influence of the phosphate group on the H-6 signal. Allo-uridine is phosphorylated by the phosphotransferases from carrot and from malt sprouts only in the 6'-position. The phosphate ester is hydrolysed by unspecific phosphatases but not by 5'-nucleotidase. A (3' leads to 6')-dinucleoside phosphate is formed by pancreatic ribonuclease with 2',3'-cyclic cytidylic acid and allo-uridine. It is split by nuclease S1, but not by snake-venom phosphodiesterase. It has no primer activity for polynucleotide phosphorylase. All-uridine 6'-diphosphate could not be prepared enzymatically by nucleotide kinase or by chemical methods, where 5',6'-cyclic phosphates are formed, which are hydrolysed exclusively to 6'-monophosphates.     

Luminescence of stable stacking aggregates of adenine and uracil in water

Luminescence and excitation spectra of the highly luminescent stacking dimers of adenine and uracil in water solutions are studied. By the luminescence excitation spectra method it is shown that the stacking aggregates of adenine and uracil are formed with participation of rare forms of monomer molecules: N7H tautomers of adenine and the uracil molecules in rare forms of hydratation, for example molecules without H-bonds with water. The study of temperature dependence of luminescence intensity of monomers and stacking dimers of uracil has shown that stacking dimers do not dissociate even at 85 degrees C similarly as described earlier for adenine and adenosine. Stable stacking aggregates of nucleic bases are most likely to be the precursors of RNA molecules in chemical evolution. This hypothesis is supported by new data on their stability.     

Acetic anhydride requirement in the colorimetric determination of tryptophan

Nucleic acid research frequently necessitates the analytical resolution of nucleic acid derivatives. Thin-layer chromatography (tlc), for its simplicity, short development time, and superior resolving power, is often preferable to other methods (1–3). Although the literature contains a large number of methods that have been devised for the separation of purine and pyrimidine derivatives (4,5) no tlc technique has hitherto been described for the concomitant separation of bases, nucleosides, nucleoside 5′-monophosphates, nucleoside 3′-monophosphates, nucleoside diphosphates, and nucleoside triphosphates.The present communication deals with methods devised for the simultaneous separation of the above-mentioned pyrimidine derivatives. They enable the resolution of either the six uracil derivatives or the six cytosine derivatives, on commercial cellulose tlc sheets. Alternatively, the six pyrimidine derivatives can be separated on cellulose layers 0.75 mm thick. Since formic acid extracts of bacterial cells do not interfere with the separation, these methods can be used for the direct estimation of extracts of biological materials.