Since PCR products, that were obtained using combination of our own reagents (Taq.pol from New England Biolabs, MgCl2 from NCB and so on), were faint on gel I decided to use Qiagen PCR amplification kit, which I found in the freezer. I run two reactions at the same. As the result bands for PCR products from Qiagen were more visible and stronger.
Conclusion: use Qiagen reagent kit for further PCR amplifications
Problem: still having multiple bands and smears
According to Qiagen kit the primer concentration for PCR amplification should be 0.5uM. So I did PCR amplification for primer concentration that we have been using and primer concentration according to Qiagen protocol. PCR amplification worked only with 20uM primer concentration.
Conclusion: keep using primers that you have been using
Problem: still having multiple bands
To resolve problem with multiple banding I decided to use two different cycles 15 and 20. Then I further gel purified band from 15 cycle run (shown in red box)
Conclusion: In 15 cycle PCR amplification program there is less by product comparing to 20 cycle PCR amplification program
Problem: Still having multiple bands
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