I have a primer of Ubq 1 and I used it to amplify two different rice cDNA groups by PCR. The first group samples produce single band around 200 bp while second group sample produce single band around 77 bp. Can anyone please help me to undertstand this problem?
Hi,
Putri Wijayanti ,
Can you please provide the gel pics, it will be easy to understand your question and also to answer it.
Thank you
i do not recognise the size standard but the most likely explanation is that the small band is a primer dimer...where is your negative sample control? PD can look bigger than it really is because it diffuses easily and the answer is to use a hot start enzyme or redesign your primers if possible. An alternative is that your gene exists with exons deleted in one copy, your gene has alternative splicing or just that the primers can anneal elsewhere in your dna sample...perhaps in gdna contamination but I really think that this is primer dimer
Paul Rutland, the negative control is in the last well of left pic and the second well of the right pict. I just wondering if they are PD, why there is no band in the negative control?
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