I'm trying to design a primer set from the human COL1A1 gene. I want to use the same primer set to perform PCR whether I'm using DNA sample or RNA sample obtained from a patient. Should I put the primers between different exons and include the introns as well in order to use the primers for DNA amplification and RNA amplification?
Primers should indeed be from 2 exons to distinguish products derived from cDNA and genomic DNA.
Uwe Borgmeyer would the intron between them cause any problem? should I remove the introns?
You can not remove exons. It is helpful for your interpretation to distinguish whether your template is derived from cDNA or not.
By PCR you can detect a specific sequence in the genome or in your experimental generated cDNA derived from RNA.
Example: Using one primer in exon 2 and one in exon 3 spanning an intron of 162 base pairs you may expect a fragment of e.g. 400 bp. Using cDNA you can expect a fragment of 248 bp. If you get both bands when using a cDNA template you may have still some genomic DNA or cDNA from unspliced RNA which is unlikely when you start with polyA-RNA.
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