The efficient and specific silencing of genes via RNA interference (RNAi) for functional genomics and therapeutics depends on careful consideration of the factors that affect the functionality of small interfering RNA (siRNA). These factors include (1) the length of sequence available for siRNA targeting of an mRNA, (2) the structural and thermodynamic properties of target and siRNA sequences, (3) the mechanisms of siRNA off-target effects, and (4) the susceptibility of siRNA degradation when exposed to nucleases in serum and inside cells. Incorporation of Unlocked Nucleobase analogs (UNAs) in the siRNA design offers an attractive approach to design highly efficacious siRNAs with dramatically reduced off-target activity. Here, we describe methods and principles pertaining to the design, selection and screening of optimal siRNAs containing UNA.