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At least 19 recordsLinked to original sources
PubMed1968

2-deoxyribose gene-enzyme complex in Salmonella typhimurium. I. Isolation and enzymatic characterization of 2-deoxyribose-negative mutants.

Salmonella typhimurium was found to utilize 2-deoxyribose as a sole carbon and energy source. Cells grown in the presence of deoxyribose contained increased levels of deoxyribose kinase, thymidine phosphorylase, and two forms of deoxyribose-5-phosphate aldolase (DR5P aldolase). One form of DR5P aldolase was induced by deoxyribose and coordinately regulated with deoxyribose kinase. The second form of DR5P aldolase was induced by deoxyribose-5-phosphate and coordinately regulated with thymidine phosphorylase. Mutants unable to ferment deoxyribose have been isolated and shown to be lacking either deoxyribose kinase or deoxyribose permease, but none has been found from which DR5P aldolase is missing. Thymine-requiring mutants which are able to grow on low levels of thymine have been isolated and shown, in some cases, to be lacking one or both DR5P aldolases.

Aldehyde-Lyases↗
PubMed1984

Deoxyribose 1-phosphate: radioenzymatic and spectrophotometric assays.

A method has been developed to measure deoxyribose 1-phosphate in the presence of ribose 1-phosphate and other sugar phosphates. The specificity of the method is based on the observation that only deoxyribose 1-phosphate is hydrolyzed by heating at pH 7.4, while both deoxyribose 1-phosphate and ribose 1-phosphate remain unchanged when heated at pH 10. A tissue extract is heated at pH 10. The amount of deoxyribose 1-phosphate plus ribose 1-phosphate is determined from that of deoxyinosine plus inosine formed in a coupled enzymatic reaction, based on the following two-stage transformation: deoxyribose 1-phosphate (ribose 1-phosphate) + adenine in equilibrium deoxyadenosine (adenosine) + inorganic phosphate, catalyzed by adenosine phosphorylase; deoxyadenosine (adenosine) + H2O----deoxyinosine (inosine), catalyzed by adenosine deaminase. By taking advantage of its unique heat lability, deoxyribose 1-phosphate is eliminated by heating the tissue extract at pH 7.4, and ribose 1-phosphate is determined as above. The amount of deoxyribose 1-phosphate stems from the difference between the amount of deoxyinosine plus inosine measured in the tissue extract heated at pH 10 and that of inosine measured in the tissue extract heated at pH 7.4. Free deoxyribose 1-phosphate has been found in rat tissues, as well as in Bacillus cereus during stationary phase of growth.

Animals↗
PubMed1990

The influence of pH on OH. scavenger inhibition of damage to deoxyribose by Fenton reaction.

Hydroxyl radicals (OH.) can be formed in aqueous solution by direct reaction of hydrogen peroxide (H2O2) with ferrous salt (Fenton reaction). OH. damage to deoxyribose, measured as formation of thiobarbituric acid-reactive material, was evaluated at different pHs to study the mechanism of action of classical OH. scavengers. OH. scavenger effect on Fe2+ oxidation was also evaluated in the same experimental conditions. In the absence of OH. scavengers, OH. damage to deoxyribose is higher at acidic compared to neutral and moderately basic pH. At acidic pH deoxiribose is per se able to inhibit Fe2+ oxidation by H2O2. Most of OH. scavengers tested inhibit deoxyribose damage and Fe2+ oxidation in a similar manner: both inhibitions are most relevant at acidic pH and decrease by increasing the pH. These results are not due to OH. scavenger inhibition of Fenton reaction. The influence of pH on the parameters studied appears to be due to the competition of deoxyribose and OH. scavengers for iron. These results suggest the prominent role of iron binding in the degradation of deoxyribose and in the OH. scavenging ability of different compounds. Results obtained with triethylenetetramine, a iron chelator with a low rate constant with OH., confirm that both deoxyribose and the OH. scavengers interact with iron bringing about a site specific Fenton reaction; that the OH. formed at these sites oxidize these molecules to their radical forms which in turn reduce the Fe3+ produced by Fenton reaction. The results presented indicate that most of classical OH. scavengers exert their effect predominantly by preventing the site specific reaction between Fe2+ and H2O2 on the deoxyribose molecule.

