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. 2020 Oct 3;48(19):10662–10679. doi: 10.1093/nar/gkaa780

Figure 7.

Figure 7.

(A) An optimal ‘in-line’ geometry (59) essential to promote catalyzed transesterification in RNA sequences. (B–D) The probability of ‘in-line’ conformation evaluated for the RNA nucleotides within the bulge-loop regions of the complexes formed between RNA and Type 1 conjugates (B) and Type 2 conjugates from BC-α (C) and BC-β (D) series. (E and F) The probability of ‘in-line’ geometry evaluated for the RNA nucleotides from the dangling ends of the complexes formed between RNA and Type 1 conjugates (E) and Type 2 conjugates from BC-α (F) and BC-β (G) series. The probabilities of achieving an ‘in-line’ geometry optimal for catalysis, estimated from the favorable values of Θ (when Θ >155°), which can be achieved during the MD simulation, were calculated as the ratio between the number of structures with Θ > 155° in MD trajectory to the overall number of all structures.