ArticleBiochemistry2006
Pairwise coupling analysis of helical junction hydrogen bonding interactions in luteoviral RNA pseudoknots.
Article in Biochemistry, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 13 citations in OpenAlex.
- Ribosome-induced mRNA pseudoknot interactions visualized by DMS MaP-Seq.bioRxiv : the preprint server for biology · 2025Article
- Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for -1 ribosomal frameshifting stimulation.Scientific reports · 2016Article
- Experimental approaches for measuring pKa's in RNA and DNA.Methods in enzymology · 2014Article
- The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin.PloS one · 2012Article
- Predicting loop-helix tertiary structural contacts in RNA pseudoknots.RNA (New York, N.Y.) · 2010Article
- Frameshifting RNA pseudoknots: structure and mechanism.Virus research · 2009Review
- The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical.RNA (New York, N.Y.) · 2006Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
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 >or=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 approximately 2.3 A 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 (delta(AB)(i)) 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, delta(AB)(i) 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.
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