No abstract

Preferential cleavage sites have been determined for Fe 2؉ /H 2 O 2 -mediated oxidations of DNA. In 50 mM H 2 O 2 , preferential cleavages occurred at the nucleoside 5 to each of the dG moieties in the sequence RGGG, a sequence found in a majority of telomere repeats. Within a plasmid containing a (TTAGGG) 81 human telomere insert, 7-fold more strand breakage occurred in the restriction fragment with the insert than in a similar-sized control fragment. This result implies that telomeric DNA could protect coding DNA from oxidative damage and might also link oxidative damage and iron load to telomere shortening and aging. In micromolar H 2 O 2 , preferential cleavage occurred at the thymidine within the sequence RTGR, a sequence frequently found to be required in promoters for normal responses of many procaryotic and eucaryotic genes to iron or oxygen stress. Computer modeling of the interaction of Fe 2؉ with RTGR in B-DNA suggests that due to steric hindrance with the thymine methyl, Fe 2؉ associates in a specific manner with the thymine flipped out from the base stack so as to allow an octahedrally-oriented coordination of the Fe 2؉ with the three purine N 7 residues. Fe 2؉ -dependent changes in NMR spectra of duplex oligonucleotides containing ATGA versus those containing AUGA or A 5m CGA were consistent with this model.

Damage by iron-mediated Fenton reactions under aerobic or anaerobic conditions to deoxycytidine, deoxycytidine-5'-monophosphate, d-CpC, d-CpCpC, and dCMP residues in DNA resulted in at least 26 distinguishable products. Of these, 24 were identified by high performance liquid chromatography retention times, radiolabeling, UV absorption spectra, chemical synthesis, fast atom bombardment mass spectrometry, high resolution fast atom bombardment mass spectrometry, and/or NMR. The nature of the products was qualitatively similar for each substrate except for d-CpC (and possibly d-CpCpC) under anaerobic conditions for which 5-hydroxy-deoxycytidine was uniquely present and 1-carbamoyl-1-carboxy-4-(2-deoxy-beta-D-erythropentofuranosyl) glycinamide was uniquely absent. Damage to dC, d-CpC, and d-CpCpC but not to dCMP or DNA was largely quenched by ethanol, indicating that iron is strongly associated only with dCMP and DNA. The presence of oxygen had little effect with dC or dCMP but had quantitative and qualitative effects with d-CpC and a significantly quantitative but not a qualitative effect with DNA. NADH could drive the Fenton reaction to cause damage to the dC family in vitro, consistent with a previous proposal that NADH was the reducing agent for the Fenton reaction in vivo (Imlay, J.A., and Linn, S. (1988) Science 240, 1302-1309). Finally, the damage spectrum of the dC family by the Fenton reaction is compared with that by ionizing radiation and chemical mechanisms leading to the formation of the 24 identified products are proposed.

Protein abundance changes during disease or experimental perturbation are increasingly analyzed by label-free LC/MS approaches. Here we demonstrate the use of LC/MALDI MS for label-free detection of protein expression differences using Escherichia coli cultures grown on arabinose, fructose or glucose as a carbon source. The advantages of MALDI, such as detection of only singly charged ions, and MALDI plate archiving to facilitate retrospective MS/MS data collection are illustrated. MALDI spectra from RP chromatography of tryptic digests of the E. coli lysates were aligned and quantitated using the Rosetta Elucidator system. Approximately 5000 peptide signals were detected in all LC/MALDI runs spanning over 3 orders of magnitude of signal intensity. The average coefficients of variation for all signals across the entire intensity range in all technical replicates were found to be <25%. Pearson correlation coefficients from 0.93 to 0.98 for pairwise comparisons illustrate high replicate reproducibility. Expression differences determined by Analysis of Variance highlighted over 500 isotope clusters ( p < 0.01), which represented candidates for targeted peptide identification using MS/MS. Biologically interpretable protein identifications that could be derived underpin the general utility of this label-free LC/MALDI strategy.

