Preferential interaction of loach DNA polymerase δ with DNA duplexes containing single‐stranded gaps

We studied the interaction of DNA polymerase δ (pol δ) purified from the eggs of the teleost fish Misgurnus fossilis (loach) with DNA duplexes containing single‐stranded gaps of 1–13 nucleotides (nt). In the absence of processivity factors (PCNA, RF‐C, and ATP), pol δ elongated primers on single‐stranded DNA templates in a distributive manner. However, the enzyme was capable of processive synthesis by filling gaps of 5–9 nt in DNA duplexes. These data suggest that, upon filling a small gap, pol δ interacts with the 5′‐terminus downstream of the gap as well as with the 3′‐terminus of the primer. Interaction of pol δ with the proximal 5′‐terminus restricting the gap was confirmed by electrophoretic mobility shift assay. Analysis of the enzyme binding to DNA duplexes containing gaps of various sizes showed a much higher affinity of pol δ for duplexes with gaps of about 10 nt than for DNA substrates with primers annealed to single‐stranded templates. The most efficient pol δ binding was observed in experiments with DNA substrates containing unpaired 3′‐tails in primers. The data obtained suggest that DNA molecules with small gaps and single‐stranded tails may serve as substrates for direct action of pol δ in the course of DNA repair.

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