When modifying an RNAi duplex (miRNA or siRNA), it's possible that the antisense strand's interaction with RISC and alignment with its mRNA target may be affected, impacting functionality. Therefore, we suggest labeling the 5' end of the sense strand for siRNA (or passenger strand for miRNA). As the 5' end of the antisense (guide strand) is recognized by RISC, it's best to add the fluorescent modification to the end of the duplex on the strand that doesn't interact with RISC. You can also compare a labeled and non-labeled RNAi duplex to assess if the modification affects the siRNA or miRNA functionality.