Characterization of Labeled Residues from 5-Diazouracil-2-C Incorporated into Ribonucleic Acids of Filamentous Escherichia coli

E. coli B, filamented with 5-diazouracil (DZU)-2-¹⁴C, yielded ribonucleic acid (RNA)-(DZU-2-¹⁴C) which was converted by pancreatic ribonuclease to ¹⁴C-mono-and oligo-nucleotides. The mixed ¹⁴C-mononucleotides isolated by diethylaminoethyl-cellulose fractionation were identified as cytidylic, uridylic, and hydroxyuridylic acids, by using a combination of paper chromatography and treatment with alkaline phosphatase and cytidine deaminase. Rifampin blocked incorporation of DZU-2-¹⁴C under conditions which inhibit RNA synthesis. Division inhibition by DZU-2-¹⁴C and the incorporation into Escherichia coli B were retarded by uracil but not by other RNA bases. In a pyrimidine-requiring E. coli, DZU substituted for uracil or cytosine to an extent limited by toxic effects. Cytosine and uracil retarded these effects and retarded the incorporation of DZU-2-¹⁴C into the pyrimidineless strain. A small proportion of DZU-2-¹⁴C was converted by the latter strain into hydroxyuridylic acid, but the bulk of the incorporated label was in cytidylic and uridylic acid, as in the wild strain.     

Removal of uracil by uracil DNA glycosylase limits pemetrexed cytotoxicity: overriding the limit with methoxyamine to inhibit base excision repair

Uracil DNA glycosylase (UDG) specifically removes uracil bases from DNA, and its repair activity determines the sensitivity of the cell to anticancer agents that are capable of introducing uracil into DNA. In the present study, the participation of UDG in the response to pemetrexed-induced incorporation of uracil into DNA was studied using isogenic human tumor cell lines with or without UDG (UDG^+/+/UDG^−/−). UDG^−/− cells were very sensitive to pemetrexed. Cell killing by pemetrexed was associated with genomic uracil accumulation, stalled DNA replication, and catastrophic DNA strand breaks. By contrast, UDG^+/+ cells were >10 times more resistant to pemetrexed due to the rapid removal of uracil from DNA by UDG and subsequent repair of the resultant AP sites (abasic sites) via the base excision repair (BER). The resistance to pemetrexed in UDG^+/+ cells could be reversed by the addition of methoxyamine (MX), which binds to AP sites and interrupts BER pathway. Furthermore, MX-bound AP sites induced cell death was related to their cytotoxic effect of dual inactivation of UDG and topoisomerase IIα, two genes that are highly expressed in lung cancer cells in comparison with normal cells. Thus, targeting BER-based therapy exhibits more selective cytotoxicity on cancer cells through a synthetic lethal mechanism.     

Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil

Archaeal family-B DNA polymerases bind tightly to deaminated bases and stall replication on encountering uracil in template strands, four bases ahead of the primer-template junction. Should the polymerase progress further towards the uracil, for example, to position uracil only two bases in front of the junction, 3′–5′ proof-reading exonuclease activity becomes stimulated, trimming the primer and re-setting uracil to the +4 position. Uracil sensing prevents copying of the deaminated base and permanent mutation in 50% of the progeny. This publication uses both steady-state and time-resolved 2-aminopurine fluorescence to show pronounced unwinding of primer-templates with Pyrococcus furiosus (Pfu) polymerase–DNA complexes containing uracil at +2; much less strand separation is seen with uracil at +4. DNA unwinding has long been recognized as necessary for proof-reading exonuclease activity. The roles of M247 and Y261, amino acids suggested by structural studies to play a role in primer-template unwinding, have been probed. M247 appears to be unimportant, but 2-aminopurine fluorescence measurements show that Y261 plays a role in primer-template strand separation. Y261 is also required for full exonuclease activity and contributes to the fidelity of the polymerase.     

