I need do gradient temperature for knowing the exact annealing temperature of my actin primer. So, I do amplification both on DNA and cDNA.
But I got the band are larger in cDNA than in DNA, which is around 200 bp different. Is it possible?
I think it is possible.
It depends on your gene.
Be careful in many cases primers that use for detecting DNA cant be used for cDNA because the sequence of cDNA is different from DNA.
More details is very important for your answering.
Good luck.
I think that it is possible.cDNA is a small genome so the primers are more likely to anneal to the right place and amplify the right amplimer but gDNA is much larger so primers can anneal in the unexpected place and may produce the wrong size product , Alternatively is thre a chance that you have mis labelled/mixed up your dna samples?
agee with Alireza Mordadi, it is possible and depending on the gene
regards
@Alireza Mordadi: yes, I designed my primer from cdna sequence.
The thing is: I will do gene expression analysis on plant X, but it has unknown sequence. so my actin primer are designed from other plants (external) that has same family with plant X.
Therefore, I don't have enough info about my gene interest
@Paul Rutland: I am sure that I am already labeled it right. Even I did PCR re-amplification to increase specifity of the product, I still get the band greater in cdna than dna
But, now I am on the process of sequecing both dna and cdna product to know the exact sequence
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