Synergistic SHAPE/Single-Molecule Deconvolution of RNA Conformation under Physiological Conditions.

Mario Vieweger, David J Nesbitt

Open access · bronzeAbstract read

In one paragraph

Article in Biophysical journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it

0cells of the map it votes in

2citing papers in PubMed

0.5field-weighted citation impact, top 37% of its field

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

2 citing papers in PubMed, 5 citations in OpenAlex.

On the Problem of Reconstructing a Mixture of RNA Structures.Bulletin of mathematical biology · 2020
Article
Challenges and approaches to predicting RNA with multiple functional structures.RNA (New York, N.Y.) · 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

2 authors at 2 institutions in 1 country.

Mario ViewegerJILA, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado.

David J NesbittJILA, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado; Department of Physics, University of Colorado, Boulder, Colorado. Electronic address: djn@colorado.edu.

National Institute of Standards and Technology · USUniversity of Colorado Boulder · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Structural RNA domains are widely involved in the regulation of biological functions, such as gene expression, gene modification, and gene repair. Activity of these dynamic regions depends sensitively on the global fold of the RNA, in particular, on the binding affinity of individual conformations to effector molecules in solution. Consequently, both the 1) structure and 2) conformational dynamics of noncoding RNAs prove to be essential in understanding the coupling that results in biological function. Toward this end, we recently reported observation of three conformational states in the metal-induced folding pathway of the tRNA-like structure domain of Brome Mosaic Virus, via single-molecule fluorescence resonance energy transfer studies. We report herein selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE)-directed structure predictions as a function of metal ion concentrations ([M

Indexed as

Nucleic Acid ConformationBase SequenceBromovirusDiffusionDNA PrimersHydroxyl RadicalDNA PrimersHydroxyl Radical

Identifiers

PMID29694857

DOI10.1016/j.bpj.2018.02.022

PMCPMC5937115

OpenAlexW2801738710

What OpenQuestion holds

Textmetadata

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.