Evidence map›Paper›PMID 29988105›Full record

ArticleNature protocols2018

Programming DNA origami assembly for shape-resolved nanomechanical imaging labels.

Jie Chao, Honglu Zhang, Yikang Xing, Qian Li, Huajie Liu, Lihua Wang, Lianhui Wang, Chunhai Fan

Abstract read
PubMed Publisher
In one paragraph

Article in Nature protocols, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
1.3field-weighted citation impact, top 20% 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

5 citing papers in PubMed, 26 citations in OpenAlex.

  1. Article
  2. Single-Molecule Nanomechanical Genotyping with DNA Origami-Based Shape IDs.Methods in molecular biology (Clifton, N.J.) · 2023
    Article
  3. Review
  4. Article
  5. DNA nanostructures: A versatile lab-bench for interrogating biological reactions.Computational and structural biotechnology journal · 2019
    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

8 authors at 2 institutions in 1 country.

Jie ChaoKey Laboratory for Organic Electronics and Information Displays (KLOEID), Institute of Advanced Materials (IAM), Jiangsu Key Laboratory for Biosensors, School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, China.
Honglu ZhangDivision of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.
Yikang XingKey Laboratory for Organic Electronics and Information Displays (KLOEID), Institute of Advanced Materials (IAM), Jiangsu Key Laboratory for Biosensors, School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, China.
Qian LiDivision of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.
Huajie LiuDivision of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.
Lihua WangDivision of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.
Lianhui WangKey Laboratory for Organic Electronics and Information Displays (KLOEID), Institute of Advanced Materials (IAM), Jiangsu Key Laboratory for Biosensors, School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, China. iamlhwang@njupt.edu.cn.ORCID http://orcid.org/0000-0001-9030-9172
Chunhai FanDivision of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China. fchh@sinap.ac.cn.ORCID http://orcid.org/0000-0002-7171-7338
Nanjing University of Posts and Telecommunications · CNShanghai Institute of Applied Physics · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Atomic force microscopy (AFM)-based nanomechanical imaging provides a high-resolution approach for imaging biomolecules with nanometer resolution. Nevertheless, the lack of appropriate nanomechanical labels poses a limit to biological applications. Here, we describe how to generate a set of shape-resolved nanomechanical labels by exploiting self-assembled DNA origami technology. By designing 'mediator' strands that can hybridize with both the origami shapes and the target DNA, these origami shape IDs can be used to site-specifically label genomic DNA with high efficiency and high throughput. When DNA origami shape IDs are used to label target sequences containing two single-nucleotide polymorphisms (SNPs), this approach is capable of differentiating adjacent labeling sites separated by only 30 nucleobases (~10 nm) under AFM imaging. This resolution is a threefold improvement of that which can be obtained with imaging-based genotyping using super-resolution imaging. We further demonstrate how to use origami shape IDs for high-resolution genotyping of SNPs in disease-associated genes in patients. The entire protocol takes ~2 d to complete.

Indexed as

DNADNA ProbesGenotyping TechniquesMicroscopy, Atomic ForceNucleic Acid HybridizationStaining and LabelingDNADNA Probes

Identifiers

PMID29988105
OpenAlexW2813591521

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.