VIPR RNA-guided DNA recognition by noncontiguous geometric triplex formation
Abstract
Viral interference programmable repeat (VIPR) systems use a noncontiguous code for RNA-guided transcriptional silencing. How the Vipr protein and a VIPR RNA (vrRNA) comprising alternating GGY and NN segments achieve precise DNA targeting is unknown. Here, we present 21 cryo–electron microscopy structures that help explain the mechanism of target engagement. Vipr protomers oligomerize along the vrRNA to form a right-handed helical filament, sequestering each GGY motif and positioning the adjacent NN bases for target base pairing. DNA binding, in which every third nucleotide is skipped, results in a gapped vrRNA-DNA hybrid helix that encircles the nontarget DNA strand to form a geometric triplex. These findings suggest that triplex-mediated target-strand handoff could enable noncontiguous and programmable RNA-guided DNA recognition in VIPR systems.
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Authors: Peter H. Yoon, Trevor Docter, Zeyuan Zhang, Kenneth J. Loi, Santiago C. Lopez, Luis E. Valentin-Alvarado, Owen T. Tuck, Stephen G. Brohawn, Jennifer A. Doudna
Institutions: University of California, San Francisco, University of California, Berkeley, Howard Hughes Medical Institute, Lawrence Berkeley National Laboratory, Gladstone Institutes, QB3, Innovative Genomics Institute