May 15, 2007 at 11:00 pm #7654
I would like to ask for an advice. I am trying to
amplify a gene (about 800 bp) for a purpose of
expression later on.
My idea was to extract the whole RNA, do RT PCR
with nested primer (about 150 BP around my gene
of interest). In the next step I wanted to use
the cDNA obtained for one more PCR to amplify the
gene, which I would then later subclone to an
The problem is that after RT PCR, for which I use
outer nested primers, I get a band of 500 BP
instead of expected 1100. The primers seem to be
unique enough to not to amplify some other
I will greatly appreciate your suggestions.
May 16, 2007 at 2:18 am #72744david23Participant
ok to narrow down the problem, you sure the primers you selected were right right? Can you post the sequence and primer here?
It’s not likely that your RNA got degraded cleaved or something I suppose.
May 16, 2007 at 8:36 am #72760
May 16, 2007 at 4:01 pm #72776david23Participant
I dont think there is anything wrong with the primer choice. But I keep on thinking back to fact that something might have happened to your RNA. Is it possible that your RNA or cDNA got degraded in some way, and only one of the primer worked, and made a partial. gene sequence. I am just throwing ideas here.
May 17, 2007 at 1:16 pm #72796blcr11Participant
Is it possible that your source tissue expresses an alternatively spliced message? It could be spliced to express a shorter protein, but retain the same upstream and downstream sequences. Or it could be spliced to remove one of your outer primer binding sites and you end up amplifying only one strand of the message. In either case, the actual message has to be smaller than you expect in order to explain what you’re seeing. I guess I would check the RNA sample to see that the size of the message(s) is consistent with what you expect. Degradation is always a possibility with RNA, but it sounds like at least one of your outside primers is working, so maybe your RNA is OK.
May 17, 2007 at 11:01 pm #72818
Thank you for your time. There are no other know splicing variants of the gene. But as both of you said, the RNA template ma be defective. I wasn’t sure what to make out of it when I repeatedly saw the PCR result but now I think it will be a good thing to start from a fresh harvest of RNA. The one I used for the template was just a presnt from the colleague.
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