Reversible DNA Encapsulation in Silica to Produce ROS-Resistant and Heat-Resistant Synthetic DNA “Fossils”
Abstract
This protocol describes a method for encapsulating DNA into amorphous silica (glass) spheres, mimicking the protection of nucleic acids within ancient fossils. In this approach, DNA encapsulation is achieved after the ammonium functionalization of silica nanoparticles. Within the glass spheres, the nucleic acid molecules are hermetically sealed and protected from chemical attack, thereby withstanding high temperatures and aggressive radical oxygen species (ROS). The encapsulates can be used as inert taggants to trace chemical and biological entities. The present protocol is applicable to short double-stranded (ds) and single-stranded (ss) DNA fragments, genomic DNA and plasmids. The nucleic acids can be recovered from the glass spheres without harm by using fluoride-containing buffered oxide etch solutions. Special emphasis is placed in this protocol on the safe handling of these buffered hydrogen fluoride solutions. After dissolution of the spheres and subsequent purification, the nucleic acids can be analyzed by standard techniques (gel electrophoresis, quantitative PCR (qPCR) and sequencing). The protocol requires 6 d for completion with a total hands-on time of 4 h.
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Grass and co-workers proposed DNA silica fossilization technology, through which they obtained stable DNA after 35 days in 65 °C (equivalent to two years at room temperature).
“Based on this discovery, Grass and co-workers proposed DNA silica fossilization technology, through which they obtained stable DNA after 35 days in 65 °C (equivalent to two years at room temperature) [38].”
From DNA Data Storage. (2023) · cites this paper as [38]
DNA-based files are encapsulated physically within discrete, impervious silica capsules, which are subsequently surface-labeled with unique single-stranded DNA barcodes that offer Boolean logic based selection on the entire data pool via simple hybridization.
“To realize this file system, we first encapsulate DNA-based files physically within discrete, impervious silica capsules9,23,24, which we subsequently surface-label with unique single-stranded DNA barcodes that offer Boolean logic based selection on the entire data pool via simple hybridization.”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [23]
Because physical encapsulation separates file sequences from external barcodes, the file system offers long-term environmental protection of encoded file sequences via silica encapsulation for permanent archival storage, where external barcodes may be renewed periodically, further protected with secondary encapsulation, or data pools may be stored using methods implemented in PCR-based random
“Because physical encapsulation separates file sequences from external barcodes that are used to describe the encapsulated information, our file system offers long-term environmental protection of encoded file sequences via silica encapsulation for permanent archival storage9,23,24, where external barcodes may be renewed periodically, further protected with secondary encapsulation, or data pools”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [23]
Because encapsulation of the DNA file sequence relies only on electrostatic interactions between positively-charged silica and the phosphate backbone of DNA, the approach can equally encapsulate any molecular weight of DNA molecule applicable to MB and larger file sizes, and is compatible with alternative DNA file compositions such as 100-200-mer oligonucleotides or multiple layers of encapsulated
“Because encapsulation of the DNA file sequence relies only on electrostatic interactions between positively-charged silica and the phosphate backbone of DNA, our approach can equally encapsulate any molecular weight of DNA molecule applicable to MB and larger file sizes, as demonstrated previously23, and is compatible with alternative DNA file compositions such as 100–200-mer oligonucleotides that”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [23]
The adaptation was accomplished by a more dilute condensation reaction as opposed to previously reported synthesis procedures.
“This was accomplished by a more dilute condensation reaction as opposed to previously reported synthesis procedures. [22,22,26]”
From Integrating DNA Encapsulates and Digital Microfluidics for Automated Data Storage in DNA (2022) · cites this paper as [26]
Once synthesized, DNA can be archived for millennia, preserving the generated randomness over generations to come.
“once synthesized, DNA can be archived for millennia, preserving the generated randomness over generations to come47,48.”
From DNA synthesis for true random number generation (2020) · cites this paper as [48]
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References 29 · Cited by 151
- Authors
- Paunescu, D., Puddu, M., Soellner, J. O. B., Stoessel, P. R., & Grass, R. N.
- Affiliations
- ETH Zurich (CH)
- Corresponding author
- Grass, Robert N
- ORCID
- Grass, Robert N
- Venue
- Nature Protocols
- Published
- 2013-11-07
- Volume
- 8
- Issue
- 12
- Pages
- 2440-2448
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- OpenAlex
- W2048735832
- Cited by
- 151
- References
- 29
- Citations by year
- 2026: 17 · 2025: 17 · 2024: 14 · 2023: 17 · 2022: 14 · 2021: 15 · 2020: 10 · 2019: 8 · 2018: 7 · 2017: 6 · 2016: 3 · 2015: 13 · 2014: 10
- FWCI
- 3.88
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Protocols (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Enzyme Catalysis and Immobilization
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Keywords
- DNA encapsulation, amorphous silica nanoparticles, heat resistance, nucleic acid preservation, fluoride etching, DNA recovery
- MeSH terms
- DNA, DNA, Single-Stranded, Fossils, Hot Temperature, Plasmids, Preservation, Biological, Silicon Dioxide, Surface Properties, Reactive Oxygen Species, Microscopy, Electron, Transmission
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