Pairwise Coupling Analysis of Helical Junction Hydrogen Bonding Interactions in Luteoviral RNA Pseudoknots

Abstract

A 28-nucleotide mRNA pseudoknot that overlaps the P1 and P2 genes of sugarcane yellow leaf virus (ScYLV) stimulates −1 ribosomal frameshifting. The in vitro frameshifting efficiency is decreased ≥8-fold upon substitution of the 3‘-most loop 2 nucleotide (C27) with adenosine, which accepts a hydrogen bond from the 2‘-OH group of C14 in stem S1. The solution structures of the wild-type (WT) and C27A ScYLV RNA pseudoknots show that while the RNAs adopt virtually identical overall structures, there are significant structural differences at the helical junctions of the two RNAs. Specifically, C8+ in loop L1 in the C8+·(G12·C28) L1−S2 major groove base triple is displaced by ≈2.3 Å relative to the accepting stem 2 base pair (G12·C28) in the C27A RNA. Here, we use a double mutant cycle approach to analyze the pairwise coupling of the C8+·(G12·C28)···C27·(C14-G7) and ···A27·(C14-G7) hydrogen bonds in the WT and C27A ScYLV RNAs, respectively, and compare these findings with previous results from the beet western yellows virus (BWYV) RNA. We find that the pairwise coupling free energy (δABi) is favorable for the WT RNA (−0.7 ± 0.1 kcal/mol), thus revealing that formation of these two hydrogen bonds is positively cooperative. In contrast, δABi is 0.9 ± 0.4 kcal/mol for the poorly functional C27A ScYLV RNA, indicative of nonadditive hydrogen bond formation. These results reveal that cooperative hydrogen bond formation across the helical stem junction in H-type pseudoknots correlates with enhanced frameshift stimulation by luteoviral mRNA pseudoknots.