Possible roles of β-elimination and δ-elimination reactions in the repair of DNA containing AP (apurinic/apyrimidinic) sites in mammalian cells

Histones and polyamines nick the phosphodiester bond 3′ to AP (apurinic/apyrimidinic) sites in DNA by inducing a beta-elimination reaction, which can be followed by delta-elimination. These beta- and delta-elimination reactions might be important for the repair of AP sites in chromatin DNA in either of two ways. In one pathway, after the phosphodiester bond 5′ to the AP site has been hydrolysed with an AP endonuclease, the 5′-terminal base-free sugar 5′-phosphate is released by beta-elimination. The one-nucleotide gap limited by 3′-OH and 5′-phosphate ends is then closed by DNA polymerase-beta and DNA ligase. We have shown in vitro that such a repair is possible. In the other pathway, the nicking 3′ to the AP site by beta-elimination occurs first. We have shown that the 3′-terminal base-free sugar so produced cannot be released by the chromatin AP endonuclease from rat liver. But it can be released by delta-elimination, leaving a gap limited by 3′-phosphate and 5′-phosphate. After conversion of the 3′-phosphate into a 3′-OH group by the chromatin 3′-phosphatase, there will be the same one-nucleotide gap, limited by 3′-OH and 5′-phosphate, as that formed by the successive actions of the AP endonuclease and the beta-elimination catalyst in the first pathway.