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Reversible DNA encapsulation in silica to produce ROS-resistant and heat-resistant synthetic DNA 'fossils'

Nature Protocols volume 8, pages 2440–2448 (2013)Cite this article

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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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Figure 1: Workflow for DNA encapsulation and release.
Figure 2: Images of DNA/SiO2 particles encapsulating a short dsDNA segment (113 bp).
Figure 3: Evidence of DNA protection against ROS activity.
Figure 4: Sequencing chromatograms obtained from plasmid DNA before encapsulation and after release from DNA/SiO2 particles.
Figure 5: Amplification curves of dissolved DNA/SiO2 dispersions at different original particle dilutions.

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Acknowledgements

We thank the Institute for Chemical and Bioengineering (ICB) at ETH Zurich, the EU-ITN network Mag(net)icFun (PITN-GA-2012-290248) and the Swiss National Science Foundation (no. 200021-150179) for financial support. We also thank W.J. Stark for helpful discussions.

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Authors and Affiliations

  1. ETH Zurich, Functional Materials Laboratory, Zurich, Switzerland

    Daniela Paunescu, Michela Puddu, Justus O B Soellner, Philipp R Stoessel & Robert N Grass

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  1. Daniela Paunescu
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  2. Michela Puddu
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  3. Justus O B Soellner
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  4. Philipp R Stoessel
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  5. Robert N Grass
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Contributions

R.N.G. elaborated the concept. D.P., M.P., J.O.B.S. and R.N.G. developed and optimized the protocol. P.R.S. performed electron microscopy. D.P., M.P., P.R.S. and R.N.G. wrote the paper.

Corresponding author

Correspondence to Robert N Grass.

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Competing interests

R.N.G. declares financial interest in the form of a patent application (no. WO2013/143014) on DNA encapsulation licensed to TurboBeads, LLC, of which R.N.G. is a shareholder and employee. The remaining authors are employed by ETH Zurich and have no competing financial interests.

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Paunescu, D., Puddu, M., Soellner, J. et al. Reversible DNA encapsulation in silica to produce ROS-resistant and heat-resistant synthetic DNA 'fossils'. Nat Protoc 8, 2440–2448 (2013). https://doi.org/10.1038/nprot.2013.154

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