2'-Deoxyguanosine, 3'-dGMP, 5'-dGMP, d-GpG, or double-stranded DNA were exposed to H2O2 in the presence of Fe2+ under anaerobic conditions or under aerobic conditions in the presence of Fe3+, Fe2+, Fe2+/NADH, or Fe3+/NADH with and without ethanol. The products were enzymatically digested to nucleosides, separated by high performance liquid chromatography (HPLC), quantified, and characterized by HPLC retention time, radiolabeling, UV absorbance spectrometry, NMR, and mass spectrometry. 20 products, constituting 78-81% of the damage, were distinguished from aerobic reactions of Fe2+/H2O2 with dG and dGMP, 16 of which were identified. The product spectra from dG, 3'-dGMP, and 5'-dGMP differ from one another, and the spectrum of the 5' nucleoside of d-GpG differs from that of the 3' nucleoside. 7, 8-Dihydro-8-oxo-2'-deoxyguanosine is the most abundant DNA-bound product aside from abasic sites, and its formation was more closely analyzed. Both NADH, which can reduce Fe3+, and ethanol, which can scavenge some free radicals, change the product profiles. Damage enhancement by NADH follows the sequence dG < d-GpG < 3'-dGMP < 5'-dGMP < DNA; the reverse sequence is observed for ethanol quenching. This sequence of susceptibility and the product differences seen for the 3' and 5' phosphate may reflect localization of iron and the damaging radicals upon the substrate.

Oxidative DNA damage is decreased by the presence of O2 during Fe(2+)-mediated Fenton reactions when H2O2 is in excess. During these reactions, the presence of DNA increases H2O2 consumption relative to Fe2+ consumption under anaerobic conditions, but decreases H2O2 consumption relative to Fe2+ consumption under aerobic conditions. The pseudobimolecular rate constant of H2O2 consumption is the same under both conditions, however, indicating that the presence of DNA affects the oxidation and/or reduction of the iron pool. To understand the basis of these effects, DNA was replaced with ethanol as a model compound. Computer simulations of Fe2+ and H2O2 consumption were experimentally verified and allowed identification of the predominant reactions leading to the changes in stoichiometry. Based upon these results and upon qualitative and quantitative differences in DNA damages between aerobic and anaerobic conditions, it was concluded that, in the presence of DNA, Fe3+ is reduced by some DNA radicals. However, if O2 is present, these radicals react instead with O2 and the product of these reactions can then oxidize Fe2+. Mechanisms proposed for the alteration by O2 of products from dC- and dG-containing substrates after exposure to Fe and H2O2 fit these general schemes. These results provide another distinction between DNA damage caused by ionizing radiation and that caused by Fenton reactions.

DNA is damaged in vivo (Fe 3؉ or Ga 3؉ ) with the adenine ring would bring it into close proximity to the redox-active nicotinamide ring in the folded form of NAD(P)H, but interaction of M 3؉ with the 2-phosphate group would avoid this close contact. In addition, as determined by absorbance spectroscopy, the energy of the charge-transfer species was significantly higher for the Fe 3؉ ⅐NADPH complex than for the Fe 3؉ ⅐NADH complex. We therefore suggest that upon exposure to H 2 O 2 the NADH pool is depleted, and NADPH, which is less reactive with Fe 3؉ , functions as the major nicotinamide nucleotide reductant.

Unaltered base release is correlated with strand breakage for gamma-irradiated bacteriophage PM2 DNA in aqueous solution at pH 7.4. The yield of DNA strand breaks is determined by the agarose gel electrophoresis method. High-performance liquid chromatography (HPLC) is used to assay the release of unaltered nucleic bases. Previously reported HPLC methods have been updated. Unaltered base release is linear with dose up to 424 Gy, where up to 0.2% of all DNA bases are released. No detectable amounts of unaltered nucleosides are released and, besides unaltered bases, only one other product released from DNA is observed. Base release yields do not reflect the PM2 GC content of 43%. Only 76% of all prompt strand breaks appear to be associated with the release of an unaltered free base, whereby the guanine, cytosine, adenine and thymine yields are 9, 27, 18 and 22% of the prompt strand break yield, respectively. Postirradiation incubation at 37 degrees C for 24 h increases the strand break yield 1.38-fold and the unaltered base release yield 1.76-fold such that 97% of the final strand breaks appear to be associated with the release of an unaltered base, whereby the guanine, cytosine, adenine and thymine yields are 10, 36, 23 and 28% of the final strand break yield, respectively. These data indicate that, given proper conditions, nearly every strand break leads to a base release. The bearing of these results on OH radical attack leading to strand breakage and base release is discussed.