ArticleThe journal of physical chemistry. B2018
How the Conformations of an Internal Junction Contribute to Fold an RNA Domain.
Article in The journal of physical chemistry. B, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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.
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Who cites it
7 citing papers in PubMed, 11 citations in OpenAlex.
- Pressure pushes tRNAProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA.The journal of physical chemistry letters · 2022Article
- Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering.IUCrJ · 2020Article
- Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics.Journal of the American Chemical Society · 2020Article
- Salt Dependence of A-Form RNA Duplexes: Structures and Implications.The journal of physical chemistry. B · 2019Article
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
- Going beyond base-pairs: topology-based characterization of base-multiplets in RNA.RNA (New York, N.Y.) · 2019Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Like proteins, some RNAs fold to compact structures. We can model functional RNAs as a series of short, rigid, base-paired elements, connected by non-base-paired nucleotides that serve as junctions. These connecting regions bend and twist, facilitating the formation of tertiary contacts that stabilize compact states. Here, we explore the roles of salt and junction sequence in determining the structures of a ubiquitous connector: an asymmetric internal loop. We focus on the J5/5a junction from the widely studied P4-P6 domain of the Tetrahymena ribozyme. Following the addition of magnesium ions to fold P4-P6, this junction bends dramatically, bringing the two halves of the RNA domain together for tertiary contact engagement. Using single-molecule fluorescence resonance energy transfer (smFRET), we examine the role of sequence and salt on model RNA constructs that contain these junction regions. We explore the wild-type J5/5a junction as well as two sequence variants. These junctions display distinct, salt-dependent conformations. Small-angle X-ray scattering (SAXS) measurements verify that these effects persist in the full-length P4-P6 domain. These measurements underscore the importance of junction sequence and interactions with ions in facilitating RNA folding.
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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.