Phosphate group, elimination reactions

Dephosphorylation can also occur from the radical a to the phosphate group (62, in Scheme 12). Oxidation of this radical (62) leads to a carbonium ion (reaction 125) which, in its subsequent reactions (126 and 127), eliminates the phosphate group, affording ribo-pentodial-dose (63). Oxidation by other radicals in this system is not very effective, and is more readily brought about by Fe3+ ions [compare G(63) in NaO and N20/Fe3+ see Table V]. 

On the basis of these results a general pathway for the formation of HDF from sugars was assumed as exemplified for fructose-1,6-biphosphate in Figure 11 [88]. Elimination of the phosphate group at C-6 of the l-deoxyosone-6-phosphate, results in acetylformoine which was established as the key intermediate in HDF formation [88]. Reduction of acetylformoine either by a disproportionation reaction with a second molecule of acetylformoine or by further reductive agents present in foods, like vitamin C, then, after elimination of water, generates HDF. 

The observation of this y-elimination reaction has raised the question, whether in DNA the related C(l ) radical can also lead to strand breakage. However due to the negative charge at the phosphate group in 3 -position, the rate of the y-elimi-nation reaction (54) should be considerably slower than that of reaction (53). 

Alkali-labile sites (ALS) may contain an AP such as 2-dRL or certain damaged bases that are released from the sugar moiety upon treatment with alkali (OH" or an organic base such as piperidine). Subsequent to this, a strand break is induced, and this procedure is often used to detect damaged bases within DNA. As the mechanism of the decomposition of 2-dRL by alkali is concerned, it is been suggested that the carbonyl function at C(l ) acidifies H2 and deprotonation [reaction (6)] leads to a (3-elimination of the phosphate group [reaction (7)]. 

This view has been challenged, and using a hexamer duplex as dsDNA model it has been shown that the 2-dRL is a perfectly stable lesion at pH 7, and at room temperature it only eliminates the (3-phosphate group at pH 9.9 [cf. reaction (66) heating at 90 °C for 30 min afforded 5-MF Oyoshi and Sugiyama 2000], In this system, scission is due to radical precursors at C(4 ) and C(5 ). 

One proposal to increase the visibility of the b and y sequence-specific ions and to provide complete sequence information is to derivatize phosphopeptides.106 Sequence analysis can also be improved by using the /3-elimination chemistry.102,107 As described above in this section, phosphoserine and phosphothreonine can be converted to S-ethylcysteine and 5-ethyl-/3-methylcysteine, respectively, upon the base-catalyzed /3-elimination of the phosphate group, followed by the reaction with ethanethiol. CID of the modified peptides results in more evenly distributed sequence-specific fragment ions. 

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