Daniela Paunescu

Robust Chemical Preservation of Digital Information on DNA in Silica with Error‐Correcting Codes

Information, such as text printed on paper or images projected onto microfilm, can survive for over 500 years. However, the storage of digital information for time frames exceeding 50 years is challenging. Here we show that digital information can be stored on DNA and recovered without errors for considerably longer time frames. To allow for the perfect recovery of the information, we encapsulate the DNA in an inorganic matrix, and employ error-correcting codes to correct storage-related errors. Specifically, we translated 83 kB of information to 4991 DNA segments, each 158 nucleotides long, which were encapsulated in silica. Accelerated aging experiments were performed to measure DNA decay kinetics, which show that data can be archived on DNA for millennia under a wide range of conditions. The original information could be recovered error free, even after treating the DNA in silica at 70 °C for one week. This is thermally equivalent to storing information on DNA in central Europe for 2000 years.

Magnetically Recoverable, Thermostable, Hydrophobic DNA/Silica Encapsulates and Their Application as Invisible Oil Tags

A method to encapsulate DNA in heat-resistant and inert magnetic particles was developed. An inexpensive synthesis technique based on co-precipitation was utilized to produce Fe2O3 nanoparticles, which were further functionalized with ammonium groups. DNA was adsorbed on this magnetic support, and the DNA/magnet nanocluster was surface coated with a dense silica layer by sol-gel chemistry. The materials were further surface modified with hexyltrimethoxysilane to achieve particle dispersibility in hydrophobic liquids. The hydrodynamic particle sizes were evaluated by analytical disc centrifugation, and the magnetic properties were investigated by vibrating sample magnetometry. The obtained nanoengineered encapsulates showed good dispersion abilities in various nonaqueous fluids and did not affect the optical properties of the hydrophobic dispersant when present at concentrations lower than 10(3) μg/L. Upon magnetic separation and particle dissolution, the DNA could be recovered unharmed and was analyzed by quantitative real-time PCR and Sanger sequencing. DNA encapsulated within the magnetic particles was stable for 2 years in decalin at room temperature, and the stability was further tested at elevated temperatures. The new magnetic DNA/silica encapsulates were utilized to developed a low-cost platform for the tracing/tagging of oils and oil-derived products, requiring 1 μg/L=1 ppb levels of the taggant and allowing quantification of taggant concentration on a logarithmic scale. The procedure was tested for the barcoding of a fuel (gasoline), a cosmetic oil (bergamot oil), and a food grade oil (extra virgin olive oil), being able to verify the authenticity of the products.

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

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.

Proacetylenic Reactivity of a Push–Pull Buta-1,2,3-triene: New Chromophores and Supramolecular Systems

Proacetylenic: An aniline-based donor-acceptor-substituted butatriene exhibits not only cumulene-like dimerization to give a [4]radialene (λ =756 nm), but also acetylene-like (proacetylenic) reactivity towards tetracyanoethene, affording via [2+2] cycloaddition- cycloreversion a NIR-absorbing zwitterionic chromophore (λ = 825 nm). The cationic charge on the imminium-type nitrogen in the zwitterion is evidenced by host-guest complexation with a tetraphosphonate cavitand. Copyright

Labeling milk along its production chain with DNA encapsulated in silica

The capability of tracing a food product along its production chain is important to ensure food safety and product authenticity. For this purpose and as an application example, recently developed Silica Particles with Encapsulated DNA (SPED) were added to milk at concentrations ranging from 0.1 to 100 ppb (μg per kg milk). Thereby the milk, as well as the milk-derived products yoghurt and cheese, could be uniquely labeled with a DNA tag. Procedures for the extraction of the DNA tags from the food matrixes were elaborated and allowed identification and quantification of previously marked products by quantitative polymerase chain reaction (qPCR) with detection limits below 1 ppb of added particles. The applicability of synthetic as well as naturally occurring DNA sequences was shown. The usage of approved food additives as DNA carrier (silica = E551) and the low cost of the technology (<0.1 USD per ton of milk labeled with 10 ppb of SPED) display the technical applicability of this food labeling technology.

