I would like to design a primer-probe for DNA detection in qPCR and RNA detection for RT-qPCR. Which sequence should I use? Genomic DNA or mRNA? Please note that I want to use the same primer set for both procedures.
For RNA detection by RT-qPCR make sure to use the mRNA sequence
for DNA detection- if you're looking for a specific sequence within the genomic DNA use the gDNA sequence
Stephanie Ackerson What should I do if I need to use the same primer set for both of these procedures? Is this possible in any way? I want to detect RNA amplification and DNA amplification using the same primers.
Nursena Kayabasi usually for RT-qPCR the primers will span two exons so that you're confirming that you're looking at the mature mRNA rather than the genomic sequence. So typically you'll use a different primer set for the mRNA vs the gDNA so you know you're not getting off target hits
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