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Pyrimidine Bases (pyrimidine + base)
Selected AbstractsFolate deficiency followed by ionizing radiation perturbs hepatic dihydrofolate reducatse activityBIOFACTORS, Issue 4 2008Vipen Batra Abstract There is lot of interest in the folate metabolism because of the essential role of folate coenzymes in nucleic acid synthesis. Gamma (,) radiation is well known for inducing damage in the DNA. To counteract these damage, a variety of DNA repair pathways have evolved that require regular supply of DNA bases whose biosynthesis in turn depends on sufficient pools of folate dependent enzymes like dihydrofolate reductase (DHFR). In the present study, we examined the ionizing radiation mediated perturbation of DHFR activity in folate deficient and folate sufficient conditions. In folate deficient animals a potent inhibition of liver DHFR activity was observed. Our results showed that combination of folate starvation and ionizing radiation might adversely affect the DHFR activity, compared to their individual treatments. Measurement of apurinic/apyrimidinic sites (AP sites), a major type of DNA damage generated by radiation induced loss of purine and/or pyrimidine base, indicated a dose dependent DNA damage in folate deficient animals. In conclusion our data suggest an interactive role of folate deficiency and radiation injury in inhibiting DHFR activity. [source] Enhanced separation of purine and pyrimidine bases using carboxylic multiwalled carbon nanotubes as additive in capillary zone electrophoresisELECTROPHORESIS, Issue 16 2006Xin Xiong Abstract This paper describes the enhanced separation of adenine (A), hypoxanthine (HX), 8-azaadenine (8-AA), thymine (T), cytosine (C), uracil (U) and guanine (G) by CZE dispersing carboxylic multiwalled carbon nanotubes (c-MWNTs) into the running buffer. The effect of important factors such as c-MWNT nanoparticle concentration, the acidity and concentration of running buffer, and separation voltage were investigated to acquire the optimum conditions. The seven purine and pyrimidine bases could be well separated within 16,min in a 35,cm effective length fused-silica capillary at a separation voltage of +8.0,kV in a 23,mM tetraborate buffer (pH,9.2) containing 8.0×10,5,g/mL c-MWNTs. Under the optimal conditions, the linear ranges were of 2,250,,g/mL for A (R2,=,0.995), 3,200,,g/mL for U (R2,=,0.990) and G (R2,=,0.992), 3,250,,g/mL for T (R2,=,0.998), 2,200,,g/mL for C (R2,=,0.985) and 4,200,,g/mL for HX (R2,=,0.988) and 8-AA (R2,=,0.990). The detection limits were 0.9,,g/mL for A (S/N,=,3), 2.4,,g/mL for U, 2.0,,g/mL for T, 1.5,,g/mL for C, 2.5,,g/mL for G and 3.0,,g/mL for HX and 8-AA. The proposed method was successfully applied for determining five purine and pyrimidine bases in yeast RNA. [source] Pyrrolidino DNA with Bases Corresponding to the 2-Oxo Deletion Mutants of Thymine and Cytosine: Synthesis and Triplex-Forming PropertiesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 24 2007Alain Mayer Abstract The dual recognition properties of pyrrolidino DNA species as parallel triplex-forming oligonucleotides were previously found to be strongly dependent upon the nature of the pyrimidine bases. In the structure,activity study presented here we were able to exclude this differential binding being due to their 2-oxo function. We had previously reported on the incorporation of pyrrolidino C -nucleosides into triplex-forming 2,-deoxyoligonucleotides (TFOs). The basic nitrogen atom that replaces the 4,-oxygen atom of the 2,-deoxysugar in such modified units introduces a positive charge in the third strand, and this is able to produce favourable electrostatic interaction with the negatively charged DNA target duplex. A first series of pyrrolidino pseudonucleosides with the bases isocytosine and uracil proved successful for GC base-pair recognition, but was unsuccessful for AT base-pair recognition within the parallel triplex binding motif. Here we report on the synthesis of the two novel 2,-deoxypyrrolidino nucleosides carrying the bases pyridin-2-one and 2-aminopyridine, their phosphoramidite building blocks and theirincorporation into TFOs. Pyrrolidinylpyridin-2-one (dp2P) and -2-aminopyridine (dp2AP), prepared as part of a structure,activity profiling of pyrrolidino DNA in triplex binding, are deletion mutants of T and C, respectively. We found by Tm measurements that neither modification increased triplex binding efficiency relative to the iso-C- and -U-containing pyrrolidino TFOs. These experiments clearly show that the C4 carbonyl function, although important for triplex binding through indirect contributions in general, is not responsible for the differential binding of the latter two aminonucleosides and suggest that TFO conformation is more important. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Synthesis and Molecular Structure of New Unsaturated Analogues of Nucleotides Containing Six-Membered RingsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 3 2005Valery K. Brel Abstract The reaction of 1-(chloromethyl)-3-(diethoxyphosphonyl)allenes 15 and 16 with purine and pyrimidine bases in the presence of cesium carbonate afforded new acyclic analogs of nucleotides containing a 1,2-alkadienic skeleton (17,24). Intramolecular cyclization of the alkoxides tethered to the allenyl moiety yielded dihydropyrans 33,38 and dihydrofurans 39 and 40. Dealkylation of the dihydropyrans led to the corresponding phosphonic acids. The molecular structures of new nucleotide analogs 33 and 36 were determined by single-crystal X-ray analyses. