Hydrogen deoxyribose

The stmctures of ribose and deoxyribose. The hydrogen atoms that are eliminated during condensation are highlighted. 

Three classes of nucleic acid triple helices have been described for oligonucleotides containing only natural units. They differ according to the base sequences and the relative orientation of the phosphate-deoxyribose backbone of the third strand. All the three classes involve Hoogsteen or reverse Hoogsteen-like hydrogen bonding interaction between the triple helix form-... 

General Considerations Regarding Hydrogen Atom Abstraction from the 2 -Deoxyribose Sugar... 

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... 

DNA is a helical polyanion built by the union of two linear polymeric strands that are composed of sugars (deoxyribose) finked by phosphates. Each sugar contains an aromatic base (G,C,A, or T) bound to C-l of the sugar. The two strands are normally complementary so that when they combine to form the duplex, each base on one strand forms Watson-Crick hydrogen bonds with its counterpart (G with C and A with T) on the opposite... 

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. 

The nucleotides of RNA and DNA consist of three components a carbohydrate, a phosphate group and an organic nitrogenous base. There are two types of carbohydrate molecule in nucleic acids, both of which are D-pentoses, i.e. contain five carbon atoms. The carbohydrate in RNA is ribose, while DNA contains deoxyribose, which has a hydrogen atom instead of a hydroxyl group attached to the carbon in the 2 position (Figure 13.1). 

They consist of two sugars that are identical except that the deoxyribose contains a hydrogen on carbon 2 (thus the name deoxy or without one oxy or hydroxyl Figure 10.7). These specific compounds were originally obtained from yeast (DNA) and the thymus gland (RNA). 

Where nucleic acids are concerned, the enhanced hydrophobicity of abiotic polyfluorinated aromatic bases (e.g., tetrafluorobenzene or tetrafluoroindole deoxyribose derivatives) was exploited as an alternative to natural hydrogen bonding to achieve selective and stable nucleic acid base pairing in duplex DNA [85], The DNA replication was examined using polyfluorinated-nucleotide analogs as substrates. A DNA polymerase active site was able to process the polyfluorinated base pairs more effectively than the analogous hydrocarbon pairs, demonstrating hydrophobic selectivity of polyfluorinated bases for other polyfluorinated bases [86]. 

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. 

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