Evidence map›Paper›PMID 35361863›Full record

ArticleCommunications biology2022

Improving the specificity of nucleic acid detection with endonuclease-actuated degradation.

Roger S Zou, Momcilo Gavrilov, Yang Liu, Dominique Rasoloson, Madison Conte, Justin Hardick, Leo Shen, Siqi Chen, Andrew Pekosz, Geraldine Seydoux and 2 more

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

Article in Communications biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.6field-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

3 citing papers in PubMed, 7 citations in OpenAlex.

  1. Review
  2. Expression and Functional Analysis of the Compact ThermophilicInternational journal of molecular sciences · 2023
    Article
  3. Multiplexed electrochemical assays for clinical applications.Current opinion in electrochemistry · 2023
    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

12 authors at 2 institutions in 1 country.

Roger S ZouDepartment of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0003-1338-6398
Momcilo GavrilovDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-5816-3406
Yang LiuDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-3889-9707
Dominique RasolosonDepartment of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Madison ConteDivision of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Justin HardickDivision of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Leo ShenDepartment of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-9563-6276
Siqi ChenDepartment of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Andrew PekoszDepartment of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.ORCID http://orcid.org/0000-0003-3248-1761
Geraldine SeydouxDepartment of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Yukari C ManabeDivision of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Taekjip HaDepartment of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA. tjha@jhu.edu.ORCID http://orcid.org/0000-0003-2195-6258
Johns Hopkins University · USHoward Hughes Medical Institute · US

Funding

TrainingU54EB007958 · NIBIB · JOHNS HOPKINS UNIVERSITY · PI Susan Anne Tuddenham · 2007 to 2026
$34.6M
Medical Scientist Training ProgramT32GM136577 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI ANDREA L COX · 2020 to 2026
$13.4M
Regulation of Germ Cell Fate During EmbryogenesisR37HD037047 · NICHD · JOHNS HOPKINS UNIVERSITY · PI SEYDOUX, GERALDINE CATHERINE JOELLE · 2016 to 2025
$3.8M
Single Molecule Studies of Nucleic Acids RemodelingR35GM122569 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Taekjip Ha · 2017 to 2026
$3.5M
High-throughput characterization of epigenetic context on DNA double strand break repair dynamicsF30CA254160 · NCI · JOHNS HOPKINS UNIVERSITY · PI ZOU, ROGER · 2020 to 2022
$151k
NCI NIH HHS F30 CA254160NIBIB NIH HHS U54 EB007958NICHD NIH HHS R37 HD037047NIGMS NIH HHS R35 GM122569NIGMS NIH HHS T32 GM136577
6 · The paper itself

Abstract

Nucleic acid detection is essential for numerous biomedical applications, but often requires complex protocols and/or suffers false-positive readouts. Here, we describe SENTINEL, an approach that combines isothermal amplification with a sequence-specific degradation method to detect nucleic acids with high sensitivity and sequence-specificity. Target single-stranded RNA or double-stranded DNA molecules are amplified by loop-mediated isothermal amplification (LAMP) and subsequently degraded by the combined action of lambda exonuclease and a sequence-specific DNA endonuclease (e.g., Cas9). By combining the sensitivity of LAMP with the precision of DNA endonucleases, the protocol achieves attomolar limits of detection while differentiating between sequences that differ by only one or two base pairs. The protocol requires less than an hour to complete using a 65 °C heat block and fluorometer, and detects SARS-CoV-2 virus particles in human saliva and nasopharyngeal swabs with high sensitivity.

Indexed as

COVID-19Molecular Diagnostic TechniquesNucleic Acid Amplification TechniquesNucleic AcidsDNAEndonucleasesHumansSARS-CoV-2DNAEndonucleasesNucleic Acids

Identifiers

PMID35361863
PMCPMC8971390
OpenAlexW4220662869

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.