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[marikab]

I phosphorylated my primers using T4 polynucleotide kinase - don't think it worked... Read somewhere that during the synthesis/desalting of primers they use ammonium hydroxide. Ammonium ions inhibit PNK. Any suggestions for removal of ammonium ions from primers?

[tfitzwater]

1. The ammonium hydroxide is evaporated off during drying.
2. It takes a high concentration of ammonium to inhibit PNK.  (Yes, I have performed the titration.)  
You are unlikely to encounter the concentration levels necessary to inhibit the enzyme.