Figure 4.

For sites 2, 4 and 5, we altered the sense strand of the siRNA duplex to reverse the duplex-end stabilities. For example, sites 2 and 5 had an A substituted for a U in the third position of the sense strand. This created an A–A mismatch in the duplex, weakening the stability of the 5′ antisense end (see Figure 3). Our results show that the changes in duplex-end stability reduced the effectiveness of the siRNA duplexes. However, for site 4, the change from unfavorable duplex energies to favorable duplex energies did not result in an increase in the effectiveness of the siRNA.