SHAPE to Probe RNA Structure and RNA-Protein Interactions In Vitro.

Kaushik Saha, Gourisankar Ghosh

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact, top 87% 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

0 citing papers in PubMed, 0 citations in OpenAlex.

No citing paper in PubMed yet.

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 1 institution in 1 country.

Kaushik SahaDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.

Gourisankar GhoshDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA. gghosh@ucsd.edu.

University of California San Diego · US

Funding

Investigation of Gene Regulation by NF-kappaB Transcription factorsR01GM085490 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GHOSH, GOURISANKAR · 2009 to 2023

$3.8M

NIGMS NIH HHS R01 GM085490

6 · The paper itself

Abstract

Selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) is used to distinguish between the levels of flexibility of nucleotides regulated by base pairing or protein binding. In this method, a reagent reacts with the 2' hydroxyl group to form an adduct, which is then detected by reverse transcription reaction. The number of RNA molecules with an adduct at a specific nucleotide position indicates the SHAPE reactivity of that nucleotide. Here, we describe the method for probing the structure of an RNA in a protein-free or a protein-bound state by in vitro SHAPE.

Indexed as

RNARNA FoldingAcylationNucleic Acid ConformationNucleotidesNucleotidesRNAPhosphorimagingReverse transcriptionRNA end-labelingRNA–protein interactionRNA structureSelective 2′ hydroxyl acylation analyzed by primer extension (SHAPE)Sequencing gel

Identifiers

PMID37166657

DOI10.1093/bioinformatics/btp250

OpenAlexW4376132802

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.