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Where to add dye label on the siRNA oligonucleotide

Labeling siRNA duplexeswith dye label at the 3’ end or the 5’ end of the sense strand does not influence gene silencing. We generally recommend the 3' end of the sense strand since new data suggests that a 3' end-labeled sense strand minimizes any chance of steric hindrance or interference with RNAi. Literature indicates that a free 5'-OH group on the antisense strand is required for the siRNA to be functional.

Reference:
  1. Chiu Y L, and Rana T M, 2002. RNAi in Human Cells: Basic Structural and Functional Features of Small Interfering RNA. Molecular Cell, 10, 549–5

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