I designed primers which have the tm 69 is and the gc content is 41%. I tried increasing gc content upto 50% but then its increasing primer tm to 72. If I keep gc content 41%, will my primers work? or should I increase gc content and let primer tm be 72 degrees. I am having taq polymerase and phusion polymerase which I can use for setting up pcr.
your primers will work.%GC is only a guide and any secondary structure problems can be sorted using dmso and/or 1M betaine (high GC buffer contains both). If the primers BLAST as unique then I would use them and sort out any problems with additional bands with increased anneling temperature,high GC additives or touchdown pcr
Seems like your primers are quite long, more than 20 base pairs if the tm is 68 at 41% GC. That length should give you good target site specificity. Just try out the PCR with a 68-degree annealing and no additives or special considerations. If it doesn't work, then you can try optimizing conditions and/or redesign primers.