Evidence map›Paper›PMID 29185740›Full record

ArticleJournal of the American Chemical Society2017

Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway.

Steve Bonilla, Charles Limouse, Namita Bisaria, Magdalena Gebala, Hideo Mabuchi, Daniel Herschlag

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of the American Chemical Society, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements.Proceedings of the National Academy of Sciences of the United States of America · 2023
    Article
  5. Review
  6. Article
  7. Article
  8. Article
  9. Article
  10. The Story of RNA Folding, as Told in Epochs.Cold Spring Harbor perspectives in biology · 2018
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Steve BonillaDepartment of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States.ORCID 0000-0002-6526-7158
Charles LimouseDepartment of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States.
Namita BisariaDepartment of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States.
Magdalena GebalaDepartment of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States.
Hideo MabuchiDepartment of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States.
Daniel HerschlagDepartment of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Decades of study of the RNA folding problem have revealed that diverse and complex structured RNAs are built from a common set of recurring structural motifs, leading to the perspective that a generalizable model of RNA folding may be developed from understanding of the folding properties of individual structural motifs. We used single-molecule fluorescence to dissect the kinetic and thermodynamic properties of a set of variants of a common tertiary structural motif, the tetraloop/tetraloop-receptor (TL/TLR). Our results revealed a multistep TL/TLR folding pathway in which preorganization of the ubiquitous AA-platform submotif precedes the formation of the docking transition state and tertiary A-minor hydrogen bond interactions form after the docking transition state. Differences in ion dependences between TL/TLR variants indicated the occurrence of sequence-dependent conformational rearrangements prior to and after the formation of the docking transition state. Nevertheless, varying the junction connecting the TL/TLR produced a common kinetic and ionic effect for all variants, suggesting that the global conformational search and compaction electrostatics are energetically independent from the formation of the tertiary motif contacts. We also found that in vitro-selected variants, despite their similar stability at high Mg

Indexed as

Nucleic Acid ConformationNucleotide MotifsRNA FoldingSingle Molecule ImagingFluorescenceKineticsRNARNA StabilityStatic ElectricityThermodynamicsRNA

Identifiers

PMID29185740
PMCPMC5748328

What OpenQuestion holds

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Read underepoch 390

Registered trials

None linked

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.