Prevalence of dual-donating amines in key regions of functional RNAs

Abstract

RNA performs many critical functions, nearly all of which are enabled by complex H-bonded structures. Nucleotides possess far fewer H-bond donors than acceptors, and the exocyclic amine is the only functional group that can donate two H-bonds, suggesting a specialized role. To assess the prevalence and structural contexts of dual-donating amines within structured RNAs, we created a computational workflow that mines and analyzes experimental RNA-containing structures. We evaluated H-bonding in over 250,000 amines from more than 1800 structures. Dual-donating amines were found most frequently in G's where they regularly interacted with diverse pairs of acceptors. In contrast, the dual-donating amines of A's and C's were less frequent, and they interacted with a more select set of acceptors. For all three nucleobases, amines that were dual-donating had both reduced solvent accessibility and higher atom density relative to amines that were single- or non-donating, indicating a tendency of dual donors to be more buried and help compact the RNA. Analysis of RNA pseudotorsion angles revealed that dual-donating amines are enriched in two non-A-form conformations, both of which are present in S-motifs found in the sarcin–ricin loop of rRNA. We find that dual-donating amines populate additional structural motifs including the GNRA tetraloop-receptor complex, the kink-turn, and the WC/H A-minor motif, which are present in the self-splicing group I intron, the SAM riboswitch, and the poly(A)-bound ENE. We suggest that dual-donating amines may enhance interactions by reducing conformational entropy loss of the RNA as well as strengthening nearby H-bonds.