Copper↗
PubMed1991

Factors that influence the deoxyribose oxidation assay for Fenton reaction products.

The mechanism of oxidation of deoxyribose to thiobarbituric acid-reactive products by Fenton systems consisting of H2O2 and either Fe2+ or Fe2+ (EDTA) has been studied. With Fe2+ (EDTA), dependences of product yield on reactant concentrations are consistent with a reaction involving OH.. With Fe2+ in 5-50 mM phosphate buffer, yields of oxidation products were much higher and increased with increasing deoxyribose concentration up to 30 mM. The product yield varied with H2O2 and Fe2+ concentrations in a way to suggest competition between deoxyribose and both reactants. Deoxyribose oxidation by Fe2+ and H2O2 was enhanced 1.5-fold by adding superoxide dismutase, even though superoxide generated by xanthine oxidase increased deoxyribose oxidation. These results are not as expected for a reaction involving free OH. or site localized OH. product on the deoxyribose. They can be accommodated by a mechanism of deoxyribose oxidation involving an iron(IV) species formed from H2O2 and Fe2+, but the overall conclusion is that the system is too complex for definitive identification of the Fenton oxidant.

Deoxyribose↗
PubMed1994

Deoxyribose degradation catalyzed by Fe(III)-EDTA: kinetic aspects and potential usefulness for submicromolar iron measurements.

Iron ions play a central role in .OH radicals formation and induction of oxidative stress in living organisms. Iron-catalyzed .OH radical formation degrades deoxyribose to thiobarbituric acid reactive substances (TBA-RS). This paper analyzes kinetic properties of the Fe(III)-EDTA-catalyzed deoxyribose degradation in the presence of ascorbate. The yield of TBA-RS formation in the presence of EDTA was 4-fold higher than in its absence, contrasting with results reported elsewhere, Cu(II)-EDTA and Fe(III)-citrate were unable to catalyze deoxyribose degradation. The dependence on deoxyribose concentration was fitted to a Lineweaver Burk-like plot and it was calculated that approximately 4.5 mM deoxyribose scavenged half of the .OH radicals formed. The data for Fe(III)-EDTA concentration dependence could also be fitted to a rectangular hyperbolic function. This function was linear up to 1 microM added FeCl3 and this property could be utilized as an assay for the estimation of submicromolar iron concentrations. Submicromolar concentrations of iron could induce measurable yields of TBA-RS. Differences of as little as 0.1 microM Fe(III)-EDTA could be reproducibly detected under optimum experimental conditions, above a consistent background absorbance that was equivalent to 0.35 +/- 0.05 microM Fe(III)-EDTA and represented contaminating iron in the reactants that could not be removed with Chelex-100. The low method determination limit makes the deoxyribose degradation reaction potentially useful as a new, highly sensitive and cost effective assay for iron quantification.

Ascorbic Acid↗
PubMed1997

DNA synthesis arrest at C4'-modified deoxyribose residues.