Purine and pyrimidine metabolism in cultured white spruce (Picea glauca) cells: Metabolic fate of 14C-labeled precursors and activity of key enzymes

In order to examine the biosynthesis, interconversion, and degradation of purine and pyrimidine nucleotides in white spruce cells, radiolabeled adenine, adenosine, inosine, uracil, uridine, and orotic acid were supplied exogenously to the cells and the overall metabolism of these compounds was monitored. [8‐¹⁴C]adenine and [8‐¹⁴C]adenosine were metabolized to adenylates and part of the adenylates were converted to guanylates and incorporated into both adenine and guanine bases of nucleic acids. A small amount of [8‐¹⁴C]inosine was converted into nucleotides and incorporated into both adenine and guanine bases of nucleic acids. High adenosine kinase and adenine phosphoribosyltransferase activities in the extract suggested that adenosine and adenine were converted to AMP by these enzymes. No adenosine nucleosidase activity was detected. Inosine was apparently converted to AMP by inosine kinase and/or a non‐specific nucleoside phosphotransferase. The radioactivity of [8‐¹⁴C]adenosine, [8‐¹⁴C]adenine, and [8‐¹⁴C]inosine was also detected in ureide, especially allantoic acid, and CO₂. Among these 3 precursors, the radioactivity from [8‐¹⁴C]inosine was predominantly incorporated into CO₂. These results suggest the operation of a conventional degradation pathway. Both [2‐¹⁴C]uracil and [2‐¹⁴C]uridine were converted to uridine nucleotides and incorporated into uracil and cytosine bases of nucleic acids. The salvage enzymes, uridine kinase and uracil phosphoribosyltransferase, were detected in white spruce extracts. [6‐¹⁴C]orotic acid, an intermediate of the de novo pyrimidine biosynthesis, was efficiently converted into uridine nucleotides and also incorporated into uracil and cytosine bases of nucleic acids. High activity of orotate phosphoribosyltransferase was observed in the extracts. A large proportion of radioactivity from [2‐¹⁴C]uracil was recovered as CO₂ and β‐ureidopropionate. Thus, a reductive pathway of uracil degradation is functional in these cells. Therefore, white spruce cells in culture demonstrate both the de novo and salvage pathways of purine and pyrimidine metabolism, as well as some degradation of the substrates into CO₂.     

Polymethylene derivatives of nucleic bases with ω-functional groups: VII. Cytotoxicity in the series of <Emphasis Type="Italic">N</Emphasis>-(2-oxocyclohexyl)-ω-oxoalkyl-substituted purines and pyrimidines

New polymethylene derivatives of the nucleic bases with β-diketo function in the ω-position have been synthesized by alkylation of uracil, thymine, cytosine, hypoxanthine, adenine, and N ²-isobutyryl guanine with 2-(ω-chloroalkanoyl)cyclohexanones. The physicochemical characteristics of compounds synthesized and their effect on tumor K562 and HCT116 cell lines have been studied.     

Measurement of urinary pyrimidine bases and nucleosides by high-performance liquid chromatography

A rapid procedure for the isolation, separation, identification and measurement of urinary pyrimidine bases and nucleosides by high-performance liquid chromatography (HPLC) is presented. The initial isolation of these compounds from urine was accomplished with small disposable ion-exchange columns. HPLC was performed on a silica gel column with a mobile phase composed of methylene chloride, methanol and 1 M aqueous ammonium formate buffer. Peaks were recorded at both 254 nm and 280 nm and the response ratio was used in conjunction with the elution volume for compound identification. The minimum detectable amount (signal-to-noise ratio = 2) ranged from 0.2 ng for uracil to 2.2 ng for cytidine. Linearity and recovery for thymine, uracil, uridine, pseudouridine, orotic acid and orotidine added to urine was demonstrated over almost a 10³ concentration range. The potential application of this method for the study of inborn errors in the urea cycle is discussed.     

One-dimensional separation of nine DNA bases on strong cation-exchange thin-layers.

