How to study the function of two isoforms of a protein, when it is difficult to design a primer for both of them?
Is the gene sequence for these proteins known? You can try purifying these by proteomic approach if it is feasible in your system OR go for antibodies against these specific isoforms and study their roles in a probable signaling pathway in which they might be functioning. Try blocking those with small molecule inhibitors and see the downstream effect.
Dear Donia,
I assume that you with isoforms you mean alternatively spliced isoforms of the protein? And when you talk about using primers, you want to do RT-qPCR?
If you post the sequence of the two isoforms you want to detect I'll have a look and see if it is possible to design specific qPCR primers. Unless the sequences are extremely similar is should be doable...
Go to BLAST, search your protein isoforms and make a primer for them.
It´s depends of the isoforms you can measure both in the same qPCR.
Cause not, you need to purify your proteins and do a antibody for both, like Swapnil said.
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