I have a problem with my PCR and tried so many trials to get my product..I am working on RAG 1 gene in birds...my PCR doesnt work at all..however..I used many recipes and programs to get the right product, but non of them is working ..
I agree with all that Katie A S Burnette says. One essential need for pcr is a good quality clean dna sample then at least you know that a pcr should work. Is there anyone in your lab that also works on avian dna who can give you a small amount to help set up your pcr?. If not then I would try a pcr with a very low annealing temperature 8c below the calculated annealing temperature and too much magnesiy=um salt ( 3mM) and only 25ng of dna. Once you have a dirty pcr with too many bands then it is much easier to clean it up to get one good amplimer but at the moment you have too many reasons why the pcr does not work
You did not specify your problem! However, if you mean that you have obtained no any bands, then this means that there is no amplification of your target DNA. This may be because of many reasons like very high annealing temperature, very low MgCl or Taq polymerase used or your primers were not optimal (low concentration or bad quality). Also, you may have used insufficient PCR cycles!
Start up from your primers. You can use softwares like Primer 3 to design your primers especially if they are longer than 25 bp. then blast them (go to NCBI) to be sure that they are very specific. Make sure that they do not form secondary structures (like hairpins or loops mainly at the 3- end of R ang F primers) using softwares as Gene Runner and finally do some In Silico PCR.
And in order to minimize optimization steps, you can get some optimized MasterMixes (like those of Qiagen or Invetrogen,..etc). You can follow their cycling programmes which depend on how many base pairs you want to amplify.