How should I calculate a touchdown PCR reaction with a low dna quantity?

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Nihan Şahin

No, i didn't, reading now, Thank you.

Matthew E. Kaplan

A a touchdown PCR reaction will have more to do with your primer sequence and target amplicon than the DNA quantity. I'm not sure if I understand how much DNA you have. Is it 1.5 ng/µl?If so you should be just fine with 2 µl in a 10 or 25 µl reaction.

Is this a reaction that works on other samples or are you starting from scratch?

If you are starting from scratch can you get one sample with a lot of DNA to optimize?

Yes i have 1.5ng/ul DNA. I confused about samples concentrations, but if 3ng/ul is enough, i can optimize my samples for this value.

3 ng into the reaction should be fine if your PCR is reliable.