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siRNA detection......which strand shuld labelled - (Aug/26/2013 )



i need guidance, i have very limited number of reactions for labelleing oligos for sirna detection. i want to confirm that which sirna strand shuld be labelled in order to detect sirna , in cells after their transfection. i feel any of two strand can be equally good for labelling  for confirmation of sirna in northern blot procedure,i am doing this whole thing first time, can some one guide me, i will be very greatfull and thankfull.



Since you know which strand is the guide (When you design a siRNA duplex, usually the antisense strand is the guide which is complementary to your target mRNA), you may want to label the guide strand. Another thing you may want to think about is that the labeling should be at the 3' end of the guide so that the labeling does not interfere with Ago loading of the siRNA. 


thank u soo much , i will read more in this direction.