ArticleProceedings of the National Academy of Sciences of the United States of America2005
A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
62 citing papers in PubMed, 102 citations in OpenAlex.
- pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing.Nucleic acids research · 2026Article
- Ribosome-induced mRNA pseudoknot interactions visualized by DMS MaP-Seq.bioRxiv : the preprint server for biology · 2025Article
- Elaborated pseudoknots that stimulate -1 programmed ribosomal frameshifting or stop codon readthrough in RNA viruses.Journal of biomolecular structure & dynamics · 2025Article
- Characterization of the proteins encoded by a recently emerged cotton-infecting Polerovirus.Virus genes · 2024Article
- The Tautomeric State ofACS central science · 2024Article
- Complete nucleotide sequence of chrysanthemum virus D, a polero-like virus.Archives of virology · 2024Article
- Possible involvement of three-stemmed pseudoknots in regulating translational initiation in human mRNAs.PloS one · 2024Article
- Structural and Functional Insights into Viral Programmed Ribosomal Frameshifting.Annual review of virology · 2023Review
- RNA-As-Graphs Motif Atlas-Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications.International journal of molecular sciences · 2022Article
- RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.Briefings in bioinformatics · 2020Review
- An RNA pseudoknot stimulates HTLV-1RNA (New York, N.Y.) · 2020Article
- Alternate RNA Structures.Cold Spring Harbor perspectives in biology · 2020Review
- Complex dynamics under tension in a high-efficiency frameshift stimulatory structure.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- QRNAS: software tool for refinement of nucleic acid structures.BMC structural biology · 2019Article
- Translocation kinetics and structural dynamics of ribosomes are modulated by the conformational plasticity of downstream pseudoknots.Nucleic acids research · 2018Article
- Adenine protonation enables cyclic-di-GMP binding to cyclic-GAMP sensing riboswitches.RNA (New York, N.Y.) · 2018Article
- Effects of flanking regions on HDV cotranscriptional folding kinetics.RNA (New York, N.Y.) · 2018Article
- Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.PLoS computational biology · 2018Article
- Nanopore electric snapshots of an RNA tertiary folding pathway.Nature communications · 2017Article
- Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot.Nucleic acids research · 2017Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The molecular determinants of stimulation of -1 programmed ribosomal frameshifting (-1 PRF) by RNA pseudoknots are poorly understood. Sugarcane yellow leaf virus (ScYLV) encodes a 28-nt mRNA pseudoknot that promotes -1 PRF between the P1 (protease) and P2 (polymerase) genes in plant luteoviruses. The solution structure of the ScYLV pseudoknot reveals a well ordered loop 2 (L2) that exhibits continuous stacking of A20 through C27 in the minor groove of the upper stem 1 (S1), with C25 flipped out of the triple-stranded stack. Five consecutive triple base pairs flank the helical junction where the 3' nucleotide of L2, C27, adopts a cytidine 27 N3-cytidine 14 2'-OH hydrogen bonding interaction with the C14-G7 base pair. This interaction is isosteric with the adenosine N1-2'-OH interaction in the related mRNA from beet western yellows virus (BWYV); however, the ScYLV and BWYV mRNA structures differ in their detailed L2-S1 hydrogen bonding and L2 stacking interactions. Functional analyses of ScYLV/BWYV chimeric pseudoknots reveal that the ScYLV RNA stimulates a higher level of -1 PRF (15 +/- 2%) relative to the BWYV pseudoknot (6 +/- 1%), a difference traced largely to the identity of the 3' nucleotide of L2 (C27 vs. A25 in BWYV). Strikingly, C27A ScYLV RNA is a poor frameshift stimulator (2.0%) and is destabilized by approximately 1.5 kcal x mol(-1) (pH 7.0, 37 degrees C) with respect to the wild-type pseudoknot. These studies establish that the precise network of weak interactions nearest the helical junction in structurally similar pseudoknots make an important contribution to setting the frameshift efficiency in mRNAs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.