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Proceedings of the National Academy of... Apr 2006To elucidate the mechanism of DNA strand breaks by low-energy electrons (LEE), theoretical investigations of the LEE attachment-induced C(5')-O(5') sigma bond breaking...
To elucidate the mechanism of DNA strand breaks by low-energy electrons (LEE), theoretical investigations of the LEE attachment-induced C(5')-O(5') sigma bond breaking of pyrimidine nucleotides (5'-dCMPH and 5'-dTMPH) were performed by using the B3LYP/DZP++ approach. The results indicate that the pyrimidine nucleotides are able to capture electrons characterized by near-0-eV energy to form electronically stable radical anions in both the gas phase and aqueous solution. The mechanism of the LEE-induced single-strand bond breaking in DNA might involve the attachment of an electron to the bases of DNA and the formation of base-centered radical anions in the first step. Subsequently, these radical anions undergo either C-O or glycosidic bond breaking, yielding neutral ribose radical fragments and the corresponding phosphoric anions or base anions. The C-O bond cleavage is expected to dominate because of its low activation energy. In aqueous solutions, the significant increases in the electron affinities of pyrimidine nucleotides ensure the formation of electronically more stable radical anions of the nucleotides. The low activation energy barriers for the C(5')-O(5') bond breaking predicted in this work are relevant when the counterions are close enough to the phosphate moiety of DNA.
Topics: DNA; DNA Damage; Electrons; Models, Molecular; Nucleic Acid Conformation; Pyrimidine Nucleotides; Thermodynamics
PubMed: 16585526
DOI: 10.1073/pnas.0510406103 -
Journal of Molecular and Cellular... Nov 1992The metabolism of pyrimidine nucleotides was studied in non-contracting myocytes isolated from adult rat hearts and compared to that observed in freshly prepared...
The metabolism of pyrimidine nucleotides was studied in non-contracting myocytes isolated from adult rat hearts and compared to that observed in freshly prepared myocardium. The myocytes were cultured for up to 96 hrs in a commercial medium containing 50 microM cytidine, uridine, adenosine and adenine; 20 microM guanosine, thymidine and D-ribose; and 5 microM hypoxanthine, xanthine, guanine, thymine and uracil. Nucleotide pool sizes were measured by HPLC. Nucleotide and RNA labelling were followed by incorporation of [U-14C]-cytidine or [U-14C]-uridine added in trace amounts to the medium. The adenine nucleotide pool was 2.4-fold larger than in situ after 7 hrs of incubation and then returned to values 30% higher than that found in the myocardium after 25 hrs. Cytosine and uracil nucleotide pools after 25 hrs of culture were respectively 2 and 4-fold larger than in situ and remained at these levels thereafter. Intracellular cytidylate and uridylate equilibrated very rapidly with exogenous [U-14C]-cytidine but not with [U-14C]-uridine. We conclude that, under the experimental conditions used here, the synthesis of pyrimidine nucleotides in isolated myocytes is mainly supplied by exogenous nucleosides. Furthermore, extracellular cytidine is rapidly converted to both uracil and cytosine nucleotides while uridine serves only as the precursor for uracil nucleotide synthesis.
Topics: Adenine Nucleotides; Animals; Cells, Cultured; Cytidine; Cytosine; Energy Metabolism; Myocardium; Pyrimidine Nucleotides; Rats; Uracil; Uridine
PubMed: 1479625
DOI: 10.1016/0022-2828(92)93099-6 -
Chembiochem : a European Journal of... Aug 2017Twice as apt: Nucleic acid aptamers with high binding affinity, specificity, epitope coverage and nuclease resistance were developed by using libraries containing...
Twice as apt: Nucleic acid aptamers with high binding affinity, specificity, epitope coverage and nuclease resistance were developed by using libraries containing oligonucleotides in which two bases in the pyrimidine nucleotide had been modified.
Topics: Animals; Aptamers, Nucleotide; Drug Design; Haplorhini; Humans; Lipoproteins, LDL; Mice; PCSK9 Inhibitors; Proprotein Convertase 9; Pyrimidine Nucleotides; Rats
PubMed: 28544018
DOI: 10.1002/cbic.201700276 -
The Journal of Pediatrics Jul 1977It was found that ATP and cyclic AMP were greatly increased in human blood lymphocytes which were deficient in ADA. Certain other purine and pyrimidine nucleotides were...
