Interaction of loach DNA polymerase delta with DNA duplexes with single-strand gaps.

The interaction of DNA polymerase delta purified from eggs of the teleost fish Misgurnus fossilis (loach) with DNA duplexes with single-strand gaps of 1-13 nucleotides was studied. In the absence of template-restricting DNA, the enzyme elongated primers on single-stranded DNA templates in a distributive manner. However, in the presence of the proximal 5;-terminus restricting the template, the enzyme activity significantly increased. In this case, the enzyme was capable of processive synthesis by filling gaps of 5-9 nucleotides in DNA duplexes. These data indicate that DNA polymerase delta can interact with both the 3;- and 5;-termini located upstream and downstream from the gap. Analysis of the complexes formed by DNA polymerase delta and different DNA substrates by electrophoretic mobility shift assay confirmed the assumption that this enzyme can interact with the proximal 5;-terminus restricting the gap. DNA polymerase delta displayed much higher affinity in duplexes with gaps of approximately 10 nucleotides compared to the standard template-primer complexes. Maximal affinity was observed in experiments with DNA substrates containing unpaired 3;-tails in primers. The results of this study suggest that DNA polymerase delta exerts high activity in the cell nuclei during repair of DNA intermediates with single-strand gaps and unpaired 3;-termini.