Hi
We have purchased an Addgene plasmid and cannot find out in articles referencing it whether this is an ss or sc vector.How do I quickly find out whether an AAV plasmid is single-stranded or self-complementary?
Thank you!
Hi Fahimeh,
Have you tried just emailing the Addgene depositor of the plasmid? That is probably your fastest option :).
You can try to differentiate between them by the size of your transgene. If the sequence in between the ITRs (promoter, gene,polyA,WPRE...) is bigger than 2.7-3kb, it is pretty likely that it is not self-complementary. It won't package well or not at all if bigger than that.
If your transgene is small, another option is to sequence the ITR region to differentiate self complementary from regular, but it is hard to do due to the secondary structure of the ITRs. Ask your sequencing facility to perform a dGTP protocol (for GC-rich sequence) when submitting your samples, it sometimes works really well.
Worse case scenario, you can always clone your transgene in a AAV plasmid you know whether is self complementary or not.
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