In contrast to the large number of base modifications in RNA, only a limited number of modified bases have been identified in DNA. 5-Methyl-cytosine and N⁶-methyl-adenine have been found to be minor components. On the other hand, in some bacteriophages complete replacement of one of the pyrimidines occurs: 5-methylcytosine or 5-hydroxymethyl-cytosine replaces cytosine and uracil and 5-hydroxymethyl-uracil substitutes for thymine (1). ¹N-thyminylputrescine (2) and dihydroxypentyluracil (3) have been isolated from bacteriophages ΦW-14 and SP-15. The present paper does not deal with these compounds.     

A smiple specific assay for uracil tRNA methylases of enteric bacteria: use of ribothymidine-deficient tRNA

A simple quantitative assay that is about 95% specific for uracil tRNA methylases of E. coli and A. aerogenes has been developed. tRNA was isolated from a strain of E. coli carrying the trm^? mutation. These organisms have a low level of uracil methylase and consequently produce tRNA with a selective deficiency of ribothymidine. This RNA acted as a specific substrate for uracil tRNA methylases, when exposed to cell extracts from E. coli or A. aerogenes containing tRNA-methylating enzymes of multiple specificities. This assay can be used to screen organisms for trm^? mutations and for studies with inhibitors.     

DNA intermediates at the Escherichia coli replication fork. II. Studies using dut and ung mutants in vitro.

The incorporation of uracil into and excision from DNA were studied in vitro using lysates on cellophane discs made from Escherichia coli strains with defects in the enzymes dUTPase (dut) and uracil-DNA glycosylase (ung).Results with dut ung lysates indicate that dUTP is competitively incorporated with dTTP at the replication fork. Such incorporation is not due to DNA polymerase I. There is a mild discrimination (2.5-fold) against incorporation of dUTP versus dTTP. These data, together with in vivo uracil incorporation data (Tye et al., 1978) permit a rough estimate of the pool of dUTP in vivo (~0.5% of the dTTP pool).These in vitro data indicate that uracil-DNA glycosylase is the initial step in at least 90% of uracil excision events. However, in a strain defective in uracil-DNA glycosylase (ung-1), uracil-containing DNA is still more subject to single-strand scission than non-uracil-containing DNA, albeit at a rate at least tenfold less than in an ung⁺ strain.A number of qualitative statements may also be made about different steps in uracil incorporation and subsequent excision and repair events. When high levels of dUTP are added in vitro, a dut ung⁺ strain has a higher steady-state level of uracil in newly synthesized DNA than does an isogenic dut⁺ ung strain. Thus the dUTPase in these lysates has a higher capacity to be overloaded than does the excision system (i.e. uracil DNA glycosylase). However, the DNA sealing system (presumably DNA polymerase I and DNA ligase) apparently can handle all single-strand interruptions being introduced by uracil excision at the maximal rate, at least so that DNA synthesis can continue.     

Errata

Mutants of Escherichia coli K-12 which are defective in components of transport systems for uracil and uridine were isolated and utilized to characterized the transport mechanism of uracil and uridine. Mutant U^?, isolated from a culture of the parent strain, is resistant to 5-fluorouracil and is deficient in the uracil transport system. Mutant UR^?, isolated from a culture of the parent strain, is resistant to a low concentration of showdomycin and lacks the capacity to transport intact uridine. Mutant U^?UR^?isolated from a culture of mutant U^?, is resistant to a low concentration of showdomycin and is defective in both uracil and intact uridine transport processes. Mutant UR^?R^? was isolated from a culture of mutant UR^?, and is resistant to high concentration of showdomycin. This mutant is defective for transport of intact uridine and in addition lacks the transport system for the ribose moiety of uridine. Characteristics of uracil and uridine transport in parent and mutant cells demonstrate the existence of specific transport processes for uracil, intact uridine and the uracil and ribose moieties of uridine. Mutants U^? and UR^?, which are defective for uracil transport, lack uracil phosphoribosyltransferase activity and retain a small but significant capacity to transport uracil. The data support the conclusion that uracil is transported by two mechanisms, the major one of which requires uracil phosphoribosyltransferase activity, while the other process involves the transport of uracil as such. The characteristics of uridine transport in parent and mutant strains show that, in addition to transport as the intact nucleoside, uridine is rapidly cleaved to the uracil and ribose moieties. The latter is transported into the cell by a process which, in contrast to transport of intact uridine, does not require an energy source. The uracil moiety is released into the medium and is transported by the uracil transport system. Whole cells of the parent and mutant strains differ in their ability to cleave uridine even though cell-free extracts of all the strains have similar uridine phosphorylase activity. The data implicate a uridine cleavage enzyme in a group transport of the ribose moiety of uridine, a process which is nonfunctional in mutants which lack the capacity to transport the ribose moiety of uridine. A common transport component for this process and the transport of intact uridine is indicated by similarities in the inhibitory effects of heterologous nucleosides on these process.     

