I have RNA template to which I designed several primers to make short cDNA fragments. The reverse transcriptases that I know have strong displacement activities producing long cDNA fragments. Say I have primers at the very 5´ end and in the middle and at the very 3´end, so if I use superscriptIII for instance I will have full length cDNA and short length cDNAs. So my question; is there any reverse transcriptase which will stop before the other primer instead of displacing it?
I think all RT have displacement activity (I am not aware of one that doesn't). If nobody suggest a specif RT with this characteristics it's easier if you just clone the full length cDNA and amplify the short fragments by PCR afterwards.
Hyde Chen , I dont think it exists. What do you need for? In my case, the long and short cDNA fragments could affect the downstream assay where I was targeting different sites with several padlock probes which could hinder each other from their amplification. So, I wanted to have short cDNA fragments that could be generated by RT lacking displacement activity but eventually, I used RT with displacement activity.
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