so I started my PCR last week, I'm analysing capsicum species using RAPD markers, but I'm a little confuse of how should I procede with my PCR.
First of all, my professor said that I couldn't make the mix all at once and then distribute to micro tubes with my DNA samples, she said that I should prepare the mix separately. Well that's quite annoying, because I have a lot of samples and I must amplify each primer 3 times. Is it really necessary prepare the mix for each sample?
Second, for my project my professor selected 20 primers to analyze the polimorphism and etc. will each primer have its own temperature of annealing, desnaturation etc. or should I configure my termocycler once and use the same program for all primers?
and last but not least, this was my first electrophoresys of a PCR:
this was just a test, I used 11 samples: some of them amplified, some of them not... but I'm not actually worried about that, I want to know why those wich amplified didn't show clear bands, and why my blank (the sample right before the ladder) stained.
Oh, I used the primer OPA 020 for this first test