I would like to design and select primers for qRT-PCR of genes from Cyanobacteria which is Prokaryotic organism. I need to know which parameters are crucial to select the best primers. I would like to use SYBR Green method for PCR running. It would be highly appreciated if someone give me some suggestions detailing the procedure of selecting that primers.
I would suggest that you read something like http://www.sigmaaldrich.com/life-science/molecular-biology/pcr/quantitative-pcr/qpcr-technical-guide.html
Which will give you an overview of the general parameters for primer design in qPCR. There is no special requirement for cyanobacteria than any other bacteria. But if you are trying to detect some photosynthetic genes then you will need to choose the region you target for primers carefully, as cyanos often contatin multiple copies of photosynthetic genes.
Your question is slightly confusing as cyanobacteria are prokaryotic . Are you trying to detect a cyanobacteria within a eukaryotic organism or a do you mean a plastid ?
@Andrew Millard, Thanks for your suggestion, I would follow that
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