Hey guys,
I am very new in knockdown experiments and I am planning to knockdown a protein by using siRNA.
I have two known siRNA sequences from another paper, where it seems to work very well.
The sequences have however only 19 nt and for ordering I need 21 nt at least. I guess the 19 nt is only the core sequence without 3' overhang.
Is it possible to add 2 nt at the 3' end (e.g. dTdT) without changing the outcome of my knockdown experiment?
Thank you very much for you help.
Different factors, including a distance of target region to transcription start site, nucleotide composition, absence of off-target effects and secondary structures in the target site and siRNA and the presence of asymmetry and energy valley within the siRNA affect the efficacy of knock downing. Usually siRNA of 19-25 nucleotides work well for eukaryotic gene silencing. Modifications in the sequence may affect the efficacy. Try first with 19 nt and Good chance!