Trapping of an intermediate in the reaction catalyzed by flavin-dependent thymidylate synthase.

Thymidylate is a DNA nucleotide that is essential to all organisms and is synthesized by the enzyme thymidylate synthase (TSase). Several human pathogens rely on an alternative flavin-dependent thymidylate synthase (FDTS), which differs from the human TSase both in structure and molecular mechanism. It has recently been shown that FDTS catalysis does not rely on an enzymatic nucleophile and that the proposed reaction intermediates are not covalently bound to the enzyme during catalysis, an important distinction from the human TSase. Here we report the chemical trapping, isolation, and identification of a derivative of such an intermediate in the FDTS-catalyzed reaction. The chemically modified reaction intermediate is consistent with currently proposed FDTS mechanisms that do not involve an enzymatic nucleophile, and it has never been observed during any other TSase reaction. These findings establish the timing of the methylene transfer during FDTS catalysis. The presented methodology provides an important experimental tool for further studies of FDTS, which may assist efforts directed toward the rational design of inhibitors as leads for future antibiotics.

High-performance capillary electrophoretic method for the quantification of global DNA methylation: application to methotrexate-resistant cells.

Global DNA hypomethylation in tumor tissue is a common characteristic in a variety of malignancies such as breast, colon, oral, lung, and blood cancers. A rapid and sensitive method has been developed for the determination of global DNA methylation in cells. Five substances--2'-deoxycytidine (dC), 5-methyl 2'-deoxycytidine (mdC), 2'-deoxyadenosine (dA), 2'-deoxythymidine (dT), and 2'-deoxyguanosine (dG)--were completely separated by high-performance capillary electrophoresis in 10 min. Intraday coefficient of variation was less than 1%, and interday coefficient of variation was less than 2%. The minimal detection limit was 1 microM. Acquired drug resistance to methotrexate (MTX) is one of the most serious problems in cancer chemotherapy. Under optimal conditions, we analyzed global DNA methylation levels in A549 and A549/MTX cells, and only 10(5) cells are needed to obtain reliable results. The percentage of 5-methyl-2'-deoxycytidine (5-mC) was 4.80+/-0.52% in A549 cells, and this decreased to 4.20+/-0.44% in A549/MTX cells. It was considered as statistically significant. This demonstrated that the mechanisms of acquired drug resistance to MTX might be concerned with DNA methylation.

Synthesis of phosphorothioamidites derived from 3'-thio-3'-deoxythymidine and 3'-thio-2',3'-dideoxycytidine and the automated synthesis of oligodeoxynucleotides containing a 3'-S-phosphorothiolate linkage.

The synthesis of N4-benzoyl-5'-O-dimethoxytrityl-2',3'-dideoxy-3'-thiocytidine and its phosphorothioamidite is described for the first time, together with a shortened procedure for the preparation of 5'-O-dimethoxytrityl-3'-deoxy-3'-thiothymidine and its corresponding phosphorothioamidite. The first fully automated coupling procedure for the incorporation of a phosphorothioamidite into a synthetic oligodeoxynucleotide has been developed, which conveniently uses routine activators and reagents. Coupling yields using this protocol were in the range of 85-90% and good yields of singularly modified oligonucleotides were obtained. Coupling yields were also equally good when performed on either a 0.2 or 1 micro mol reaction column, thus facilitating large scale syntheses required for mechanistic studies.

Synthesis of fluorescently labeled alkylated DNA adduct standards and separation by capillary electrophoresis.

DNA adducts are regarded as individual internal dosimeters for the exposure to chemical carcinogens. To date, the most sensitive method for DNA adduct analysis is the radioactive 32P-postlabeling method, which allows the detection of one adduct in 10(10) unmodified nucleotides in microg amounts of DNA. However, this technique suffers from disadvantages such as working with radioactive phosphorus and time-consuming chromatographic separation procedures. In addition, the simultaneous detection of adducts from different classes of carcinogens in a DNA sample is difficult. In order to overcome these drawbacks, we are developing a new detection method, comprising fluorescence labeling of DNA adducts, capillary electrophoretic (CE) separation, and on-line detection by monitoring laser-induced fluorescence (LIF). So far, we have evaluated the separation power and the detection limit of CE with fluorescently labeled standard compounds such as unmodified nucleotides or alkylated thymidines. For this purpose, we developed a universal method for labeling 5'-OH-mononucleosid-3'-dicyanoethyl-phosphates with fluorescent dyes based on the phosphoramidite technology for DNA synthesis. The separation of N3-methylated, N3-, O2- and O4-butylated thymidines from the unmodified nucleotide within a few minutes recommends CE-LIF as a powerful method for DNA adduct analysis.

