Improved measurement of thymidylate synthetase activity by a modified tritium-release assay

Accurate quantitation of thymidylate synthetase activity using a tritium-release assay is dependent upon measurement of only that tritium released from deoxy[5-³H]uridine monophosphate ([³H]dUMP) during the biosynthesis of thymidylate. Removal of remaining [³H]dUMP on completion of the assay by charcoal adsorption and correction for the nonenzymatic release of tritium are necessary. Although over 99% of [³H]dUMP is removed immediately following addition of charcoal, these studies demonstrate that sufficient [³H]dUMP can remain to prevent accurate measurement of low levels of thymidylate synthetase activity. By delaying measurement of radioactivity for at least 24 h following addition of charcoal, this problem is minimized. To account for nonenzymatic release of tritium, a blank containing enzyme extract with omission of $\text{±,}\text{l}\text{-5,10-}\text{methylenetetrahydrofolate}$ is demonstrated to be more effective than the commonly used blank in which water is substituted for enzyme extract. In samples containing 5-fluoro-2′-deoxyuridine monophosphate (FdUMP), a potent inhibitor of thymidylate synthetase activity, an alternative blank containing a high concentration of FdUMP (approximately 1mM) is useful in demonstrating a theoretical maximal or complete inhibition of thymidylate synthetase activity.     

Synthesis and Properties of DNA Containing Cyclonucleosides

Here, we present efficient syntheses of the R and S diastereomers of 8,5′-cyclo-2′-deoxyadenosine and 6,5′-cyclo-2′-deoxyuridine. We incorporated these interesting nucleosides into DNA to study how the cyclo linkage affects the stability of duplex formation.     

Iododeoxyuridine administered to mice is de-iodinated and incorporated into DNA primarily as thymidylate.

Iododeoxyuridylic acid, a structural analog of thymidylic acid, is extensively de-iodinated in vivo by the enzyme thymidylate synthetase. Substantial amounts of the deoxyuridylic acid formed by this process are subsequently methylated and incorporated into DNA as thymidine. As a result, when mice are given tritiated iododeoxyuridine, most of the tritium incorporated into their DNA is present in thymidine rather than in iododeoxyuridine. Some, but not nearly as much, tritium from tritiated bromodeoxyuridine is also incorporated into DNA thymidine.     

Cellular Response to Efficient dUTPase RNAi Silencing in Stable HeLa Cell Lines Perturbs Expression Levels of Genes Involved in Thymidylate Metabolism

dUTPase is involved in preserving DNA integrity in cells. We report an efficient dUTPase silencing by RNAi-based system in stable human cell line. Repression of dUTPase induced specific expression level increments for thymidylate kinase and thymidine kinase, and also an increased sensitization to 5-fluoro-2′-deoxyuridine and 5-fluoro-uracil. The catalytic mechanism of dUTPase was investigated for 5-fluoro-dUTP. The 5F-substitution on the uracil ring of the substrate did not change the kinetic mechanism of dUTP hydrolysis by dUTPase. Results indicate that RNAi silencing of dUTPase induces a complex cellular response wherein sensitivity towards fluoropyrimidines and gene expression levels of related enzymes are both modulated.     

Lack of mutagenicity of vinyl chloride in two strains of Neurospora crassa.

No detectable induction of mutations could be found in two strains of Neurospora crassa after their conidia were treated with vinyl chloride, in ethanol solution and in its gaseous form. The results suggest that although N. crassa seems to lativating systems does not increase mutagenic activity of vinyl chloride in the two strains tested. At the same time these strains were mutated easily by UV and methyl methanesulfonate.     

19F NMR of the 5-fluorodeoxyuridylate-thymidylate synthetase binary complex.

Formation of the 5-fluorodeoxyuridylate-thymidylate synthetase binary complex generates a ¹⁹F nmr resonance 1.3–1.4 ppm to higher shielding from free ligand, probably as the result of rotation of the pyrimidine ring about the glycosyl bond. Addition of sodium dodecyl sulfate to the complex produces the spectrum of free ligand indicating that in contrast to the ternary complex of enzyme:nucleotide:cofactor, the binary complex does not contain a covalent bond linking the nucleotide to the enzyme. In the presence of a 2.5 molar excess of nucleotide, 1.55 moles were bound per mole of enzyme in Tris-Cl buffer. Under comparable conditions in sodium phosphate, 0.64 moles were bound, suggesting a specific buffer effect by phosphate.     

