Deoxyribose radicals

Aruoma, O. 1. (1994). Deoxyribose assay for detecting hydroxyl radicals. Methods in Enzymology, Vol. 233, pp. 57-66, ISBN 978-0-12-182148-7. 

Gutteridge, J.M. Halliwell, B. (1988). The deoxyribose assay an assay both for free hydroxyl radical and for site-specific hydroxyl radical production. Biochemical Journal, Vol. 253, (April 1988), pp. 932-933, ISSN 0264-6021. 

Many compounds that damage DNA via radical intermediates have been identified. Some of the agents, such as bleomycin and the enediynes, damage DNA primarily through abstraction of hydrogen atoms. ° In these cases, chemical reactions are directed to certain positions on the DNA backbone by noncovalent binding that places the reactive intermediates in close proximity to particular deoxyribose sugar residues. Similar to the reactions of HO described above, small radicals, such as... 

Comprehensive discussions of radical reactions at the deoxyribose residues in DNA ... 

In 1977, Kellogg and Fridovich [28] showed that superoxide produced by the XO-acetaldehyde system initiated the oxidation of liposomes and hemolysis of erythrocytes. Lipid peroxidation was inhibited by SOD and catalase but not the hydroxyl radical scavenger mannitol. Gutteridge et al. [29] showed that the superoxide-generating system (aldehyde-XO) oxidized lipid micelles and decomposed deoxyribose. Superoxide and iron ions are apparently involved in the NADPH-dependent lipid peroxidation in human placental mitochondria [30], Ohyashiki and Nunomura [31] have found that the ferric ion-dependent lipid peroxidation of phospholipid liposomes was enhanced under acidic conditions (from pH 7.4 to 5.5). This reaction was inhibited by SOD, catalase, and hydroxyl radical scavengers. Ohyashiki and Nunomura suggested that superoxide, hydrogen peroxide, and hydroxyl radicals participate in the initiation of liposome oxidation. It has also been shown [32] that SOD inhibited the chain oxidation of methyl linoleate (but not methyl oleate) in phosphate buffer. 

Ponka et al. [372] showed that pyridoxal isonicotinoyl hydrazone (PIH, Figure 19.23) is an iron chelating agent. Numerous studies showed the possibility of using this chelator for the treatment of iron overload disease [373], In subsequent studies the antioxidant activity of PIN has been confirmed. For example, Hermes-Lima et al. [374,375] showed that PIN protected plasmid pUC-18 DNA and 2-deoxyribose against hydroxyl radical damage. 

In eukaryotes, ribonucleotide reductase is a tetramer consisting of two R1 and two R2 subunits. In addition to the disulfide bond mentioned, a tyrosine radical in the enzyme also participates in the reaction (2). It initially produces a substrate radical (3). This cleaves a water molecule and thereby becomes radical cation. Finally, the deoxyribose residue is produced by reduction, and the tyrosine radical is regenerated. 

Trifluridine is synthesized by radical trifluoromethylation of uracil, followed by coupling with the protected deoxyribose (enzymatic or chemical) or by trifluoromethylation of the protected iodonucleoside (Fig. 28) [91]. 

Figure 1 Free radical structures, parent compounds, and stable end products for the various components of DNA (a) deoxyribose, (b) guanine, (c) adenine, (d) thymine, and (e) cytosine. Panel (f) shows trapping of the electron and hole by proton transfer in the GC base pair in duplex DNA.

In single crystals of deoxyadenosine [45], the site of oxidation seems to be the deoxyribose moiety. This brings up an interesting point. In studies of the radiation-induced defects in nucleosides and nucleotides, one often sees evidence of damage to the ribose or deoxyribose moiety. These radicals have not been discussed here because much less is known about sugar-centered radicals in irradiated DNA. 

An alternative method to investigate DNA strand breakage by OH radicals considers the surface accessibility of hydrogen atoms of the DNA backbone [102]. The solvent accessibility is 80% for the sugar-phosphates and —20% for the bases. This method allows a more direct determination of reaction of OH radicals with the individual deoxyribose hydrogens [103,104]. Recent studies show trends in reactivity of OH radicals closely follow the accessibility of the solvent to various deoxyribose hydrogens [105,106]. 

Steenken et al. have concluded that in double-stranded DNA direct hydrogen atom abstraction from 2 -deoxyribose by G(-H) radical is very unlikely due to steric hindrance effects and a small thermodynamic driving force [94]. The EPR studies performed in neutral aqueous solutions at room temperature have shown that, in the absence of specific reactive molecules, the lifetime of the G(-H) radical in double-stranded DNA is as long as -5 s [80]. Therefore, the fates of G(-H) radicals are mostly determined by the presence of other reactive species and radicals. Thus, the G(-H) radical can be a key precursor of diverse guanine lesions in DNA. In the next section we begin from a discussion of the site-selective generation of the G(-H) radical in DNA, and then continue with a discussion of the reaction pathways of this guanine radical. 

Major emphasis has been on the isolation and identification of the main decomposition products arising from one electron oxidation reactions with the pyrimidine and purine bases of isolated DNA and related model compounds13,14D. In recent years, major interest has been devoted on the delineation of the mechanistic features of charge transfer within double stranded DNA. This is mostly achieved using defined-sequence oligonucleotides in which radical cations are generated in most cases by photo-ionization of selected nucleobases and 2-deoxyribose. For more information on these systems, the reader is encouraged to read the recent review article by Cadet et al.134 and other references mentioned there in. 

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