Will dsRNA form in my amplified product, and if so, will it negatively impact reverse transcription and microarray hybridization?
It’s certainly possible, though we have not tested this directly. In our experience, our reverse transcription typically yields around 80-85% for reverse transcrition of aRNA amplified from sonicated dsDNA having an average size of 600 bp. We did test and determine, in our hands, that a low-complexity mixture (~300 unique DNA species) may have a reduced dynamic range of 60-70% of a corresponding mixture where each species was single-stranded and missing its complementary strand. However, most genomic DNA mixtures are likely to be more complex and consequently less likely to suffer from this problem. Furthermore, R-PCR and LM-PCR (described in [1.4]) would also have the same problem since they also amplify both strands of the dsDNA template.