Thymidylic Acid Synthesis in Eimeria tenella (Coccidia) Cultured In Vitro*

The source of thymidylic acid for DNA synthesis in 1st generation stages of Eimeria tenella cultured in vitro was investigated using 5-bromo-2′-deoxyuridine, a thymidine analog, and 5-fluoro-2′-deoxyuridine, an inhibitor of de novo thymidylic acid synthesis. Results show that the parasite is unable to utilize either exogenous thymidine or 5-bromo-2′-deoxyuridine but is dependent upon the methylation of deoxyuridylic acid via the thymidylate synthetase reaction to supply thymidine for DNA synthesis.     

Properties of Triple Helices Formed by Oligonucleotides Containing 8-Aminopurines

Abstract

The synthesis of parallel hairpins carrying 8-aminopurines is described. These hairpins have a high affinity for specific polypyrimidine sequences resulting in the formation of very stable triplexes.     

A Simple Method for Enzymatic Synthesis of Unlabeled and Radiolabeled Hydroxycinnamate-CoA

Hydroxycinnamate coenzyme A (CoA) thioesters are substrates for biosynthesis of lignin and hydroxycinnamate esters of polysaccharides and other polymers. Hence, a supply of these substrates is essential for investigation of cell wall biosynthesis. In this study, three recombinant enzymes, caffeic acid 3-O-methyltransferase, 4-coumarate-CoA ligase 1, and 4-coumarate-CoA ligase 5, were cloned from wheat, tobacco, and Arabidopsis, respectively, and were used to synthesize ¹⁴C-feruloyl-CoA, caffeoyl-CoA, p-coumaroyl-CoA, feruloyl-CoA, and sinapoyl-CoA. The corresponding hydroxycinnamoyl-CoA thioesters were high-performance liquid chromatography purified, the only extraction/purification step necessary, with total yields between 88–95%. Radiolabeled ¹⁴C-feruloyl-CoA was generated from caffeic acid and S-adenosyl-¹⁴C-methionine under the combined action of caffeic acid 3-O-methyltransferase and 4-coumarate-CoA ligase 1. About 70% of ¹⁴C-methyl groups from S-adenosyl methionine were incorporated into the final product. The methods presented are simple, fast, and efficient for the preparation of the hydroxycinnamate thioesters.     

A Rapid Method for Mounting Pollen Grains: With Special Regard To Sterility Studies

A method is described for the simultaneous mounting and double staining of mature pollen grains. The medium consists of 50 ml. of glycerol jelly to which 2.5 ml. of methyl green and 2 ml. of phloxine, both in 50% alcoholic solutions, have been added. Prior to the application of the jelly-dye mixture, the pollen is washed with 70% ethanol to remove adhering oils and resins. The staining reaction is differential and permits the rapid classification of pollen grains. The “functional” pollen expands and stains with both dyes whereas the aborted grains remain shrunken and take only the methyl green wall stain. The same reaction functions with orchid seed.     

Characterization of the fluorodihydrouracil substituent in 5-fluorouracil-containing Escherichia coli transfer RNA

The fluorodihydrouridine derivative previously detected in one of two isoaccepting forms of FUra-substituted Escherichia coli tRNA^Met_f has been further characterized. This substituent is responsible for the ¹⁹F resonance observed 15 ppm upfield from free FUra (= 0 ppm) in the high resolution ¹⁹F-NMR spectra of FUra-substituted tRNA purified by chromatography on DEAE-cellulose, at pH 8.9, to remove normal tRNA. Similar highfield ¹⁹F signals have now been observed in the spectra of two other purified fluorinated E. coli tRNAs, tRNA^Met_m and tRNA^Val_l, as well as in unfractionated tRNA, indicating the widespread occurrence of the constituent. Comparison with ¹⁹F spectrum of the model compound 5′-deoxy-5-fluoro-5,6-dihydrouridine (dH⁵₆FUrd) (δ_FUra = ? 31.4 ppm; J_HF = 48 Hz) indicates that the substituent does not contain an intact fluorodihydrouridine ring. dH⁵₆FUrd is considerably more alkali labile than 5,6-dihydrouridine (H⁵₆Urd). At pH 8.9, where H⁵₆Urd is stable, dH⁵₆FUrd is degraded to a derivative, presumably a fluoroureidopropionic acid, with a ¹⁹F resonance at ? 15.7 ppm that nearly coincides with the upfield peak in the spectrum of pH 8.9-treated tRNA. The ¹⁹F-NMR spectrum of fluorinated tRNA, not exposed to pH 8.9, exhibits two peaks 31 and 32 ppm upfield of FUra, in place of the ¹⁹F signal at ? 15 ppm. Hydrolysis of this tRNA with RNAase T₂ produces a sharp doublet 33 ppm upfield (J_HF = 45 Hz). Similarities of the ¹⁹F chemical shift and coupling constant to those of dH⁵₆FUrd, allows assignment of the peak at ? 33 ppm to an intact fluorodihydrouridine residue in the tRNA. Our results demonstrate that FUra residues incorporated into E. coli tRNA at sites normally occupied by dihydrouridine can be recognized by tRNA-modifying enzymes and reduced to fluorodihydrouridine. This substituent is labile at moderately alkaline pH values and undergoes ring-opening during purification of the tRNA.     