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] DNA tertiary structure and changes in DNA supercoiling upon interaction with ethidium bromide and gyrase monitored by UV resonance Raman spectroscopyJOURNAL OF RAMAN SPECTROSCOPY, Issue 10 2007U. Neugebauer Abstract The tertiary structure of DNA is important for many of its biological functions. In this work supercoiled and relaxed forms of purified plasmid DNA pBR322 in dilute aqueous solutions are investigated by means of UVRR spectroscopy to assess changes in B-DNA conformation. Spectral variation in the CO and exocyclic NH2 vibration above 1600 cm,1 indicate changes in hydrogen bonding. A minor shift of the CN stretching mode of adenosine and guanosine at 1487 cm,1 supports these findings. Changes in ribose conformation are visible in the spectral region 1320,1360 cm,1 by vibrational coupling of the ribose pucker to the vibrations of the purine and pyrimidine bases. The intercalating phenanthridinium drug ethidium bromide is known to reduce the negative supercoiling of DNA. This change in DNA topology is reflected in variations of the UVRR marker bands of DNA identified above. Principal component analysis helped to extract the features of interest from the complex spectra of the intercalation complex. Within the bacterial cells the change in DNA topology is achieved by the action of topoisomerases. In this work, the DNA-binding subunit GyrA of the enzyme gyrase was extracted from E. coli and applied to relaxed and supercoiled pBR322. The observed changes in the vibrational signature of the relaxed DNA in the presence of GyrA indicate a change of topology towards the supercoiled form. With already supercoiled DNA no further change in DNA topology is observed. Copyright © 2007 John Wiley & Sons, Ltd. [source] Regulation of pyrimidine nucleotide formation in Pseudomonas reptilivoraLETTERS IN APPLIED MICROBIOLOGY, Issue 2 2004T.P. West Abstract Aims:, To study the regulation of de novo pyrimidine biosynthesis in the pathogenic bacterium Pseudomonas reptilivora ATCC 14836. Methods and Results:, The pyrimidine biosynthetic pathway enzymes were assayed in extracts of Ps. reptilivora ATCC 14836 cells and of cells from an auxotroph lacking aspartate transcarbamoylase activity. Pyrimidine biosynthetic pathway enzyme activities in ATCC 14836 were influenced by the addition of pyrimidine bases to the culture medium with orotic acid addition inducing dihydroorotase activity. Pyrimidine starvation of the transcarbamoylase mutant strain increased its de novo enzyme activities suggesting that the de novo pathway was also subject to repression by a pyrimidine-related compound. Aspartate transcarbamoylase activity in ATCC 14836 was inhibited in vitro by pyrophosphate and ATP. Conclusions:, Regulation of pyrimidine biosynthesis in Ps. reptilivora was observed at the level of enzyme synthesis and at the level of activity for aspartate transcarbamoylase. Its regulation of enzyme synthesis seemed to be more highly controlled than what was observed in the related species Ps. fluorescens. Significance and Impact of the Study:, This investigation found that pyrimidine biosynthesis is controlled in Ps. reptilivora. This could prove helpful to future studies exploring its pathogenicity. [source] Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodonsACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2007Yoshiteru Sato In protein synthesis, 20 types of aminoacyl-tRNA synthetase (aaRS) are generally required in order to distinguish between the 20 types of amino acid so that each achieves strict recognition of the cognate amino acid and the cognate tRNA. In the crenarchaeon Sulfolobus tokodaii strain 7 (St), however, asparaginyl-tRNA synthetase (AsnRS) is missing. It is believed that AspRS instead produces Asp-tRNAAsn in addition to Asp-tRNAAsp. In order to reveal the recognition mechanism for the two anticodons, GUC for aspartate and GUU for asparagine, the crystal structure of St -AspRS (nondiscriminating type) has been determined at 2.3,Å resolution as the first example of the nondiscriminating type of AspRS from crenarchaea. A structural comparison with structures of discriminating AspRSs indicates that the structures are similar to each other overall and that the catalytic domain is highly conserved as expected. In the N-terminal domain, however, the binding site for the third anticodon nucleotide is modified to accept two pyrimidine bases, C and U, but not purine bases. The C base can bind to form a hydrogen bond to the surrounding main-chain amide group in the discriminating AspRS, while in the nondiscriminating AspRS the corresponding amino-acid residue is replaced by proline, which has no amide H atom for hydrogen-bond formation, thus allowing the U base to be accommodated in this site. In addition, the residues that cover the base plane are missing in the nondiscriminating AspRS. These amino-acid changes make it possible for both C and U to be accepted by the nondiscriminating AspRS. It is speculated that this type of nondiscriminating AspRS has been introduced into Thermus thermophilus through horizontal gene transfer. [source] | |||||||||||||