ArticleNucleic acids research2024
Single-molecule visualization of sequence-specific RNA binding by a designer PPR protein.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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.
The trial behind it
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Who cites it
8 citing papers in PubMed.
- Pentatricopeptide repeat proteins in crops: Advances in functional mechanisms and breeding applications.Journal of integrative plant biology · 2026Review
- Expanding the palette of cis-elements to tune the expression of chloroplast transgenes in tobacco.The Plant journal : for cell and molecular biology · 2026Article
- Structural basis of plant organelle C-to-U RNA editing by PPR-DYW proteins.Nature communications · 2026Article
- Structures of pentatricopeptide repeat proteins.Acta crystallographica. Section F, Structural biology communications · 2026Review
- Can transcriptome size and off-target effects explain the contrasting evolution of mitochondrial vs nuclear RNA editing?Journal of evolutionary biology · 2025Article
- Synthetic Pentatricopeptide Repeat Proteins: Building a Toolkit for Precise RNA Control.International journal of molecular sciences · 2025Review
- RECODE: a programmable guide-free C-to-U RNA editing tool.Nucleic acids research · 2025Article
- GRASP: a modular toolkit for building synthetic pentatricopeptide repeat RNA-binding proteins.Nucleic acids research · 2025Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Pentatricopeptide repeat proteins (PPR) are a large family of modular RNA-binding proteins, whereby each module can be modified to bind to a specific ssRNA nucleobase. As such, there is interest in developing 'designer' PPRs (dPPRs) for a range of biotechnology applications, including diagnostics or in vivo localization of ssRNA species; however, the mechanistic details regarding how PPRs search for and bind to target sequences is unclear. To address this, we determined the structure of a dPPR bound to its target sequence and used two- and three-color single-molecule fluorescence resonance energy transfer to interrogate the mechanism of ssRNA binding to individual dPPRs in real time. We demonstrate that dPPRs are slower to bind longer ssRNA sequences (or could not bind at all) and that this is, in part, due to their propensity to form stable secondary structures that sequester the target sequence from dPPR. Importantly, dPPR binds only to its target sequence (i.e. it does not associate with non-target ssRNA sequences) and does not 'scan' longer ssRNA oligonucleotides for the target sequence. The kinetic constraints imposed by random 3D diffusion may explain the long-standing conundrum of why PPR proteins are abundant in organelles, but almost unknown outside them (i.e. in the cytosol and nucleus).
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Identifiers
What Socratic holds
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 Socratic graph.