RNA structural motifs that entail hydrogen bonds involving sugar-phosphate backbone atoms of RNA

Abstract

The growing number of high-resolution crystal structures of large RNA molecules provides much information for understanding the principles of structural organization of these complex molecules. Several in-depth analyses of nucleobase-centered RNA structural motifs and backbone conformations have been published based on this information, including a systematic classification of base pairs by Leontis and Westhof. However, hydrogen bonds involving sugar-phosphate backbone atoms of RNA have not been analyzed systematically until recently, although such hydrogen bonds appear to be common both in local and tertiary interactions. Here we review some backbone structural motifs discussed in the literature and analyze a set of eight high-resolution multi-domain RNA structures. The analyzed RNAs are highly structured: among 5372 nucleotides in this set, 89% are involved in at least one "long-range" RNA-RNA hydrogen bond, i.e., hydrogen bonds between atoms in the same residue or sequential residues are ignored. These long-range hydrogen bonds frequently use backbone atoms as hydrogen bond acceptors, i.e., OP1, OP2, O2', O3', O4', or O5', or as a donor (2'OH). A surprisingly large number of such hydrogen bonds are found, considering that neither single-stranded nor double-stranded regions will contain such hydrogen bonds unless additional interactions with other residues exist. Among 8327 long-range hydrogen bonds found in this set of structures, 2811, or about one-third, are hydrogen bonds entailing RNA backbone atoms; they involve 39% of all nucleotides in the structures. The majority of them (2111) are hydrogen bonds entailing ribose hydroxyl groups, which can be used either as a donor or an acceptor; they constitute 25% of all hydrogen bonds and involve 31% of all nucleotides. The phosphate oxygens OP1 or OP2 are used as hydrogen bond acceptors in 12% of all nucleotides, and the ribose ring oxygen O4' and phosphodiester oxygens O3' and O5' are used in 4%, 4%, and 1% of all nucleotides, respectively. Distributions of geometric parameters and some examples of such hydrogen bonds are presented in this report. A novel motif involving backbone hydrogen bonds, the ribose-phosphate zipper, is also identified.

Fig. 1

Histograms of H-bond heavy atom distances (A–F) and scatter plots of H-bond angle versus heavy atom distance (G–I). The histograms are shown for BH-bonds 2′OH–O with nucleobase acceptors (A) and backbone acceptors excluding O2′ (B), BH-bonds 2′OH–O2′ (C), H-bonds NH–O with nucleobase acceptors (D), BH-bonds NH–O with backbone acceptors (E), and H-bonds NH–N (F). The scatter plots are shown for H-bonds NH–O with nucleobase acceptors (G), BH-bonds NH–O with backbone acceptors (H), and H-bonds NH–N (I). Superimposed on the scatter plots are the lines of equal energy calculated for isolated H-bonds. The energy increments relative to the H-bond with the optimal geometry are +1, +3, +5, and +10 kcal mol⁻¹ for the four lines, respectively; the energy labels are shown only in H for clarity. In each case, the total number of relevant H-bonds is shown in parentheses.

Fig. 2

Examples of adenine H-bonds with ribose atoms: N1–O2′ (A), N3–O2′ (B), N6–O2′ (C and D), and N6–O4′ (E). The hydroxyl oxygen O2′ serves as an H-bond donor (A, B) or acceptor (C, D). In (A), adenine and guanine make a group 12 AG pair (trans-sugar edge/sugar edge), which is part of the A-minor I motif with G14 Watson–Crick-base paired to C78 and hydroxyl group of C78 making additional H-bonds with the A81 ribose (not shown); G14–C78 is part of a GC-rich helix in the lysine riboswitch (PDB 3DIL). In (B), the unclassified AC pair is part of the A-minor II motif, with A551 interacting with the minor groove of 8-base pair helix (not shown) in 23S rRNA (PDB 1VQ8). In (C), A and G form a group 6 AG pair (trans-Watson–Crick/sugar edge) in 16S rRNA (PDB 2VQE). In (D and E), A and G form group 10 AG pair (trans-Hoogsteen/sugar edge); both are from 23S rRNA (PDB 1VQ8). In (D), the AN1–O2′ H-bond is formed, and in (E), the AN1–O4′ H-bond is formed instead, which is correlated with C2′–endo sugar pucker of G47. Here, and in other molecular graphics, the numbering scheme from the PDB files is used.

Fig. 3

Examples of guanine–ribose interactions: the original G-ribo interaction with GN2–O4′ and GO2′–O2′ H-bonds (A); “reverse G-ribo” interaction with GN2–O2′ and GO2′–O4′ H-bonds (B); a variant G-ribo with three H-bonds, GN2–O3′, GN3–O2′, and GO2′–O2′ (C). All examples are from 23S rRNA, PDB 1VQ8.

Fig. 4

Examples of group 8 AA base pairs (trans-Hoogsteen/Hoogsteen) from 23S rRNA in the large ribosomal subunit, PDB 1VQ8. In addition to the Hoogsteen edge/sugar edge H-bonds, these pairs are stabilized by one (A) or two (B) H-bonds between the adenine amino proton and phosphate OP2 oxygen.

Fig. 5

Group 10 AG base pair (the same as shown in Fig. 2D). The phosphate oxygen OP2 of the residue immediately upstream of A is making bifurcated H-bonds with imino and amino protons of G. The nucleobase atoms of the upstream residue, labeled X48, are omitted for clarity.

Fig. 6

Examples of major-groove triples AU–U (A) and GC–U (B) with additional O2′–OP2 H-bonds stabilizing the triples. Both examples are from 23S rRNA, PDB 1VQ8.

Fig. 7

Stabilization of bulged-out bases with O2′–OP2 (A) or O2′–OP1 H-bond. The examples are from the lysine riboswitch, PDB 3DIL (A), and 16S rRNA, PDB 2VQE (B).

Fig. 8

Ribose–phosphate zipper motifs with side-by-side O2′–OP1 (A), O2′–OP2 (B) and mixed O2′–OP1/OP2 interactions (C). The examples are from tRNA^Tyr, PDB 1J1U (A), and 23S rRNA, PDB 1VQ8 (B and C).