A robust,sensitive assay for genomic uracil determination by LC/MS/MS reveals lower levels than previously reported

Considerable progress has been made in understanding the origins of genomic uracil and its role in genome stability and host defense; however, the main question concerning the basal level of uracil in DNA remains disputed. Results from assays designed to quantify genomic uracil vary by almost three orders of magnitude. To address the issues leading to this inconsistency, we explored possible shortcomings with existing methods and developed a sensitive LC/MS/MS-based method for the absolute quantification of genomic 2′-deoxyuridine (dUrd). To this end, DNA was enzymatically hydrolyzed to 2′-deoxyribonucleosides and dUrd was purified in a preparative HPLC step and analyzed by LC/MS/MS. The standard curve was linear over four orders of magnitude with a quantification limit of 5 fmol dUrd. Control samples demonstrated high inter-experimental accuracy (94.3%) and precision (CV 9.7%). An alternative method that employed UNG2 to excise uracil from DNA for LC/MS/MS analysis gave similar results, but the intra-assay variability was significantly greater. We quantified genomic dUrd in Ung^+/+ and Ung^?/? mouse embryonic fibroblasts and human lymphoblastoid cell lines carrying UNG mutations. DNA-dUrd is 5-fold higher in Ung^?/? than in Ung^+/+ fibroblasts and 11-fold higher in UNG2 dysfunctional than in UNG2 functional lymphoblastoid cells. We report approximately 400–600 dUrd per human or murine genome in repair-proficient cells, which is lower than results using other methods and suggests that genomic uracil levels may have previously been overestimated.     

Structural basis for uracil DNA glycosylase interaction with uracil: NMR study

Two dimensional (2D) NMR and molecular dynamics simulations have been used to determine the three dimensional (3D) structure of a hairpin DNA, d-CTA-GAGGATCC-TUTT-GGATCCT (22mer; abbreviated as U2-hairpin), which has uracil at the second position from the 5′ end of the tetraloop. The ¹H resonances of this hairpin have been assigned almost completely. NMR restrained molecular dynamics and energy minimization procedures have been used to describe the 3D structure of U2-hairpin. This study establishes that the stem of the hairpin adopts a right-handed B-DNA conformation, while the T₁₂ and T₁₅ nucleotides stack upon 3′ and 5′ ends of the stem, respectively. Further, T₁₄ stacks upon both T₁₂ and T₁₅. Though U₁₃ partially stacks upon T₁₄, no stacking interaction is observed between U₁₃ and T₁₂. All the individual nucleotide bases belonging to the stem and T₁₂ and T₁₅ of the loop adopt ‘anti’ conformation with respect to their sugar moiety, while the U₁₃ and T₁₄ of the loop are in ‘syn’ conformation. The turning phosphate in the loop is located between T₁₃ and T₁₄. This study and a concurrent NMR structural study on yet another hairpin DNA d-CTAGAGGAATAA-TTTU-GGATCCT (22mer; abbreviated as U4-hairpin), with uracil at the fourth position from the 5′ end of the tetraloop throw light upon various interactions which have been reported between Escherichia coli uracil DNA glycosylase (UDG) and uracil containing DNA. The of T₁₂ and α, β, γ, and ζ of U₁₃ and γ of T₁₄, which partially influence the local conformation of U₁₃ in U2-hairpin are all locked in ‘trans’ conformation. Such stretched out backbone conformation in the vicinity of U₁₃ could be the reason as to why the U2-hairpin is found to be the poor substrate for its interaction with UDG compared to the other substrates in which the uracil is at first, third and fourth positions of the tetraloop from its 5′ end, as reported earlier by Vinay and Varshney. This study shows that UDG actively promotes the flipping of uracil from a stacked conformation and rules out the possibility of UDG recognizing the flipped out uracil bases.     

