Very efficient template/primer-independent DNA synthesis by thermophilic DNA polymerase in the presence of a thermophilic restriction endonuclease

Biochemistry. 2004 Oct 26;43(42):13459-66. doi: 10.1021/bi0489614.


We have found that, in the presence of a thermophilic restriction endonuclease, thermophilic DNA polymerase efficiently synthesizes and amplifies DNA in the absence of any added template and primer nucleic acid under isothermal conditions. More than 10 microg of DNA can be synthesized by 1 unit of DNA polymerase in 1 h, and the reaction proceeds until available dNTPs are consumed. We used mostly the Tsp509I restriction endonuclease (recognition sequence: decreasing AATT), the TspRI restriction endonuclease (recognition sequence: NNCA(G/C)TGNN decreasing), and Vent (exo(-)) and Vent DNA polymerase. The synthesized double-stranded DNA has a highly repetitive palindromic sequence, e.g. (AAAAATTTTT)(n) and (ATACACTGTATATACAGTGTAT)(n). In every repeating unit, there are one or two recognition sites for the restriction enzyme. Our data show that the high efficiency of the restriction-endonuclease-DNA-polymerase (RE-pol) DNA synthesis results from an efficient exponential amplification involving digestion-elongation cycles: a longer DNA with numerous recognition sites for the restriction enzyme is digested to short fragments, and the short fragments are used as seeds for elongation to synthesize longer DNA. A possible role of RE-pol DNA synthesis in the evolutionary development of genetic materials is briefly discussed.

MeSH terms

  • Archaeal Proteins / metabolism*
  • Cloning, Molecular
  • DNA / biosynthesis*
  • DNA / chemistry
  • DNA Polymerase I / metabolism
  • DNA Primers / metabolism*
  • DNA Replication*
  • DNA-Directed DNA Polymerase / metabolism*
  • Deoxyribonucleases, Type II Site-Specific / metabolism*
  • Peptide Chain Elongation, Translational / genetics
  • Sequence Analysis, DNA
  • Tandem Repeat Sequences
  • Templates, Genetic*
  • Thermococcus / enzymology*


  • Archaeal Proteins
  • DNA Primers
  • DNA
  • DNA Polymerase I
  • Tli polymerase
  • DNA-Directed DNA Polymerase
  • Deoxyribonucleases, Type II Site-Specific