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Loop sequences - siRNA hairpin loop sequences (Feb/18/2005 )

Can anybody suggest best loop sequence for my small hairpin RNA ?

-ashwin raut-

Ah loop sequences - the holy grail of shRNA design... I'm afraid different loop sequences work differently with different shRNAs. For the sequence we recommend and to generate your sequences goto


you can see the sequence from brummelkamp et al.Science 296, 550-3
you can see the paper of denti et al Mol Ther. 2004 Jul;10(1):191-9.

I first try the one from brummelkap and al and recently chaged for the one from denti and al. without changing my siRNA sequence. That works correctly in both cases.