Why do SMARTpool reagents work? Could the duplexes interfere with each other?
In general, we have found that transfection of four rationally designed siRNAs targeting a single gene, as in a SMARTpool reagent, results in knockdown comparable to with the best duplex of the mixture. The assumption is that there is little or no difference between the presence of a single siRNA and multiple siRNAs that target the same gene but at distinct sites. The duplexes are designed to have equal probabilities of silencing and are not expected to interfere with the activity of each other.