Many genotoxic agents form base lesions that inhibit DNA polymerases. To study the mechanism underlying termination of DNA synthesis on defective templates, we tested the capacity of a model enzyme (Klenow fragment of Escherichia coli DNA polymerase I) to catalyze primer elongation across a series of C4' deoxyribose derivatives. A site with inverted C4' configuration or two different C4' deoxyribose adducts were introduced into the backbone of synthetic templates without modifying the chemistry of the corresponding bases. Inverted deoxyribose moieties may arise in cellular DNA as a product of C4' radical attack. We found that DNA synthesis by the Klenow polymerase was arrested transiently at the C4' inversion and was essentially blocked at C4' deoxyribose adducts. Major termination sites were located one position downstream of a C4' selenophenyl adduct and immediately 3' to or opposite a C4' pivaloyl adduct. Primer extension studies in the presence of single deoxyribonucleotides showed intact base pairing fidelity opposite all three C4' variants regardless of whether the Klenow fragment or its proofreading-deficient mutant was tested. These results imply that the coding ability of template bases is maintained at altered C4' deoxyribose moieties. However, their capacity to impede DNA polymerase progression indicates that backbone distortion and steric hindrance are important determinants of DNA synthesis arrest on damaged templates. The strong inhibition by C4' adducts suggests a potential target for new chemotherapeutic strategies.

DNA Polymerase I↗
PubMed1969

2-Deoxyribose gene-enzyme complex in Salmonella typhimurium: regulation of phosphodeoxyribomutase.

Phosphodeoxyribomutase, the enzyme which catalyzes the interconversion of 2-deoxyribose-1-phosphate to 2-deoxyribose-5-phosphate, has been partially purified from Salmonella typhimurium. The enzyme had an absolute requirement for manganese ion and was stimulated by glucose-1, 6-diphosphate. Phosphodeoxyribomutase was induced by deoxyribose-5-phosphate and was coordinately regulated with the enzymes thymidine phosphorylase and deoxyribose-5-phosphate aldolase, type II. Mutants deficient in these three enzymes were isolated and mapped close to the threonine locus in S. typhimurium. The three enzymes thymidine phosphorylase, deoxyribose-5-phosphate aldolase, type II, and phosphodeoxyribomutase are controlled by a series of linked genes and appear to constitute an operon.

Aldehyde-Lyases↗
PubMed1982

Deoxyribose breakdown by the adriamycin semiquinone and H2O2: evidence for hydroxyl radical participation.

We report our finding that the reaction between the adriamycin semiquinone (produced by reduction of the drug by xanthine oxidase) and H2O2 in N2 causes deoxyribose degradation to a thiobarbituric acid-reactive chromogen. Deoxyribose breakdown was inhibited by scavengers of hydroxyl radicals, providing evidence for the participation of hydroxyl radicals. The reaction was detected in air, but was less efficient in air than in N2. Deoxyribose degradation did not require a metal catalyst, and was inhibited by superoxide dismutase in air, but not N2. A similar reaction with deoxyribose in DNA may be of major importance in the antitumour action of adriamycin.

Air↗
PubMed1986

Copper + zinc and manganese superoxide dismutases inhibit deoxyribose degradation by the superoxide-driven Fenton reaction at two different stages. Implications for the redox states of copper and manganese.

When OH. radicals are formed in a superoxide-driven Fenton reaction, in which O2.- is generated enzymically, deoxyribose degradation is effectively inhibited by CuZn- and Mn-superoxide dismutases. The products of this reaction are H2O2 and a Fe3+-EDTA chelate. The mixing of H2O2 and a Fe3+-EDTA chelate also generates OH. radicals able to degrade deoxyribose with the release of thiobarbituric acid-reactive material. This reaction too is inhibited by CuZn- and Mn-superoxide dismutases, suggesting that most of the OH. is formed by a non-enzymic O2.--dependent reduction of the Fe3+-EDTA chelate. Since the reaction between the Fe3+-EDTA chelate and H2O2 leads to a superoxide dismutase-inhibitable formation of OH. radicals, it could suggest a much wider protective role for the superoxide dismutase enzymes in biological systems. Urate produced during the reaction of xanthine oxidase and hypoxanthine limits deoxyribose degradation as well as the effectiveness of the superoxide dismutase enzymes to inhibit damage to deoxyribose by H2O2 and the Fe3+-EDTA chelate. Some of this damage may result from an O2.--independent pathway to OH. formation in which urate reduces the ferric complex.

