The guide RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex

Abstract

SUMMARYThe RNA-induced silencing complex (RISC), which powers RNA interference (RNAi), consists of a guide RNA and an Argonaute protein that slices target RNAs complementary to the guide. We find that for different guide-RNA sequences, slicing rates of perfectly complementary, bound targets can be surprisingly different (>250-fold range), and that faster slicing confers better knockdown in cells. Nucleotide sequence identities at guide-RNA positions 7, 10, and 17 underlie much of this variation in slicing rates. Analysis of one of these determinants implicates a structural distortion at guide nucleotides 6-7 in promoting slicing. Moreover, slicing directed by different guide sequences has an unanticipated, 600-fold range in 3'-mismatch tolerance, attributable to guides with weak (AU-rich) central pairing requiring extensive 3' complementarity (pairing beyond position 16) to more fully populate the slicing-competent conformation. Together, our analyses identify sequence determinants of RISC activity and provide biochemical and conformational rationale for their action. HIGHLIGHTSO_LISequence of guide RNA can alter slicing rate of fully paired substrate by 250-fold C_LIO_LISequences that cause more rapid slicing direct more efficient RNAi in cells C_LIO_LIStrong central pairing imparts tolerance for mismatches to the guide 3' region C_LIO_LIThis tolerance is attributable to more fully populating the slicing conformation C_LI