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For PCR protocol: https://www.neb.com/protocols/2012/09/06/protocol-phusion-high-fidelity-pcr-master-mix-with-hf-buffer-m0531

 

 

Hairpins and dimers

IDT's Oligoanalyzer:  http://www.idtdna.com/calc/analyzer

How to interpret the delta G values you get:  http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html