An official website of the United States government
Abstract DNA has emerged as a promising material to address growing data storage demands. We recently demonstrated a structure-based DNA data storage approach where DNA probes are spatially oriented on the surface of DNA origami and decoded using DNA-PAINT. In this approach, larger origami structures could improve the efficiency of reading and writing data. However, larger origami require long single-stranded DNA scaffolds that are not commonly available. Here, we report the engineering of a novel longer DNA scaffold designed to produce a larger rectangle origami needed to expand the origami-based digital nucleic acid memory (dNAM) approach. We confirmed that this scaffold self-assembled into the correct origami platform and correctly positioned DNA data strands using atomic force microscopy and DNA-PAINT super-resolution microscopy. This larger structure enables a 67% increase in the number of data points per origami and will support efforts to efficiently scale up origami-based dNAM.
more »
« less
High-speed 3D DNA PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography
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.
more »
« less
- Award ID(s):
- 2239518
- PAR ID:
- 10656346
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Nature Communications
- Volume:
- 16
- Issue:
- 1
- ISSN:
- 2041-1723
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract DNA is a compelling alternative to non-volatile information storage technologies due to its information density, stability, and energy efficiency. Previous studies have used artificially synthesized DNA to store data and automated next-generation sequencing to read it back. Here, we report digital Nucleic Acid Memory (dNAM) for applications that require a limited amount of data to have high information density, redundancy, and copy number. In dNAM, data is encoded by selecting combinations of single-stranded DNA with (1) or without (0) docking-site domains. When self-assembled with scaffold DNA, staple strands form DNA origami breadboards. Information encoded into the breadboards is read by monitoring the binding of fluorescent imager probes using DNA-PAINT super-resolution microscopy. To enhance data retention, a multi-layer error correction scheme that combines fountain and bi-level parity codes is used. As a prototype, fifteen origami encoded with ‘Data is in our DNA!\n’ are analyzed. Each origami encodes unique data-droplet, index, orientation, and error-correction information. The error-correction algorithms fully recover the message when individual docking sites, or entire origami, are missing. Unlike other approaches to DNA-based data storage, reading dNAM does not require sequencing. As such, it offers an additional path to explore the advantages and disadvantages of DNA as an emerging memory material.more » « less
-
DNA nanotechnology has broad applications in biomedical drug delivery and pro- grammable materials. Characterization of the self-assembly of DNA origami and quan- tum dots (QDs) is necessary for the development of new DNA-based nanostructures. We use computation and experiment to show that the self-assembly of 3D hierarchi- cal nanostructures can be controlled by programming the binding site number and their positions on DNA origami. Using biotinylated pentagonal pyramid wireframe DNA origamis and streptavidin capped QDs, we demonstrate that DNA origami with 1 binding site at the outer vertex can assemble multi-meric origamis with up to 6 DNA origamis on 1 QD, and DNA origami with 1 binding site at the inner center can only assemble monomeric and dimeric origamis. Meanwhile, the yield percentages of differ- ent multi-meric origamis are controlled by the QD:DNA-origami stoichiometric mixing ratio. DNA origamis with 2 binding sites at the αγ positions (of the pentagon) make larger nanostructures than those with binding sites at the αβ positions. In general, increasing the number of binding sites leads to increases in the nanostructure size. At high DNA origami concentration, the QD number in each cluster becomes the limiting factor for the growth of nanostructures. We find that reducing the QD size can also affect the self-assembly because of the reduced access to the binding sites from more densely packed origamis.more » « less
-
DNA is an incredibly dense storage medium for digital data. However, computing on the stored information is expensive and slow, requiring rounds of sequencing, in silico computation, and DNA synthesis. Prior work on accessing and modifying data using DNA hybridization or enzymatic reactions had limited computation capabilities. Inspired by the computational power of “DNA strand displacement,” we augment DNA storage with “in-memory” molecular computation using strand displacement reactions to algorithmically modify data in a parallel manner. We show programs for binary counting and Turing universal cellular automaton Rule 110, the latter of which is, in principle, capable of implementing any computer algorithm. Information is stored in the nicks of DNA, and a secondary sequence-level encoding allows high-throughput sequencing-based readout. We conducted multiple rounds of computation on 4-bit data registers, as well as random access of data (selective access and erasure). We demonstrate that large strand displacement cascades with 244 distinct strand exchanges (sequential and in parallel) can use naturally occurring DNA sequence from M13 bacteriophage without stringent sequence design, which has the potential to improve the scale of computation and decrease cost. Our work merges DNA storage and DNA computing, setting the foundation of entirely molecular algorithms for parallel manipulation of digital information preserved in DNA.<more » « less
-
Abstract The field of nucleic acid self‐assembly has advanced significantly, enabling the creation of multi‐dimensional nanostructures with precise sizes and shapes. These nanostructures hold great potential for various applications, including biocatalysis, smart materials, molecular diagnosis, and therapeutics. Here, dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA) are employed to investigate DNA origami nanostructures, focusing on size distribution and particle concentration. Compared to DLS, NTA provided higher resolution in size measurement with a smaller full‐width at half‐maximum (FWHM), making it particularly suitable for characterizing DNA nanostructure. To enhance sensitivity, a fluorescent NTA method is developed by incorporating an intercalation dye to amplify the fluorescence signals of DNA origami. This method is validated by analyzing various DNA origami structures, ranging from 1 and 2D flexible structures to 3D compact shapes, and evaluating structural assembly yields. Additionally, NTA is used to analyze dynamic DNA nanocages that undergo conformational switches among linear, square, and pyramid shapes in response to the addition of trigger strands. Quantitative size distribution data is crucial not only for production quality control but also for providing mechanistic insights into the various applications of DNA nanomaterials.more » « less
