I have amplified 2.8 Kb fragment by SOE PCR using 72 degree (2 step method) annealing temp using Phusion enzyme and their GC buffer and getting ~3 Kb band .When I am using this as template after gel purification, I am getting non specific 1- 2 Kb bands. using 2mM mgcl2, 98deg-10sec and 72 deg -60 sec.Can any body suggest something?

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