Classification and energetics of the base-phosphate interactions in RNA

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Classification and energetics of the
base-phosphate interactions in RNA 

• Jesse Stombaugh

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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).
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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.
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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.
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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.
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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.
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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.