If my primer has the specificty with transcript variance of its own, then what should be the the possiblity dissociation curve of my real time pcr and how its effects my results?
What this means is you need to design new primers. You CAN"T predict the efficiency of a primer with multiple targets.
Dear Katie
my concern is i have a primer which has a blast similarity with its tranccript variance. so is there any problem in my real timee pcr dissociation curve?
If you primer is not make one specific product, then you can't accurately calculate it's efficiency in your qPCR reactions.
The "dissociation curve" aka "melt curve" is the least useful part of qPCR. You will get a mixed population of molecules, each with a specific melting pattern.
Bottom line: do you want to publish ANY of these results? If so, then you need to go back and design new primers specific to ONE transcript varient.
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