Although DNA is generally viewed as a stable molecule, many conditions can cause loss of DNA bases or strand breakage.
- Depurination involves the loss of purine bases forming abasic sites.
- Depurination is one of the two limiting factors in chemical synthesis of long DNA oligos (the other is coupling efficiency).
- DNA under physiological conditions has been found to depurinate at a rate of /sec at 70C and pH 7.4 .
- Cytosine can be spontaneously deaminated to form uracil.
- Abasic sites are alkali-labile. Under mildly alkaline conditions, β-elimination occurs which nicks 3' to the abasic site leaving a 5'-P on the downstream fragment
- Under strong alkaline conditions, δ-elimination will occur after β-elimination which completely removes the abasic site leaving a 3'-P on the upstream fragment and a 5'-P on the downstream fragment