The Development of Inducibility for Glutamine Synthetase in Embryonic Neural Retina: Inhibition by BrdU

The hydrocortisone-mediated induction of glutamine synthetase (GS) in the neural retina of the chick embryo is a characteristic and unique feature of differentiation of this tissue. The induction involves genomic activity elicited by the inducer resulting in synthesis and accumulation of the enzyme. We describe correlations between the growth of embryonic retina tissue in vivo and in vitro and the development of its inducibility for GS, and demonstrate that this development proceeds through two phases: competence-acquisition phase (before the 7th day of development), and maturation phase. BrdU applied for 24 h to retinas of 5-day embryos irreversibly suppresses the development of induction-competence. However, BrdU does not affect the progressive maturation of inducibility when applied to retinas that already are fully induction-competent (8 days and older). The short treatment with BrdU of 5-day retinas also causes defective histogenesis resulting in drastic malformation of the tissue. The nature of the processes involved in competence-acquisition and in the maturation of inducibility for GS are examined. Possible mechanisms by which BrdU prevents the development of induction-competence for GS in the early embryonic retina and elicits defective histogenesis are discussed.     

Versatile Solid Supports for Oligonucleotide Synthesis that Incorporate Urea Bridge

The universal solid support, USIII, representing a new and improved version of commercial USII, as well as 2 ′-deoxynucleoside and 2 ′-deoxy-2 ′-fluoronucleoside bound supports, incorporating a labile phenoxyacetyl fragment, was synthesized by an aminomethyl polystyrene carbamoylation with corresponding azides in the presence of aqueous triethylammonium bicarbonate. All three solid phases incorporate a stable urea tether, thus bridging the polymer and functional linker. These new matrices proved to be potent solid phases for the synthesis of DNA, RNA, or modified oligonucleotides as well as randomized mixed 2 ′-ribo/2 ′-deoxy-2 ′-fluoro-RNA libraries and/or DNA libraries, randomized with trinucleotides (codons).     

Insight into the recognition mechanism of DNA cytosine-5 methyltransferases (DNMTs) by incorporation of acyclic 5-fluorocytosine (FC) nucleosides into DNA

DNA cytosine-5 methyltransferase (DNMT) catalyzes methylation at the C5 position of cytosine in the CpG sequence in double stranded DNA to give 5-methylCpG (mCpG) in the epigenetic regulation step in human cells. The entire reaction mechanism of DNMT is divided into six steps, which are scanning, recognition, flipping, loop locking, methylation, and releasing. The methylation and releasing mechanism are well-investigated; however, few reports are known about other reaction steps. To obtain insight into the reaction mechanism, we planned the incorporation of acyclic nucleosides, which make it easy to flip out the target nucleobase, into oligodeoxynucleotides (ODNs) and investigated the interaction between the ODN and DNMT. Here, we describe the design and synthesis of ODNs containing new acyclic 5-fluorocytosine nucleosides and their physiological and biological properties, including their interactions with DNMT. We found that the ODNs containing the acyclic 5-fluorocytosine nucleoside showed higher flexibility than those that contain 5-fluoro-2′-deoxycytidine. The observed flexibility of ODNs is expected to influence the scanning and recognition steps due to the decrease in helicity of the B-form.     

Selection of mitotic Chinese hamster ovary cells from microcarriers. Cell cycle-dependent induction of mutation by 5-bromo-2'-deoxyuridine and ethyl methanesulfonate

Large quantities of mitotic cells may be collected by mitotic detachment from a population of Chinese hamster ovary cells growing on positively charged dextran microcarriers in suspension culture. Exponentially growing cells are treated for 2.5 h with colcemid and mitotic cells are detached from the microcarriers by increasing the stirring speed. A yield of 4-6% of the total population is obtained and, of the cells collected, 85-95% are arrested in metaphase. Using this means to synchronize cells we have determined the cell cycle dependence of the toxic and mutagenic effects of 5-bromo-2'-deoxyuridine (BUdR) and ethyl methanesulfonate (EMS). Mutation was measured at two independent loci: resistance to 6-thioguanine and resistance to ouabain. Both mutagens were more toxic during S phase as compared to G1 or G2 or mitosis. BUdR induced significant mutation only during S phase. The maximum induction of 6-thioguanine resistance was observed in cultures treated 10 h after plating of mitotic cells (2 h into S phase), while the maximum induction of ouabain resistance was observed in cultures treated 10-12 h after plating of mitotic cells (2-4 h into S phase). EMS induced significant mutation at all points in the cell cycle. Mutation induction reached a minimum during S phase but the magnitude of difference between any two points in the cell cycle was found to be less than two-fold.     

