Duplex end breathing determines serum stability and intracellular potency of siRNA-Au NPs

Structural requirements of siRNA-functionalized gold nanoparticles (siRNA-Au NPs) for Dicer recognition and serum stability were studied. We show that the 3' overhang on the nucleic acids of these particles is preferentially recognized by Dicer but also makes the siRNA duplexes more susceptible to nonspecific serum degradation. Dicer and serum nucleases show lower preference for blunt duplexes as opposed to those with 3' overhangs. Importantly, gold nanoparticles functionalized with blunt duplexes with relatively less thermal breathing are up to 15 times more stable against serum degradation without compromising Dicer recognition. This increased stability leads to a 300% increase in cellular uptake of siRNA-Au NPs and improved gene knockdown.