Fig. 2: Structure of the Cas9d sgRNA.
a, b Schematic representation (a) and atomic model (b) of the Cas9d sgRNA. The guide sequence is depicted in black and white, with black-filled circles indicating the seed region. Stem loop 1, Stem 1, Stem 2, Stem 3, Stem loop 2, and Stem 4 are highlighted in green, pink, purple, yellow, teal, and light blue, respectively. Canonical Watson–Crick base pairs are illustrated with solid lines, while non-canonical base interactions are shown with dashed lines. Nucleic acids that are not visible in the cryo-EM map have been omitted from the atomic model. c Comparison of sgRNA scaffolds between Cas9d (teal and grey) and SpyCas9 (pink, PDB: 6O0Z). The sgRNA of Cas9d is shown in two parts: the grey region resembles the sgRNA of SpyCas9, while the teal regions are absent in SpyCas9. d In vitro cleavage assays were performed using WT Cas9d in combination with various sgRNA truncations. The catalytically inactive mutant D10A/H375A served as a control. The sgRNAs were truncated at the nucleotide positions indicated, as shown in a. The representative gel from three biological replicates is shown. The molecular weight markers are labeled on the right side of the gel. The uncropped gel image and cleavage percentages are included in the source data. Source data are provided as a Source Data file.