Cations, Divalent↗
PubMed1990

The horseradish peroxidase catalysed oxidation of deoxyribose sugars.

The ability of horseradish peroxidase (E.C. 1.11.1.7, Donor: H2O2 oxidoreductase) to catalytically oxidize 2-deoxyribose sugars to a free radical species was investigated. The ESR spin-trapping technique was used to demonstrate that free radical species were formed. Results with the spin trap 3,5-dibromo-4-nitrosobenzene sulphonic acid showed that horseradish peroxidase can catalyse the oxidation of 2-deoxyribose to produce an ESR spectrum characteristic of a nitroxide radical spectrum. This spectrum was shown to be a composite of spin adducts resulting from two carbon-centered species, one spin adduct being characterized by the hyperfine coupling constants aN = 13.6 G and aH beta = 11.0 G, and the other by aN = 13.4 G and aH beta = 5.8 G. When 2-deoxyribose-5-phosphate was used as the substrate, the spectrum produced was found to be primarily one species characterized by the hyperfine coupling constants aN = 13.4 G and aH beta = 5.2. All the radical species produced were carbon-centered spin adducts with a beta hydrogen, suggesting that oxidation occurred at the C(2) or C(5) moiety of the sugar. Interestingly, it was found that under the same experimental conditions, horseradish peroxidase apparently did not catalyze the oxidation of either 3-deoxyribose or D-ribose to a free radical since no spin adducts were found in these cases.

Catalysis↗
PubMed1995

Kinetics of the competitive degradation of deoxyribose and other molecules by hydroxyl radicals produced by the Fenton reaction in the presence of ascorbic acid.

The competition method in which the Fenton reaction is employed as an .OH radical generator and deoxyribose as a detecting molecule, has been used to determine the rate constants for reactions of the .OH radical with its scavengers. Nonlinear competition plots were obtained for those scavengers which reacted with the Fenton reagents (Fe2+ or H2O2). Ascorbic acid is believed to overcome this problem. We have investigated the kinetics of deoxyribose degradation by .OH radicals generated by the Fenton reaction in the presence of ascorbic acid, and observed that the inclusion of ascorbic acid in the Fenton system greatly increased the rate of .OH radical generation. As a result, the interaction between some scavengers and the Fenton reagents became negligeable and linear competition plots of A degree/A vs scavenger concentrations were obtained. The effects of experimental conditions such as, the concentrations of ascorbic acid, deoxyribose, H2O2 and Fe(2+)-EDTA, the EDTA/Fe2+ ratio as well as the incubation time, on the deoxyribose degradation and the determination of the rate constant for mercaptoethanol chosen as a reference compound were studied. The small standard error, (6.76 +/- 0.21) x 10(9) M-1s-1, observed for the rate constant values for mercaptoethanol determined under 13 different experimental conditions, indicates the latter did not influence the rate constant determination. This is in fact assured by introducing a term, kx, into the kinetic equation. This term represents the rate of .OH reactions with other reagents such as ascorbic acid, Fe(2+)-EDTA, H2O2 etc. The agreement of the rate constants obtained in this work with that determined by pulse radiolysis techniques for cysteine, thiourea and many other scavengers, suggests that this simple competition method is applicable to a wide range of compounds, including those which react with the Fenton reagents and those whose solubility in water is low.

Ascorbic Acid↗
PubMed1983

DNA concentrations in the human cerebellum. Computation from kinetics of deoxyribose extraction in hot acid.

DNA can be measured in mammalian tissues by extracting deoxyribose from unfixed, lyophilized tissue specimens with 0.5 N perchloric acid at 90 degrees C. Deoxyribose concentrations in the extract are determined photometrically by reaction with diphenylamine. Inevitably, some deoxyribose is destroyed during exposure to the hot acid. A computer program has been written which corrects photometric absorbance data for such loss of deoxyribose. When extrapolated to infinite duration of extraction, the corrected absorbances yield a measure of the DNA content of the specimen. This method was used to estimate DNA concentrations in human cerebellar cortex and white matter. The results are discussed in relation to stable carbon isotope ratios of human cerebellar DNA.

