Evidence map›Paper›PMID 41390661›Full record

ArticleNature communications2025

High-speed 3D DNA PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography.

Gde Bimananda Mahardika Wisna, Daria Sukhareva, Jonathan Zhao, Prathamesh Chopade, Deeksha Satyabola, Michael Matthies, Subhajit Roy, Chao Wang, Petr Šulc, Hao Yan and 1 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Two-dimensional data storage using a DNA molecular register.Frontiers in bioengineering and biotechnology · 2026
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Gde Bimananda Mahardika WisnaDepartment of Physics, Arizona State University, Tempe, AZ, USA. gwisna@asu.edu.ORCID http://orcid.org/0000-0003-4463-944X
Daria SukharevaCenter for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA.ORCID http://orcid.org/0009-0002-9828-3725
Jonathan ZhaoCenter for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA.
Prathamesh ChopadeCenter for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA.ORCID http://orcid.org/0000-0002-2825-6791
Deeksha SatyabolaCenter for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA.ORCID http://orcid.org/0000-0003-0960-8103
Michael MatthiesCenter for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA.ORCID http://orcid.org/0000-0001-5979-1757
Subhajit RoyDepartment of Physics, Arizona State University, Tempe, AZ, USA.ORCID http://orcid.org/0000-0002-5887-4232
Chao WangCenter for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA.ORCID http://orcid.org/0000-0001-5020-961X
Petr ŠulcCenter for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA.ORCID http://orcid.org/0000-0003-1565-6769
Hao YanCenter for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA.ORCID http://orcid.org/0000-0001-7397-9852
Rizal F HariadiDepartment of Physics, Arizona State University, Tempe, AZ, USA. rhariadi@asu.edu.ORCID http://orcid.org/0000-0001-7840-859X

Funding

Nanoscale reconstruction of mechanical systems involved in disease pathogenesisDP2AI144247 · NIAID · ARIZONA STATE UNIVERSITY-TEMPE CAMPUS · PI HARIADI, RIZAL FAJAR · 2018 to 2018
$2.4M
Integrated Nano-Opto-Fluidic System on Sapphire towards Single-Molecule Protein SequencingDP2GM149552 · NIGMS · ARIZONA STATE UNIVERSITY-TEMPE CAMPUS · PI WANG, CHAO · 2022 to 2025
$2.2M
American Heart Association (American Heart Association, Inc.) 23PRE1029870National Science Foundation (NSF) CAREER - 2341002National Science Foundation (NSF) SemiSynBio-II 2027215National Science Foundation (NSF) Semisynbio III- 2227650NIAID NIH HHS DP2 AI144247NIGMS NIH HHS DP2 GM149552U.S. Department of Health & Human Services | National Institutes of Health (NIH) 1DP2AI144247-01
6 · The paper itself

Abstract

DNA origami information storage is a promising alternative to silicon-based data storage, offering a molecular cryptography technique concealing information within DNA origami. Routing, sliding, and interlacing staple strands lead to a large 700-bit key size. Practical DNA data storage requires high information density, robust security, and accurate and rapid information retrieval. Consequently, advanced readout techniques and large encryption key sizes are essential. Here, we report an enhanced DNA origami cryptography protocol in 2D and 3D DNA origami, increasing the encryption key size. We employ all-DNA-based steganography with fast readout through high-speed DNA-PAINT super-resolution imaging. By combining DNA-PAINT data with unsupervised clustering, we achieve an accuracy of up to 89%, despite the flexibility in the 3D DNA origami shown by oxDNA simulation. Furthermore, we propose criteria that ensure complete information retrieval for the DNA origami cryptography. Our findings show that DNA-based cryptography is a secure and versatile solution for storing information.

Indexed as

Computer SecurityDNAInformation Storage and RetrievalCluster AnalysisImaging, Three-DimensionalNucleic Acid ConformationDNA

Identifiers

PMID41390661
PMCPMC12749235

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.