Increased activity and fidelity of DNA polymerase β on single- nucleotide gapped DNA

DNA polymerase β (pol β) is an error-prone polymerase that plays a central role in mammalian base excision repair. To better characterize the mechanisms governing rat pol β activity, we examined polymerization on synthetic primer-templates of different structure. Steady-state kinetic analyses revealed that the catalytic efficiency of pol β (k(cat)K(m,dNTP)/(app)) is strongly influenced by gap size and the presence of a phosphate group at the 5'-margin of the gap. pol β exhibited the highest catalytic efficiency on 5'-phosphorylated 1-nucleotide gapped DNA. This efficiency was ≤500 times higher than on non-phosphorylated 1- nucleotide and 6-nucleotide (with or without PO₄) gapped DNAs and 2,500 times higher than on primer-template with no gaps. The nucleotide insertion fidelity of pol β, as judged by its ability to form G-N mispairs, was also higher (10-100 times) on 5'-phosphorylated single-nucleotide gapped DNA compared with the other DNA substrates studied. These data suggest that a primary function of mammalian pol β is to fill 5'-phosphorylated 1- nucleotide gaps.