Dye label considerations:
Fluorescent dyes at the 5' end of the antisense strand of a siRNA duplex have been shown to interfere with siRNA silencing activity, and therefore this position is not recommended.
We recommend placing the fluorescent dye at the 5' end of the sense strand, as this is the position that provides the most efficient chemical synthesis.
However, modifications at either of the 3' ends have been shown to have minimal to no effect on silencing activity and can be utilized as well.
Single-strand RNA oligos:
Fluorescent dyes located at the 5' end of an RNA oligo are incorporated during solid-phase synthesis and typically do not require purification.
However, purification is recommended or may be required for most dyes located internally or at the 3' end, as these are added post-synthesis.
Please contact Scientific Support if you would like recommendations regarding the purification of your custom oligo.