Preferential interaction of loach DNA polymerase delta with DNA duplexes containing single-stranded gaps

FEBS Lett. 2000 Dec 1;486(1):14-8. doi: 10.1016/s0014-5793(00)02232-8.


We studied the interaction of DNA polymerase delta (pol delta) 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 delta 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 delta interacts with the 5'-terminus downstream of the gap as well as with the 3'-terminus of the primer. Interaction of pol delta 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 delta for duplexes with gaps of about 10 nt than for DNA substrates with primers annealed to single-stranded templates. The most efficient pol delta 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 delta in the course of DNA repair.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / physiology
  • Animals
  • Cypriniformes* / genetics
  • Cypriniformes* / metabolism
  • DNA / genetics*
  • DNA / metabolism*
  • DNA Polymerase III / metabolism*
  • DNA Probes / genetics
  • DNA Probes / metabolism
  • DNA Repair
  • DNA-Binding Proteins / metabolism
  • DNA-Binding Proteins / physiology
  • Homeodomain Proteins*
  • Hydrolysis
  • Minor Histocompatibility Antigens
  • Proliferating Cell Nuclear Antigen / physiology
  • Protein Binding
  • Proto-Oncogene Proteins c-bcl-2*
  • Replication Protein C
  • Repressor Proteins*
  • Saccharomyces cerevisiae Proteins*
  • Sequence Deletion / genetics*
  • Substrate Specificity
  • Templates, Genetic


  • BCL2-related protein A1
  • DNA Probes
  • DNA-Binding Proteins
  • Homeodomain Proteins
  • MATA1 protein, S cerevisiae
  • Minor Histocompatibility Antigens
  • Proliferating Cell Nuclear Antigen
  • Proto-Oncogene Proteins c-bcl-2
  • Repressor Proteins
  • Saccharomyces cerevisiae Proteins
  • Adenosine Triphosphate
  • DNA
  • DNA Polymerase III
  • Replication Protein C