Cerebellar Cortex↗
PubMed1991

Enzymatic release of 5'-terminal deoxyribose phosphate residues from damaged DNA in human cells.

Activities that catalyze or promote the release of 5'-terminal deoxyribose phosphate residues from DNA abasic sites previously incised by an AP endonuclease have been identified in soluble extracts of several human cell lines and calf thymus. Such excision of base-free sugar phosphate residues from apurinic/apyrimidinic sites is expected to be obligatory prior to repair by gap filling and ligation. The most efficient excision function is due to a DNA deoxyribophosphodiesterase similar to the protein found in Escherichia coli. The human enzyme has been partially purified and freed from detectable exonuclease activity. This DNA deoxyribophosphodiesterase is a Mg(2+)-requiring hydrolytic enzyme with an apparent molecular mass of approximately 47 kDa and is located in the cell nucleus. By comparison, the major nuclear 5'----3' exonuclease, DNase IV, is unable to catalyze the release of 5'-terminal deoxyribose phosphate residues as free sugar phosphates but can liberate them at a slow rate as part of small oligonucleotides. Nonenzymatic removal of 5'-terminal deoxyribose phosphate from DNA by beta-elimination promoted by polyamines and basic proteins is a very slow mechanism of release compared to enzymatic hydrolysis. We conclude that a DNA deoxyribophosphodiesterase acts at an intermediate stage between an AP endonuclease and a DNA polymerase during DNA repair at apurinic/apyrimidinc sites in mammalian cells, but several alternative routes also exist for the excision of deoxyribose phosphate residues.

Animals↗
PubMed1990

Conformation and dynamics of the deoxyribose rings of a (nogalamycin)2-d (5'-GCATGC)2 complex studied in solution by 1H-n.m.r. spectroscopy.

The conformation and dynamics of the deoxyribose rings of a (nogalamycin)2-d(5'-GCATGC)2 complex have been determined from an analysis of 1H-1H vicinal coupling constants and sums of coupling constants (J1'-2',J1'-2",epsilon 1', epsilon 2' and epsilon 2") measured from one-dimensional n.m.r. spectra and from H-1'-H-2' and H-1'-H-2" cross-peaks in high-resolution phase-sensitive two-dimensional correlation spectroscopy (COSY) and double-quantum-filtered correlation spectroscopy (DQF-COSY) experiments. The value of J3'-4' has also been estimated from the magnitude of H-3'-H-4' cross-peaks in DQF-COSY spectra and H-1'-H-4' coherence transfer cross-peaks in two-dimensional homonuclear Hartman-Hahn spectroscopy (HOHAHA) spectra. The data were analysed, in terms of a dynamic equilibrium between North (C-3'-endo) and South (C-2'-endo) conformers, by using the graphical-analysis methods described by Rinkel & Altona [(1987) J. Biomol. Struct. Dyn. 4,621-649]. The data reveal that the sugars of the 2C-5G and 3A-4T base-pairs, which form the drug-intercalation site, have strikingly different properties. The deoxyribose rings of the 2C-5G base-pair are best described in terms of an equilibrium heavily weighted in favour of the C-2'-endo geometry (greater than 95% 'S'), with a phase angle, P, lying in the range 170-175 degrees and amplitude of pucker between 35 and 40 degrees, as typically found for B-DNA. For the deoxyribose rings of the 3A-4T base-pair, however, the analysis shows that, for 3A, the C-2'-endo and C3'-endo conformers are equally populated, whereas a more limited data set for the 4T nucleotide restricts the equilibrium to within 65-75% C-2'-endo. The deoxyribose rings of the 1G-6C base-pair have populations of 70-80% C-2'-endo, typical of nucleotides at the ends of a duplex. Although drug-base-pair stacking interactions are an important determinant of the enhanced duplex stability of the complex [Searle, Hall, Denny, & Wakelin (1988) Biochemistry 27, 4340-4349], the current findings make it clear that the same interactions can be associated with considerable variations in the degree of local structural dynamics at the level of the sugar puckers.

