siRNAs

Small interfering RNAs (siRNAs) are short, double-stranded RNA molecules, typically 21 to 23 nucleotides in length with characteristic 2-nucleotide 3' overhangs. They arise from long double-stranded RNA precursors or hairpin transcripts and are central to the RNA interference (RNAi) pathway. In many organisms, siRNAs are loaded into an effector complex known as RISC, where one strand (the guide) directs the complex to complementary target RNA.

Biogenesis and mechanism: Dicer, an RNAse III enzyme, cleaves long dsRNA or hairpin precursors into siRNA duplexes. The duplex is loaded onto RISC, which unwinds it and retains the guide strand while the passenger strand is degraded. The core Argonaute protein (Ago2 in humans) then uses the guide to locate complementary mRNA and cleave it or repress its translation, depending on the degree of complementarity. Perfect pairing often results in endonucleolytic cleavage of the target mRNA; partial pairing commonly suppresses translation.

Distribution and function: Endogenous siRNAs occur in plants, fungi, and some animals and can participate in antiviral defense and transposon silencing. In mammals, the siRNA pathway is robust mainly for exogenous or experimentally introduced dsRNA, whereas microRNA pathways predominate in natural gene regulation.

Applications and challenges: siRNAs are widely used as research tools to achieve sequence-specific gene knockdown and to study gene function. Therapeutically, siRNAs hold potential for silencing disease-causing genes, but challenges include delivery to specific tissues, stability, activation of innate immune sensors, and off-target effects. Strategies include chemical modifications to siRNAs and delivery via lipid nanoparticles or targeted conjugates.

Key distinctions: Unlike miRNAs, which usually bind with imperfect complementarity to repress translation, siRNAs are designed for near-perfect complementarity with a single target and typically induce mRNA cleavage. siRNA can be exogenous or endogenously derived; endogenous siRNAs are less common in mammals.