PNK Treatment of DNA Ends

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This protocol is used to add a phosphate group to the 5' end of a single or double stranded DNA molecule. Most primers, for example, are ordered without this being added as it requires an extra synthesis step and hence greater cost. However subsequent ligation steps are more efficient if these phosphate groups are added.

  • The above website outlines a protocol for use that is modified and summarized below.
  • If you have annealed primers, make sure to check their melting temperature as it may not be significantly above the heat inactivation step of this protocol. If this is the case, either don't bother with the PNK step, or make sure to cool the reaction mix very slowly after the heat inactivation to allow reannealing of any melted DNA.

Reaction Mix (10μl)

  • 1 μL PNK stock (10,000 U/ml)
  • 1 μL T4 Ligase Buffer
  • 8 μL Substrate

Reaction Conditions

  1. 37°C for 30mins
  2. 65°C for 20mins
  3. Store at 4°C


  • The T4 Ligase Buffer provides the required ATP and substitutes for the PNK Buffer and ATP in the NEB protocol. It is actually possible to perform the PNK step and a ligation step simultaneously although the author has not done this.