Classification and energetics of the base-phosphate interactions in RNA Jesse Stombaugh

Figure 2. Proposed nomenclature for BPh interactions and superpositions of idealized BPh interactions observed in RNA 3D crystal structures for each base. H-bonds are indicated with dashed lines. BPh categories are numbered 0 to 9, starting at the H6 (pyrimidine) or H8 (purine) base positions. BPh interactions that involve equivalent functional groups on different bases are grouped together, i.e. 0BPh (A,C,G,U), 5BPh (G,U), 6BPh (A,C), 7BPh (A,C) and 9BPh (C,U).

Figure 4. 2D annotations for (a) T-Loop from yeast Phe-tRNA (b) GNRA from T.th. 16S rRNA and (c) Sarcin/ricin motif from T.th. 16S rRNA.

Table 4. Frequencies of non-self BPh interactions in E.c. and T.th. 16S and 23S rRNAs. About 13% of all bases in the bacterial rRNA structures form BPh interactions and ~86% of these interactions are common to the E.c. and T.th. rRNA structures. For the corresponding BPh interactions, the base is ~95% conserved between E.c. and T.th.

Figure 6. BPh interactions conserved between E.c. and T.th. rRNA 3D structures mapped on the 2D structure of E.c. 16S rRNA (46). Red symbols were used to denote the edge used by each base donor (circle for Watson-Crick edge, square for Hoogsteen edge, triangle for Sugar edge and diamond for the Adenine 2BPh which straddles the WC and Sugar edges). The 1BPh interactions that are conserved at the base pair level, are marked by red triangles placed between the bases forming the WC base pair. Green circles denote the locations of phosphate acceptors.

Table 5. Corresponding BPh interactions observed in the 3D structures of E.c. and T.th. 16S and 23S rRNAs. Diagonal entries (dark green) correspond to identical BPh interactions (same base donor and BPh category). Yellow shaded cells correspond to differences in base or BPh category that preserve the geometry of the interaction. Pink cells indicate differences that do not preserve the BPh geometry.

Figure 8. Conservation of 1BPh interaction at the level of base pairs. The G2692/C2717 cWW base pair of E.c. 23S rRNA corresponds to the C2692/G2717 base pair in T.th. 23S. The G in each structure forms a conserved 1BPh interaction with the phosphate of nucleotide 2848, as shown.