[Studies on chemical constitutents in seeds of Allium tuberosum Rottl].

OBJECTIVE: To study the chemical constituents in the seed of Allium tuberosum. METHOD: Chromatography and spectral analysis were used to isolate the constituents and elucidate their structures. RESULT: Five compounds were isolated from the alcohol extracts of the seeds and identified as nicotianoside C, (22S)-cholest-5-ene-1 beta, 3 beta, 16 beta, 22-tetrol-1-O-alpha-L-rhamnopyranosyl-16-O-beta-D-glucopyranoside, daucosterol, adenosine and thymidine. CONCLUSION: All the compounds were isolated from the seed of this plant for the first time.

Preparation/analysis of chromatin replicated in vivo and in isolated nuclei.

This article outlined biochemical methodologies for the labeling, detection, and analysis of newly replicated and newly assembled nucleosomes. The isolation of specific vertebrate factors that may be involved in chromatin assembly in vivo, such as nucleoplasmin, CAF-1, and NAP-1 and their counterparts in Drosophila and yeast add a further dimension to the study of nucleosome assembly in living cells. In particular, the ability to genetically manipulate the yeast system, together with the identification of yeast enzymes that acetylate newly synthesized H4, will certainly provide exciting new avenues for the investigation of chromatin assembly in vivo.

Purification of thymine glycol DNA and nucleosides by use of boronate chromatography.

Boronate columns can be used to purify DNAs containing cis-thymine glycol residues and can also be used to purify cis-thymine glycol nucleosides. The boronate group can form a reversible complex with the cis-diol of the thymine glycol but not with the urea residue which is formed by alkaline hydrolysis of the thymine glycol. This method is rapid and appears applicable to a range of nucleic acids. In addition to the purifications of DNAs and nucleosides demonstrated here boronate chromatography may be applicable to assaying the extent and sites of oxidative damage to DNAs.

Conformational studies of dithymidine boranomonophosphate diastereoisomers.

The boranophosphate ester nucleotides are a new class of nucleic acid analogues that are isoelectronic and isostructural to normal phosphodiester nucleic acids and that maintain the anionic charge of the nucleic acid backbone. The two P-diastereoisomers of dithymidine boranomonophosphates were separated using reverse phase HPLC; the faster and slower eluting isomers are designated as d(TpBT)-1 and d(TpBT)-2, respectively. Conformations of the isomers were studied using-circular dichroism (CD) and NMR, and compared to the analogous phosphate diester, d(TpT). This comparison allowed the effects of the borane group and chirality of the boranophosphate linkage on sugar and base conformations to be assessed. The CD spectra of the diastereoisomers are consistent with both having a B-type conformation. Analysis of the 1H-1H and 1H-31P coupling constants showed that these conformations are similar to those of the unmodified parent dimer; specifically, the 2'-deoxyribose rings prefer the S (C2'-endo) conformation, and the C4'-C5' and C5'-O5' rotamers are primarily in the gamma + and beta + conformations, respectively. Conformational differences between the diastereoisomers and between the modified and unmodified dimers are manifested by differences in the preferences of the 3'-residues to adopt S sugar pucker and beta + conformations. There is reduced preference for the S sugar pucker of the 3'-residue in d(TpBT)-1 relative to d(TpBT)-2, which is similar to d(TpT). There is less preference for the beta + conformation of the 3'-residue in d(TpBT)-2 relative to d(TpBT)-1 and d(TpT). Based on the CD results, the temperature dependences of the thymidine H6 chemical shifts, and the derived sugar ring and backbone conformational parameters, we conclude that the borane group exerts a minimal influence on the sugar conformations and base stacking interactions. Preliminary assignment of the absolute configuration of the pair of SP and RP diastereoisomers to d(TpBT)-1 and d(TpBT)-2, respectively, is made on the basis of enzyme selectivity and NOE difference experiments.

[Chemical constituents of Cuscuta austrolis R.Br].

Australiside A(1), a new diterpenoid glucoside, was isolated together with thymidine(2), caffeic acid(3), p-coumaric acid(4) and caffeic-beta-D-glucoside(5) from Cuscuta australis. Based on spectral analysis and physico-chemical properties the structures of the above-cited five compounds were identified. The structure of compound 1 was deduced as 4-oic acid-7-oxo-kaurene-6 alpha-O-beta-D-glucoside. Compounds 2, 3, 4 and 5 were obtained from Cuscuta for the first time.

[Water soluble contents of Chinese drug beimu, the bulbs of Fritillaria plants].