It was found that ATP and cyclic AMP were greatly increased in human blood lymphocytes which were deficient in ADA. Certain other purine and pyrimidine nucleotides were elevated but to a lesser degree. Energy production in these cells may be inhibited by the increase in nucleotides since the ATP:ADP ratio was significantly below normal. Thus it appears that the immunologic deficiency in human ADA deficiency is related to increased nucleotide concentrations in the lymphocytes.
Topics: Adenosine Deaminase; Adenosine Diphosphate; Adenosine Triphosphate; Cyclic AMP; Guanosine Triphosphate; Humans; Immunologic Deficiency Syndromes; Infant; Lymphocytes; Male; Nucleoside Deaminases; Purines; Pyrimidine Nucleotides
PubMed: 195028
DOI: 10.1016/s0022-3476(77)80442-3 -
Journal of the American Chemical Society Feb 2007Fluorescent nucleobase analogues that respond to changes in their microenvironment are valuable for studying RNA structure, dynamics, and recognition. The most commonly...
Fluorescent nucleobase analogues that respond to changes in their microenvironment are valuable for studying RNA structure, dynamics, and recognition. The most commonly used fluorescent ribonucleoside is 2-aminopurine, a highly responsive purine analogue. Responsive isosteric fluorescent pyrimidine analogues are, however, rare. Appending five-membered aromatic heterocycles at the 5-position on a pyrimidine core has recently been found to provide a family of responsive fluorescent nucleoside analogues with emission in the visible range. To explore the potential utility of this chromophore for studying RNA-ligand interactions, an efficient incorporation method is necessary. Here we describe the synthesis of the furan-containing ribonucleoside and its triphosphate, as well as their basic photophysical characteristics. We demonstrate that T7 RNA polymerase accepts this fluorescent ribonucleoside triphosphate as a substrate in in vitro transcription reactions and very efficiently incorporates it into RNA oligonucleotides, generating fluorescent constructs. Furthermore, we utilize this triphosphate for the enzymatic preparation of a fluorescent bacterial A-site, an RNA construct of potential therapeutic utility. We show that the binding of this RNA target to aminoglycoside antibiotics, its cognate ligands, can be effectively monitored by fluorescence spectroscopy. These observations are significant since isosteric emissive U derivatives are scarce and the trivial synthesis and effective enzymatic incorporation of the furan-containing U triphosphate make it accessible to the biophysical community.
Topics: Aminoglycosides; Binding Sites; Fluorescent Dyes; Furans; Nucleic Acid Conformation; Pyrimidine Nucleotides; RNA; RNA, Messenger; Ribonucleotides; Spectrometry, Fluorescence; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 17256858
DOI: 10.1021/ja066455r -
The Biochemical Journal Jul 1993Pyrimidine nucleotide metabolism in rat hepatocytes was studied by measurement of the labelling kinetics of the various intermediates after double labelling with...
Pyrimidine nucleotide metabolism in rat hepatocytes was studied by measurement of the labelling kinetics of the various intermediates after double labelling with [14C]orotic acid and [3H]cytidine, the precursors for the de novo and the salvage pathways respectively. For the uridine nucleotides, differences were found for the 14C/3H ratios in the UDP-sugars, in UMP (of RNA) and in their precursor UTP, suggesting the existence of separated flows of the radioactive precursors through the de novo and the salvage pathways. Higher ratios in the UDP-sugars, which are synthesized in the cytoplasm, and a lower ratio in UMP (of RNA) relative to the 14C/3H ratio in UTP indicated that UTP derived from orotic acid is preferentially used for the cytoplasmic biosynthesis of the UDP-sugars. Uridine, derived from cytidine, is preferentially used for the nuclear-localized synthesis of RNA. In contrast to these findings, the 14C/3H ratios in the cytidine derivatives CMP-NeuAc and CMP (of RNA), and in the liponucleotides CDP-choline and CDP-ethanolamine, were all lower than that in the precursor CTP. This indicates a preferential utilization of the salvage-derived CTP for the synthesis of the liponucleotides as well as for RNA and CMP-NeuAc. Similar conclusions could be drawn from experiments in which the intracellular amounts of several uridine- and cytidine-nucleotide-containing derivatives were increased by preincubating the hepatocytes with unlabelled pyrimidine nucleotides or ethanolamine. Based on these data, we propose a refined model for the intracellular compartmentation of pyrimidine nucleotide biosynthesis in which three pools of UTP are distinguished: a pool of de novo-derived molecules and a pool of salvage-derived molecules, both of which are channelled to the site of utilization; in addition an 'overflow' pool exists, consisting of molecules having escaped from channelling. An overflow pool could also be distinguished for CTP, but no discrimination between de novo and salvage-derived molecules could be made.
