Figure 1.

Design of a resected RNA pseudoknot by analogy with the tRNA-like structure of BMV RNA. (a) Folding of the tRNA-like structure emphasizing mimicry with canonical tRNA (in blue) and domains maintaining the architecture of the tRNA-like core but not directly involved in tRNA mimicry (12) (in yellow). Numbering starts at the 3′-end. Domains A–E are denoted as in ref. 10. Explicit sequence is only displayed for domain A from which the RNA duplex is derived. (b) Sequence of a RNA duplex with histidine accepting capacity. Potential identity elements are circled in blue and mutations at N4 and N117 are indicated. Notice that the circular RNA (boxed in black) was designed by joining positions 101 and 124 of the complete tRNA-like molecule. The three domains S1, S2, and L1 required to built the resected pseudoknot are assigned according to refs. 25 and 26; the missing domain L3 corresponds to the N11-N100 stretch in a. (c) Model of the duplex derived from the BMV tRNA-like structure with accepting 10-mer (red) and circle mediating histidylation (blue). Putative histidine identity elements are indicated. The ribbon diagram was drawn from a full-atom model of the duplex with the algorithm DRAWNA (27).