HI!
In the lab we're doing a project where we start from a DNA sequence. When this is re-transscribed it would give us the sequency of a shRNA but I would like to know what step/methodology I could do to detect whether my re-transscribed product has shRNA conformation and not for example ssRNA or dsRNA. Thank you very much!
I used to sanity check my own shRNA designs by first identifying the loop sequence, then counting out bases from either side. Eg:
AGATCAG[loopseq]CTGATCT
one base upstream and one base downstream of loop: G, C = yes, pair
second base upstream, second base downstream: A, T = yes, pair
etc etc.
For the folding of the small RNA as a whole you could try:
Oligoanalyzer on the IDT website (has a Hairpin function - will show a folding diagram, and the delta G should be very negative if the structure will actually form)
Mxfold2: http://www.dna.bio.keio.ac.jp/mxfold2/
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