Nicks 3′ or 5′ to AP sites or to mispaired bases, and one-nucleotide gaps can be sealed by T4 DNA ligase

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Abstract
Using synthetic oligodeoxynucleotides with 3′-OH ends and 32P-labelled 5′-phosphate ends and the technique of polyacrylamide gel electrophoresis, it is shown that, in the presence of the complementary polynucleotide, an AP (apurinic or apyrimidinic) site at the 3′ or the 5′ end of the labelled oligodeoxynucleotides does not prevent their ligation by T4 DNA ligase, although the reaction rate is decreased. This decrease is more severe when the AP site is at the 3′ end; the activated intermediates accumulate showing that it is the efficiency of the adenyl-5′-phosphate attack by the 3′-OH of the base-free deoxyribose which is mostly perturbed.