Unique Substrate Spectrum and PCR Application of Nanoarchaeum equitans Family B DNA Polymerase

The known archaeal family B DNA polymerases are unable to participate in the PCR in the presence of uracil. Here, we report on a novel archaeal family B DNA polymerase from Nanoarchaeum equitans that can successfully utilize deaminated bases such as uracil and hypoxanthine and on its application to PCR. N. equitans family B DNA polymerase (Neq DNA polymerase) produced λ DNA fragments up to 10 kb with an approximately 2.2-fold-lower error rate (5.53 × 10⁻⁶) than Taq DNA polymerase (11.98 × 10⁻⁶). Uniquely, Neq DNA polymerase also amplified λ DNA fragments using dUTP (in place of dTTP) or dITP (partially replaced with dGTP). To increase PCR efficiency, Taq and Neq DNA polymerases were mixed in different ratios; a ratio of 10:1 efficiently facilitated long PCR (20 kb). In the presence of dUTP, the PCR efficiency of the enzyme mixture was two- to threefold higher than that of either Taq and Neq DNA polymerase alone. These results suggest that Neq DNA polymerase and Neq plus DNA polymerase (a mixture of Taq and Neq DNA polymerases) are useful in DNA amplification and PCR-based applications, particularly in clinical diagnoses using uracil-DNA glycosylase.     

Transport of uridine in Escherichia coli B and A showdomycin-resistant mutant

The mechanism of uridine transport in Escherichia coli B cells was studied using experimental approaches designed to limit possible ambiguities in interpretation of data obtained previously. For this purpose, the transport of [2-¹⁴C]uridine and [U-¹⁴C]uridine was determined in E. coli B and an E. coli B mutant which is resistant to the inhibitory effects of the nucleoside antibiotic, showdomycin.The majorty of the uridine transported as the intact nucleoside is cleaved to uracil and ribose l-phosphate. The uracil, in large part, is excreted, while ribose l-phosphate is retained. In addition, uridine is also rapidly cleaved to uracil and ribose l-phosphate in the periplasmic space. The uracil moiety may enter the cell, whereas ribose l-phosphate is not transported. The showdomycin-resistant mutant transports the intact nucleoside inefficiently, or not at all, but retains its ability to convert uridine to uracil in the periplasmic space.     

Arabidopsis Uracil DNA Glycosylase (UNG) Is Required for Base Excision Repair of Uracil and Increases Plant Sensitivity to 5-Fluorouracil

Uracil in DNA arises by misincorporation of dUMP during replication and by hydrolytic deamination of cytosine. This common lesion is actively removed through a base excision repair (BER) pathway initiated by a uracil DNA glycosylase (UDG) activity that excises the damage as a free base. UDGs are classified into different families differentially distributed across eubacteria, archaea, yeast, and animals, but remain to be unambiguously identified in plants. We report here the molecular characterization of AtUNG (Arabidopsis thaliana uracil DNA glycosylase), a plant member of the Family-1 of UDGs typified by Escherichia coli Ung. AtUNG exhibits the narrow substrate specificity and single-stranded DNA preference that are characteristic of Ung homologues. Cell extracts from atung^−/− mutants are devoid of UDG activity, and lack the capacity to initiate BER on uracil residues. AtUNG-deficient plants do not display any apparent phenotype, but show increased resistance to 5-fluorouracil (5-FU), a cytostatic drug that favors dUMP misincorporation into DNA. The resistance of atung^−/− mutants to 5-FU is accompanied by the accumulation of uracil residues in DNA. These results suggest that AtUNG excises uracil in vivo but generates toxic AP sites when processing abundant U:A pairs in dTTP-depleted cells. Altogether, our findings point to AtUNG as the major UDG activity in Arabidopsis.     

