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Table 3 List of C/D box sRNAs that target distant sites that are close in secondary structure space

From: C/D box sRNA-guided 2′-O-methylation patterns of archaeal rRNA molecules

Species sRNA Subunit D target D' target
Iho sR114 23S C1961 C2265
Iho sR114 23S C2275 D1937
Iho sR472 23S C897 G1017
Iho sR206 16S G*36 and 505 G482
Iho sR103 16S C1045 U1136
Pca sR53 16S A509 C34 and 530
Pca sR56 16S U894 G1358 and G925
Pca sR2 23S G747 C884 and 769
Mka sR87 23S A1241 G1385
Neq sR15 16S G1217 G930
Neq sR17 16S U1370 A915
Tte sR51 23S C1947 G2249 and 1980
Tte sR50 23S U2883 and 2783 U2753
Tte sR46 16S U547 and 984 G924
Tte sR15 16S A509 C35 and 530
  1. Five species (Iho, Pca, Mka, Neq, and Tte) have sRNAs that are predicted to target methylation to sites that are distant in the primary rRNA sequence but close in the secondary structure. Two types of interactions are observed. In the first, the D and D′ guides have single targets as exemplified by Neq sR15. In the second, one guide has a single target, whereas the second guide has two targets, one linked and one distant in the primary sequence but close in the secondary structure. An example of this is Tte 509 where the D guide is predicted to modify position 16S A509 and the D′ guide is predicted to modify at the linked position C530 and the distant position C35. In one instance, the Iho sR206 interaction with the distant site at position 16S G36 contains a mismatch base pair at the site of methylation and is predicted not to be modified although the guide-target may well occur. The asterisk (*) indicates a mismatch base pair at the target site in the region of guide-target complementarity