An Efficient Method for the Isolation and Purification of Oligoribonucleotides

Abstract

Problems associated with the use of tetrabutylammonium fluoride like incomplete desilylation and removal of the tetrabutylammonium salts during large scale syntheses of oligoribonucleotides (RNA) have been eliminated by the use of triethylamine trihydrofluoride and precipitation of the RNA with 1-butanol. An efficient anion-exchange HPLC method has been developed for the purification of chemically synthesized RNA and the resulting product precipitated directly by the addition of 1-propanol. A new activator, 5-ethylthio-1H-tetrazole significantly enhances the synthesis quality and yield of oligoribonucleotides. RNA synthesized using these improvements has been shown to be biologically active by a comparative ribozyme-substrate assay.     

Simple determination of capecitabine and its metabolites by liquid chromatography with ultraviolet detection in a single injection

Capecitabine (N4-pentoxycarbonyl-5'-deoxy-5-fluorocytidine, Xeloda), a prodrug of 5-fluorouracil (5-FU), is an oral tumor-selective fluoropyrimidine carbamate approved in the treatment of colorectal and breast cancer. It has a preferential activation to 5-FU by thymidine phosphorilase (TP) in target tumor tissues through a series of three metabolic steps minimizing the exposure of normal tissues to 5-FU. It offers the potential of less gastrointestinal toxicity and advantages in terms of convenience and quality of life for the patient, in addition to cost-effectiveness as compared with intravenous 5-FU chemotherapy. We developed a high performance liquid chromatography assay for the determination of plasma capecitabine and its nucleoside metabolite concentrations and 5-FU catabolite dihydro-5-fluorouracil in a single step extraction and a single HPLC injection. The retention times of dihydro-5-fluorouracil, 5-FU, 5'-deoxy-5-fluorouridine (5'-DFUR) and capecitabine were 3.6, 4.4, 11.4 and 20.4 min, respectively and the internal standard retention times were 8.7 and 12.2 min for 5-bromouracil (5-BU) and tegafur, respectively. The limit of detection was 0.01 microg/ml for capecitabine and its nucleoside metabolites and the limit of quantification was 0.025 microg/ml. Extraction efficiency was >80% with a single solvent mixture extraction step for all analytes of interest. The assay had good precision, the within-day and between-day standard deviation of the mean (R.S.D.) being <10% in the linear range 0.025-10 microg/ml. The authors conclude that the method described here is ideally suited for the therapeutic monitoring of capecitabine and its metabolites.     

Synthesis and Triplex Binding Properties of Oligonucleotides Containing a Novel Nucleobase

Abstract

The thiazolo-indole compound 1 bearing the complementary donor-acceptor-donor sites (dad) was designed for specific recognition of an AT inverted base pair in pyrimidine triple helix motif. It was successfully incorporated into 14-mer oligonucleotide using a serinol unit as sugar derivative. The triple helix hybridization studies were examined by means of thermal denaturation experiments with a 26-mer DNA duplex containing the AT inverted base pair.     

Synthesis and in vitro anticancer activity of new gemcitabine-nucleoside analogue dimers containing methyltriazole or ester-methyltriazole linker

Two series of novel gemcitabine-nucleoside analogue dimers were synthesized using the ‘click’ chemistry approach. In the first series of dimers (21–30), the nucleoside units were connected with a stable methyltriazole 4N-3′(or 5′)C linker whereas in the second series (31–40) with a cleavable ester-methyltriazole 4N-3′(or 5′)C linker. Dimers 21–40 were evaluated for their cytotoxic activity in five human cancer cell lines such as cervical (HeLa), nasopharyngeal (KB), lung (A549), brain (U87), liver (HepG2) and normal dermal fibroblast cell line (HDF) using the sulforhodamine B (SRB) assay. Compound 29 comprising two gemcitabine (dFdC) units exhibited the highest activity among dimers 21–30. The activity of compound 29 was higher than that of dFdC in all the studied cancer cell lines. A similar order of activity was observed for compounds 25, 28, and 30. The best activity among all the dimers synthesized was displayed by compound 39, comprising two gemcitabine units with a cleavable linker. The activity of compound 39 was 5 to 9 times higher than that of dFdC, depending on the cell line. In addition, marked cytotoxic activity was shown by compounds 31, 36, 38, and 40.