Based on platelet aggregation induced by platelet activating factor (PAF), the active fraction with inhibiting effect was screened from four species of Chinese drung Beimu, the bulbs of Fritillaria przewalskii, F. ussurienis, F. anhuiensis and F. thunbergii. According to the experimental results, the active water soluble fraction of F. ussuriensis was further studied. Two nucleosides, thymidine and adenosine were isolated. Platelet aggregation assay shows that adenosine is the chief aggregation inhibitor with 1% = 42 at 5 microns. It is suggested that nucleosides may be the other type of active constituent besides alkaloids in the Fritillaria plants.

Photooxidation of d(TpG) by riboflavin and methylene blue. Isolation and characterization of thymidylyl-(3',5')-2-amino-5-[(2-deoxy-beta-D- erythro-pentofuranosyl)amino]-4H-imidazol-4-one and its primary decomposition product thymidylyl-(3',5')-2,2-diamino-4-[(2-deoxy-beta-D- erythro-pentofuranosyl)amino]-5(2H)-oxazolone.

The major initial product of riboflavin- and methylene blue-mediated photosensitization of 2'-deoxyguanosine (dG) in oxygen-saturated aqueous solution has previously been identified as 2-amino-5-[(2-deoxy-beta-D-erythro-pentofuranosyl)amino] 4H-imidazol-4-one (dlz). At room temperature in aqueous solution dlz decomposes quantitatively to 2,2-diamino-4-[(2-deoxy-beta-D-erythro- pentofuranosyl)amino]-5(2H)-oxazolone (dZ). The data presented here show that the same guanine photooxidation products are generated following riboflavin- and methylene blue-mediated photosensitization of thymidylyl-(3',5')-2'-deoxyguanosine [d(TpG)]. As observed for the monomers, the initial product, thymidylyl-(3',5')-2-amino-5-[(2-deoxy- beta-D-erythro-pentofuranosyl)amino]-4H-imidazol-4-one [d(Tplz)], decomposes in aqueous solution at room temperature to thymidylyl-(3',5')-2,2-diamino-4- [(2-deoxy-beta-D-erythro-pentofuranosyl)amino]-5(2H)-oxazolone [d(TpZ)]. Both modified dinucleoside monophosphates have been isolated by HPLC and characterized by proton NMR spectrometry, fast atom bombardment mass spectrometry, chemical analyses and enzymatic digestions. Among the chemical and enzymatic properties of these modified dinucleoside monophosphates are: (i) d(Tplz) and d(TpZ) are alkali-labile; (ii) d(Tplz) reacts with methoxyamine, while d(TpZ) is unreactive; (iii) d(Tplz) is digested by snake venom phosphodiesterase, while d(TpZ) is unaffected; (iv) relative to d(TpG), d(TpZ) and d(Tplz) are slowly digested by spleen phosphodiesterase; (v) d(Tplz) and d(TpZ) can be 5'-phosphorylated by T4 polynucleotide kinase. The first observation suggests that dlz and dZ may be responsible for some of the strand breaks detected following hot piperidine treatment of DNA exposed to photosensitizers.

Repair of O6-methylguanine and O4-methylthymidine in F344 rat liver following treatment with 1,2-dimethylhydrazine and O6-benzylguanine.

Concentrations of O6-methylguanine, O4-methylthymidine, and N-7-methylguanine were measured in the livers of Fischer 344 rats following treatment with 1,2-dimethylhydrazine (20 mg/kg, s.c.) alone or in combination with the O6-alkylguanine transferase inhibitor O6-benzylguanine (100 mg/kg, i.p., daily). Animals were sacrificed at 12, 24, 36, or 48 h following 1,2-dimethylhydrazine exposure. Direct measurement of alkyltransferase demonstrated that daily treatment with O6-benzylguanine completely eliminated detectable alkyltransferase activity in the livers of treated rats. Adducts in liver DNA were quantitated by high performance liquid chromatography separation followed by fluorescence detection, UV absorbance, and/or specific radioimmunological assays. In animals exposed to 1,2-dimethylhydrazine alone O6-methylguanine concentrations declined rapidly, whereas animals exposed to both O6-benzylguanine and 1,2-dimethylhydrazine showed less removal of O6-methylguanine, with significant differences between the two populations appearing at 36 and 48 h. O4-Methylthymidine removal also differed significantly between the two groups, with O6-benzylguanine-treated animals exhibiting higher concentrations of adducts at 36 and 48 h. O6-Benzylguanine treatment had no effect on the removal of N-7-methylguanine. These results show that the rate of disappearance of both O6-methylguanine and O4-methylthymidine is slower following alkyltransferase depletion, suggesting that mammalian alkyltransferase is involved in the removal of O4-methylthymidine lesions as well as O6-methylguanine lesions.

Synthesis of the diastereomers of thymidine glycol, determination of concentrations and rates of interconversion of their cis-trans epimers at equilibrium and demonstration of differential alkali lability within DNA.