DNA protection against ultraviolet irradiation by encapsulation in a multilayered SiO2/TiO2 assembly

DNA is protected against UV-induced damage by encapsulation in a core-shell-shell particulate construct. The DNA is hermetically sealed in SiO2 particles coated with TiO2. The TiO2 coating acts as a physical sunscreen and prevents high energy photons from damaging the nucleic acids. DNA can be recovered unharmed from the protection system with fluoride comprising buffers, and then directly analyzed using biochemical standard techniques (quantitative PCR, gel electrophoresis and Sanger sequencing). The coatings increase the DNA UV resistance by 42 times, which is equivalent to the increase in UV resistance obtained by bacteria during sporulation. The attenuation coefficient of the 20 nm titania layer is 1.8 106 cm-1 at 254 nm UV irradiation and optical attenuation is largely attributed to light scattering on the titania surface.

Detecting and Number Counting of Single Engineered Nanoparticles by Digital Particle Polymerase Chain Reaction

The concentrations of nanoparticles present in colloidal dispersions are usually measured and given in mass concentration (e.g. mg/mL), and number concentrations can only be obtained by making assumptions about nanoparticle size and morphology. Additionally traditional nanoparticle concentration measures are not very sensitive, and only the presence/absence of millions/billions of particles occurring together can be obtained. Here, we describe a method, which not only intrinsically results in number concentrations, but is also sensitive enough to count individual nanoparticles, one by one. To make this possible, the sensitivity of the polymerase chain reaction (PCR) was combined with a binary (=0/1, yes/no) measurement arrangement, binomial statistics and DNA comprising monodisperse silica nanoparticles. With this method, individual tagged particles in the range of 60-250 nm could be detected and counted in drinking water in absolute number, utilizing a standard qPCR device within 1.5 h of measurement time. For comparison, the method was validated with single particle inductively coupled plasma mass spectrometry (sp-ICPMS).

Silica particles with encapsulated DNA as trophic tracers

Ecological networks such as food webs are extremely complex and can provide important information about the robustness and productivity of an ecosystem. In most cases, it is not feasible to observe trophic interactions between predators and prey directly and with the available methods, it is difficult to quantify the connections between them. Here, we show that submicron‐sized silica particles (100–150 nm) with encapsulated DNA (SPED) enable accurate food and organism labelling and quantification of specific animal‐to‐animal transfer over more than one trophic level. We found that SPED were readily transferable and quantifiable from the bottom to the top of a two‐level food chain of arthropods. SPED were taken up in the gut system and remained persistent in an animal over several days. When uniquely labelled SPED were applied at predefined ratios, we found that information about their relative abundance was reliably conserved after trophic level transfer and over time. SPED were also applied to investigate the flower preference of fly pollinators and proved to be a fast and accurate analysis method. SPED combine attributes of DNA barcoding and stable isotope analysis such as unique labelling, quantification via real‐time PCR and exact backtracking to the tracer source. This improves and simplifies the analysis and monitoring of ecological networks.

PCR quantification of SiO2 particle uptake in cells in the ppb and ppm range via silica encapsulated DNA barcodes

There is a strong interest in studying the cellular uptake of silica nanoparticles, particularly at medically relevant concentrations (ppb-ppm range) to understand their toxicology. At present, uptake analysis at these exposure levels is impeded by the high silica background concentration. Here we describe the use of DNA encapsulated within silica particles as a tool to quantify silica nanoparticles in in vitro cell-uptake experiments at low concentrations (down to 10 fg cell(-1)).

Self-defending anti-vandalism surfaces based on mechanically triggered mixing of reactants in polymer foils

The bombardier beetle uses attack-triggered mixing of reactants (hydrochinone, hydrogen peroxide (H2O2) and enzymes as catalysts) to defend itself against predators. Using multi-layer polymer sheets with H2O2 and catalyst (MnO2) filled compartments we developed a 2D analogous bio-inspired chemical defence mechanism for anti-vandalism applications. The reactants were separated by a brittle layer that ruptures upon mechanical attack and converts the mechanical energy trigger (usually a few Joules) into a chemical self-defence reaction involving release of steam, and optionally persistent dyes and a DNA-based marker for forensics. These surfaces effectively translate a weak mechanical trigger into an energetic chemical reaction with energy amplification of several orders of magnitude. Since the responsive materials presented here do not depend on electricity, they may provide a cost effective alternative to currently used safety systems in the public domain, automatic teller machines and protection of money transport systems. Anti-feeding protection in forestry or agriculture may similarly profit from such mechanically triggered chemical self-defending polymer surfaces.