Topics: Animals; Cells, Cultured; Chromatography, High Pressure Liquid; Liver; Male; Orotic Acid; Pyrimidine Nucleotides; Rats; Rats, Wistar
PubMed: 8328961
DOI: 10.1042/bj2930207 -
Metabolism: Clinical and Experimental Dec 1988Third-degree burn injury covering 25% of the body surface was imposed on rats. The de novo biosynthesis of purine and pyrimidine nucleotides in the liver of these rats...
Third-degree burn injury covering 25% of the body surface was imposed on rats. The de novo biosynthesis of purine and pyrimidine nucleotides in the liver of these rats was measured by the incorporation of labeled glycine and bicarbonate into the respective bases. They were increased one day after injury (day 2) and returned to the control values three days after injury (day 4). As expected, the metabolic flow through 5-phosphoribosyl l-pyrophosphate (PPRibP), estimated using [14C]ribose as a tracer, varied in a similar manner. The activities of glutamine phosphoribosylpyrophosphate amidotransferase and carbamoyl-phosphate synthetase II on day 2 did not change significantly. The nucleotide concentrations, effectors of the enzymes, also did not change significantly. The concentrations of PPRibP on days 2 and 4 were 85% higher (P less than .02) and similar to that of controls, respectively, and the elevated concentration was a major factor responsible for the increased nucleotide biosynthesis. Increased synthesis caused the elevation of PPRibP concentrations. There were, however, no significant changes in the factors so far known to regulate PPRibP synthesis.
Topics: Animals; Burns; Liver; Phosphoribosyl Pyrophosphate; Purine Nucleotides; Pyrimidine Nucleotides; Rats; Rats, Inbred Strains
PubMed: 2461507
DOI: 10.1016/0026-0495(88)90186-2 -
Analytical Biochemistry Jul 1983A procedure for a rapid and accurate determination of nucleotide pool sizes in heart muscle is described. The method involves an enzymatic cleavage of all nucleotides by...
A procedure for a rapid and accurate determination of nucleotide pool sizes in heart muscle is described. The method involves an enzymatic cleavage of all nucleotides by phosphodiesterase to nucleoside 5'-monophosphates and an HPLC separation (Partisil 10 SAX) by isocratic or two-step elution. This method permits reproducible measurements of the pools of pyrimidine nucleotides which are particularly small in cardiac tissue. Moreover, this technique may be conveniently applied in studies on the incorporation of labeled precursors into free nucleotides. Experimental evidence is presented showing the accuracy of the method.
Topics: Adenosine Monophosphate; Animals; Chromatography, High Pressure Liquid; Myocardium; Pyrimidine Nucleotides; Rats; Uridine Monophosphate
PubMed: 6625155
DOI: 10.1016/0003-2697(83)90436-0 -
Journal of the American Chemical Society Jan 1973
Topics: Cyclization; Cytosine Nucleotides; Magnetic Resonance Spectroscopy; Molecular Conformation; Nucleotides; Pyrimidine Nucleotides; Temperature; Uracil Nucleotides
PubMed: 4687676
DOI: 10.1021/ja00783a043 -
Comptes Rendus de L'Academie Bulgare... 1977
Topics: Animals; Depression, Chemical; In Vitro Techniques; Mice; Pyrimidine Nucleotides; Pyrimidines; RNA
PubMed: 852400
DOI: No ID Found