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. 2005 Nov 16;33(20):6507–6514. doi: 10.1093/nar/gki962

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© The Author 2005. Published by Oxford University Press. All rights reserved

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(A) K-turn modeled from the consensus C/D motif (28) with the C and D motifs shown in red and green, respectively. K-loop modeled from a consensus C′/D′ motif with a 3 nt-spacer. The nucleotide positions are numbered from 5′ to 3′ starting with the first one in the D or D′ motif. Positions 7, 8 and 9 correspond to the asymmetric internal loop of the K-turn with the flipped-out U (position 9). The symbols for the non-canonical base pairs (26,44) are shown in the legend at upper right. The non-canonical base pairs involving positions 5 and 7 of the K-loop are hypothetical. (B) Distribution of nucleotides in the terminal loops of 40 C/D guide RNAs from P.abyssi with a 3 nt-spacer.