Evidence map›Paper›PMID 35945159›Full record

ArticleAdvanced materials (Deerfield Beach, Fla.)2022

Massively Parallel Selection of NanoCluster Beacons.

Yu-An Kuo, Cheulhee Jung, Yu-An Chen, Hung-Che Kuo, Oliver S Zhao, Trung D Nguyen, James R Rybarski, Soonwoo Hong, Yuan-I Chen, Dennis C Wylie and 7 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Advanced materials (Deerfield Beach, Fla.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing 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

13 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Article
  6. Review
  7. Review
  8. Review
  9. Article
  10. Article
  11. Article
  12. Recent Advances in Single-Molecule Tracking and Imaging Techniques.Annual review of analytical chemistry (Palo Alto, Calif.) · 2023
    Review
  13. Massively Parallel Profiling of RNA-targeting CRISPR-Cas13d.bioRxiv : the preprint server for biology · 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

17 authors.

Yu-An KuoDepartment of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
Cheulhee JungDepartment of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea.
Yu-An ChenDepartment of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.ORCID https://orcid.org/0000-0001-7228-4696
Hung-Che KuoDepartment of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
Oliver S ZhaoDepartment of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
Trung D NguyenDepartment of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
James R RybarskiDepartment of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
Soonwoo HongDepartment of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
Yuan-I ChenDepartment of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
Dennis C WylieComputational Biology and Bioinformatics, Center for Biomedical Research Support, University of Texas at Austin, Austin, TX, 78712, USA.
John A HawkinsEuropean Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany.
Jada N WalkerDepartment of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
Samuel W J ShieldsDepartment of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
Jennifer S BrodbeltDepartment of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
Jeffrey T PettyDepartment of Chemistry, Furman University, Greenville, SC, 29617, USA.
Ilya J FinkelsteinDepartment of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
Hsin-Chih YehDepartment of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.ORCID https://orcid.org/0000-0001-6654-5626

Funding

Turning a sequence barcode into a spectral barcode for single-cell analysis.R21GM129617 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI FINKELSTEIN, ILYA J, YEH, HSIN-CHIH · 2019 to 2020
$398k
National Science Foundation CBET2029266National Science Foundation CBET2041345NIGMS NIH HHS R21 GM129617NIH HHS GM129617Texas 4000UT-Austin Catalyst GrantWelch Foundation F-1155Welch Foundation F-1808Welch Foundation F-1833
6 · The paper itself

Abstract

NanoCluster Beacons (NCBs) are multicolor silver nanocluster probes whose fluorescence can be activated or tuned by a proximal DNA strand called the activator. While a single-nucleotide difference in a pair of activators can lead to drastically different activation outcomes, termed polar opposite twins (POTs), it is difficult to discover new POT-NCBs using the conventional low-throughput characterization approaches. Here, a high-throughput selection method is reported that takes advantage of repurposed next-generation-sequencing chips to screen the activation fluorescence of ≈40 000 activator sequences. It is found that the nucleobases at positions 7-12 of the 18-nucleotide-long activator are critical to creating bright NCBs and positions 4-6 and 2-4 are hotspots to generate yellow-orange and red POTs, respectively. Based on these findings, a "zipper-bag" model is proposed that can explain how these hotspots facilitate the formation of distinct silver cluster chromophores and alter their chemical yields. Combining high-throughput screening with machine-learning algorithms, a pipeline is established to design bright and multicolor NCBs in silico.

Indexed as

Metal NanoparticlesSilverDNANucleotidesSpectrometry, FluorescenceDNANucleotidesSilverfluorescent nanomaterialshigh-throughput screeningNanoCluster Beaconsnext-generation sequencingsilver nanoclusters

Identifiers

PMID35945159
PMCPMC9588665

What OpenQuestion holds

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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.