A click chemistry approach for the synthesis of cyclic ureido tethered coumarinyl and 1-aza coumarinyl 1,2,3-triazoles as inhibitors of Mycobacterium tuberculosis H37Rv and their in silico studies

Nucleoside bases like uracil, pharmacophoric triazoles and benzimidazolones have been used during the present study to design molecular matrices for antitubercular activity, employing Click Chemistry. Click triazoles 4/7/10 have been obtained by the reaction of 4-(Azidomethyl)-2H-chromen-2-ones/quinolin-2(1H)-ones 3 and propargyl ethers 2/6/9 derived from theophylline/6-methyl uracil/2-benzimidazolone respectively. In addition to spectral data structures have been confirmed by single crystal X-ray diffraction studies in case of uracil bis alkyne (6) and theophylline mono triazole (4c). Theophylline linked mono triazoles, 4(a-d) and 6-methyl uracil linked bis triazoles, 7(a-e) have been found to inhibit Mycobacterium tuberculosis H37Rv with MIC values in the range 55.62–115.62 μM. Benzimidazolone bis triazoles, 10(a-n) showed better activity with MIC in the range 2.33–18.34 μM. Molecular modeling studies using Surflex-Dock algorithm supported our results.     

Syntheses and characterization of polymers containing nucleic acid bases

Two different types of polymers containing nucleic acid bases in the backbone or in the pendant groups were prepared. The polymers of the first type were polyureas obtained by the polyaddition reaction of uracil and adenine with hexamethylene diisocyanate (HMD1). The second type that is cationic polyurethanes containing nucleic acid bases in pendant groups, were obtained by the Menschutkin reaction of halogenated derivatives of uracil and adenine with a linear polyurethane containing tertiary nitrogen atoms which was based on HMD1 and N-methyldiethanolamine. Base base interactions were studied for the polymers by ultraviolet (u.r.), optical rotary dispersion (o.r.d.), and nuclear magnetic resonance (n.m.r.) spectra. A relatively high value of hypochromicity, ≈17% was observed for the mixture of the ionic polyurethane with uracil pendant and herring-sperm DNA. Complementary hydrogen bonding interactions were detected for the mixture of the ionic polyurethane with adenine pendant and with uracil pendant. The non-thrombogenic character of the polymers was examined according to the modified Lee White method. The ionic polyurethanes with adenine and uracil pendant exhibited a fairly good anti-clotting properly.     

Synthesis and NMR properties of the first boron analogues of uracil

Synthesis of 4-hydroxyborauracil and 4-hydroxy-3-methylborauracil, the first boron analogues of uracil, and comparison of their ¹H and ¹³C NMR properties with those of uracil, are presented. The analyses of NMR-monitored boron compound-alcohol and boron compound-amine interactions pointed to the existence of sp³-hybridized, B,B-bis-methoxyborauracils and pyridine-/n-butylamine-borauracils ate-complexes in solution.     

Polymethylene derivatives of nucleic bases bearing ω-functional groups: IX—An unusual reaction of methyl 2-thiocyano-5-chloropentanoate with uracyl and thymine

Although the search of inhibitors of the key enzymes of HIV replication has remained a topical and intensively studied topic over the last several decades, potential inhibitors of the enzymes bearing thiocyano groups have been little studied. In this work, we tried to synthesize polymethylene derivatives of nucleic bases bearing thiocyano groups at the ω-position of the polymethylene chain. The reaction of new alkylating reagents, methyl α-thiocyano-ω-chloroalkanoates, with nucleic bases led to a complicated and barely separated product mixture. The only exceptions were the reactions of uracil or thymine with methyl 2-thiocyano- 2-chloropentanoate, in which 2-(N ¹-uracilyl or -thyminyl)tetrahydrothiophene-2-carboxylates were isolated in 45–50% yields. The potential mechanism of the reaction is discussed.