Evidence map›Paper›PMID 36369947›Full record

ArticleRNA biology2022

High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavage.

Md Solayman, Thomas Litfin, Yaoqi Zhou, Jian Zhan

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in RNA biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.2field-weighted citation impact, top 51% 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

1 citing paper in PubMed, 2 citations in OpenAlex.

  1. Article
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

4 authors at 1 institution in 2 countries.

Md SolaymanInstitute for Glycomics, Griffith University, Parklands Dr, Southport, QLD, Australia.ORCID 0000-0003-4316-5211
Thomas LitfinInstitute for Glycomics, Griffith University, Parklands Dr, Southport, QLD, Australia.
Yaoqi ZhouInstitute for Glycomics, Griffith University, Parklands Dr, Southport, QLD, Australia.
Jian ZhanInstitute for Glycomics, Griffith University, Parklands Dr, Southport, QLD, Australia.
Griffith University · AU

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Given the challenges for the experimental determination of RNA tertiary structures, probing solvent accessibility has become increasingly important to gain functional insights. Among various chemical probes developed, backbone-cleaving hydroxyl radical is the only one that can provide unbiased detection of all accessible nucleotides. However, the readouts have been based on reverse transcription (RT) stop at the cleaving sites, which are prone to false positives due to PCR amplification bias, early drop-off of reverse transcriptase, and the use of random primers in RT reaction. Here, we introduced a fixed-primer method called RL-Seq by performing RtcB Ligation (RL) between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavage prior to high-throughput sequencing. The application of this method to

Indexed as

Amino Acyl-tRNA SynthetasesEscherichia coli ProteinsEscherichia coliHigh-Throughput Nucleotide SequencingHydroxyl RadicalNucleic Acid ConformationNucleotidesRNASolventsAmino Acyl-tRNA SynthetasesEscherichia coli ProteinsHydroxyl RadicalNucleotidesRNARtcB protein, E coliSolventshydroxyl radicalprobingRL-SeqSASAsolvent accessibility

Identifiers

PMID36369947
PMCPMC9662193
OpenAlexW4309073097

What Socratic holds

Textmetadata
LicenceCC BY-NC
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 Socratic graph.