5,6-dihydroxy-5,6-dihydrothymidine (thymidine glycol) is a major product of the reaction of thymidine with reactive oxygen species, including those generated by ionizing radiation. Thymidine glycol exists as 2 diastereomeric pairs by virtue of the chirality of the C(5) and C(6) atoms. A simple procedure is described for synthesizing and purifying each of the diastereomeric pairs separately. After brominating thymidine, the two trans 5-bromo-6-hydroxy-5,6-dihydrothymidine (thymidine bromohydrin) C(5) diastereomers were easily separated by High Performance Liquid Chromatography. Each thymidine bromohydrin was quantitatively converted to the corresponding diastereomeric thymidine glycol pair by reflux in aqueous solution. The concentrations at equilibrium of the cis (5S,6R),(5R,6S) and trans (5S,6S),(5R,6R) forms of the thymidine glycol diastereomers were determined and were 80% cis and 20% trans for the 5S pair and 87% cis and 13% trans for the 5R pair. At equilibrium, the rate of cis-trans epimerization of the two sets of diastereomers was essentially identical. The 5S diastereomeric pair was significantly more alkali labile than the 5R pair due to the higher concentration of the 5S trans epimer at equilibrium. This differential alkali lability was also manifest when the thymine glycol moiety was present in chemically oxidized poly(dA-dT).poly(dA-dT) indicating that the chemical differences between the diastereomeric pairs are preserved in DNA. These chemical differences may affect the biological properties of this important oxidative derivative of thymine in DNA.

Evidence for the involvement of endogenous thymidine in the density-inhibition of tumorigenic Chinese hamster V79 cells.

Two distinct low-molecular-weight growth inhibitory activities were isolated from supernatants of a density-inhibited, tumorigenic V79 Chinese hamster cell line. By chromatographic analyses, one of these was purified to homogeneity and eventually proved to be thymidine (dThd). In order to investigate the biological role of dThd in a density-inhibited culture of these cells, a dThd-kinase deficient (TK-) clone resistant to the excess of dThd was isolated from V79 cells and the effect of the supernatants on growth of these TK- or TK-proficient (TK+) cells was examined. As a result, the growth of TK- cells was not inhibited but enhanced by the supernatant at the concentrations which significantly inhibited the growth of TK+ cells. Such TK-dependent differential responses to supernatants suggest the presence of deoxyribonucleosides including a high level of dThd in the supernatants. Since it is unlikely that dThd might derive from denatured DNA of dead cells, an accumulation of endogenous dThd in confluent culture appears to be responsible for dThd triphosphates which are synthesized de novo, degraded and excreted into the medium rather than incorporated into DNA as a consequence of aberrant growth in the presence of certain growth inhibitors produced by density-inhibited V79 cells.

Separation of [Sp]-3'-O-(5'-dimethoxytritylthymidyl)-5'-O-(3'camphanoyl thymidyl)-O-methyl phosphite.

First isolation of diastereoisomerically enriched (d.p. 95%) [Sp]-3'-O-(5'-dimethoxytrityl tjymidyl)-5'-O-(3'-camphanoyl thymidyl)-O-methyl phosphite (1) allowed to assign, via sulfuration and deprotection, its absolute configuration as Sp. Its reactions with methyl iodide, dimethoxytrityl chloride, or water, respectively, allowed to confirm correctness of assignment of absolute configuration in diastereisomers of TPMeT, and to assign absolute configuration in corresponding diastereoisomers of TPDMTT and TPHT.

Synthesis of 11C-labelled thymidine for tumor visualization using positron emission tomography.

A no-carrier added synthesis of [11C]thymidine from cyclotron produced [11C]methyl iodide is presented. The bis-silylated derivative of the lithium salt of 5-bromo-2'-deoxyuridine is treated with [11C]methyl iodide in THF at -50 degrees C giving 20-30 mCi [11C]thymidine in a 40-70% radiochemical yield. Purification is performed by reversed phase chromatography on a C18 column. The whole procedure takes 25 min and the specific activity is about 20-30 mCi/mumol at the end of the synthesis.

Mass spectrometry of electrophore-labeled nucleosides. Pentafluorobenzyl and cinnamoyl derivatives.

Three structurally similar deoxynucleosides (thymidine, O4-ethylthymidine, and 2'-deoxyuridine) were studied by mass spectrometry as pentafluorobenzyl, cinnamyl, or mixed derivatives. The purpose of the work was to define the usefulness of such derivatives for structural elucidation of deoxynucleosides. The compounds were ionized in three ways: electron capture negative ion, positive ion chemical ionization, and electron impact. For each of the derivatives examined, the combined spectra were well suited for structural elucidation purposes.