Base Sequence↗
PubMed1987

The deoxyribose method: a simple "test-tube" assay for determination of rate constants for reactions of hydroxyl radicals.

Hydroxyl radicals, generated by reaction of an iron-EDTA complex with H2O2 in the presence of ascorbic acid, attack deoxyribose to form products that, upon heating with thiobarbituric acid at low pH, yield a pink chromogen. Added hydroxyl radical "scavengers" compete with deoxyribose for the hydroxyl radicals produced and diminish chromogen formation. A rate constant for reaction of the scavenger with hydroxyl radical can be deduced from the inhibition of color formation. For a wide range of compounds, rate constants obtained in this way are similar to those determined by pulse radiolysis. It is suggested that the deoxyribose assay is a simple and cheap alternative to pulse radiolysis for determination of rate constants for reaction of most biological molecules with hydroxyl radicals. Rate constants for reactions of ATP, ADP, and Good's buffers with hydroxyl radicals have been determined by this method.

Ascorbic Acid↗
PubMed1989

Binding of iron(II) ions to the pentose sugar 2-deoxyribose.

Iron(II) ions are able to form a weak complex (apparent equilibrium constant about 10(2) at pH 7.4 and 25 degrees C) with 2-deoxyribose over a range of pH values, including pH 7. Evidence for this complex formation has been obtained by spectrophotometric experiments and by studies of Fe(II) oxidation. Iron(II) ions bound to deoxyribose seem to react with H2O2, in a site-specific reaction, to form hydroxyl radicals (.OH) that immediately damage the deoxyribose molecule.

Chemical Phenomena↗
PubMed1999

EPR spin trapping and 2-deoxyribose degradation studies of the effect of pyridoxal isonicotinoyl hydrazone (PIH) on *OH formation by the Fenton reaction.

The search for effective iron chelating agents was primarily driven by the need to treat iron-loading refractory anemias such as beta-thalassemia major. However, there is a potential for therapeutic use of iron chelators in non-iron overload conditions. Iron can, under appropriate conditions, catalyze the production of toxic oxygen radicals which have been implicated in numerous pathologies and, hence, iron chelators may be useful as inhibitors of free radical-mediated tissue damage. We have developed the orally effective iron chelator pyridoxal isonicotinoyl hydrazone (PIH) and demonstrated that it inhibits iron-mediated oxyradical formation and their effects (e.g. 2-deoxyribose oxidative degradation, lipid peroxidation and plasmid DNA breaks). In this study we further characterized the mechanism of the antioxidant action of PIH and some of its analogs against *OH formation from the Fenton reaction. Using electron paramagnetic resonance (EPR) with 5, 5-dimethyl-1-pyrroline-N-oxide (DMPO) as a spin trap for *OH we showed that PIH and salicylaldehyde isonicotinoyl hydrazone (SIH) inhibited Fe(II)-dependent production of *OH from H2O2. Moreover, PIH protected 2-deoxyribose against oxidative degradation induced by Fe(II) and H2O2. The protective effect of PIH against both DMPO hydroxylation and 2-deoxyribose degradation was inversely proportional to Fe(II) concentration. However, PIH did not change the primary products of the Fenton reaction as indicated by EPR experiments on *OH-mediated ethanol radical formation. Furthermore, PIH dramatically enhanced the rate of Fe(II) oxidation to Fe(III) in the presence of oxygen, suggesting that PIH decreases the concentration of Fe(II) available for the Fenton reaction. These results suggest that PIH and SIH deserve further investigation as inhibitors of free-radical mediated tissue damage.

Cyclic N-Oxides↗