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

Păunescu, Daniela; Puddu, Michela; Soellner, Justus Oliver Butz; Stoessel, Philipp R.; Grass, Robert N.

doi:10.1038/nprot.2013.154

Cited by 111 publications

(208 citation statements)

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“…The individual technologies are a storage format on impregnated filter paper, [12] a biopolymer technology that mimics the anhydrous vitreous state of DNA in seeds and spores, [13] and a synthetic silica fossilization technology based on a procedure developed in our group. [14] Compared to the storage of solid-state DNA without additional agents, all three solid-state DNA storage technologies decreased the DNA decay rates considerably. From the temperature dependence of the decay rates, Arrhenius-type activation energies (E A ) were calculated by assuming first .…”

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confidence: 99%

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

et al. 2015

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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 8C for one week. This is thermally equivalent to storing information on DNA in central Europe for 2000 years.Prehistorical information put down by our ancestors in cave drawings, texts engraved in gold, and medieval texts are some of the strongest links with our past. An example is the Archimedes Palimpsest that originates from the tenth century. This contains the single known copy of "The Methods of Mechanical Theorems", and represents a cornerstone in the development of geometry and modern calculus. The book has survived more than 1000 years and in 1998 was valued at more than two million USD. In view of this valuation of information it may seem surprising that current efforts of guaranteeing longevity of digital information are scarce (e.g. MDisc, Syylex) and the storage half-life of information has dropped drastically since the transition from analog to digital storage systems.[1]Traditional storage technologies such as optical and magnetic devices are not reliable for long-term (> 50 years) data storage.[2] Furthermore, the development of reliable systems requires long-term testing, which is well above the current device-development timelines. DNA is the only datastorage medium for which real long-term data are available from archeology. Most recently, 300 000 year old mitochondrial DNA from bears and humans has been sequenced. [3] DNA has also previously been utilized as a coding language, for applications in forensics, [4] product tagging, [5] and DNA computing.[6] As a consequence, several approaches to store information on DNA have been proposed. [7] However, those approaches are not reliable as they cannot handle errors efficiently and do not suggest how to (physically) store the DNA to maintain its stability over time.To overcome these issues we combined an error-correcting information-encoding scheme tailored to DNA (Scheme 1) with a previously established chemical method for storing DNA in "synthetic fossils". The corresponding experiments show that only by the combination of the two concepts, could digital information be recovered from DNA stored at the Global Seed Vault (at À18 8C) after over 1 milli...

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

et al. 2015

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“…The successful incorporation of DNA into additional inorganic nanoparticles has already been shown in previous studies. 12,16 Engineered particles are commonly used as tagging systems in diverse applications ranging from biological detection and imaging techniques, such as cell labelling, 30 cell tracking, 31 and detection of DNA 32 and proteins 33 and several methods have been proposed that use nanoparticles for the amplification of measurement signals. 34,35 By the use of dpPCR, the quantification of such particles on a single particle level is simplified and will further decrease the detection limits of the particulate taggants and any measurement derived thereof.…”

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confidence: 99%

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

et al. 2015

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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).

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“…Furthermore, DNA is a relatively sensitive molecule and can degrade under the normal temperature, oxidation, radiation and chemical and enzymatic activity levels associated with ambient environmental conditions [41,42]. While DNA damages caused by these stresses may be repaired by a number of processes within living organisms, the same cannot be said of the synthetic oligonucleotides included within forensic taggants.…”

Section: Dna Taggantsmentioning

confidence: 91%

Taggant materials in forensic science: A review

Gooch

Daniel

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et al. 2016

TrAC Trends in Analytical Chemistry

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Highlights The use of forensic taggant technologies has become considerably more widespread  The application of taggant materials for forensic purposes are described  The different coding methods used in commercial marking materials to infer identity are explored  Recent developments in the field are discussed along with future perspectives AbstractThe use of taggant technology to mark objects for the purpose of identification is becoming a significant part of national crime reduction strategies. Taggants may be able to prevent or monitor criminal offences by associating an object with a specific piece of information. While the material properties of a taggant will largely vary between application purposes, a specific 'coding' element will generally be incorporated to infer marker uniqueness. With the speed, simplicity and accuracy of coding component analysis largely determining the overall efficacy of taggants, continuing advances in portable in-field analysis, nanotechnology and material science should have allowed for the development of new and improved forensic marking agents. However, the limited amount of recent research in this area suggests that this is not the case. This critical review therefore examines the current state of presently available taggants before attempting to offer insight into the future direction of forensic marking technology.

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

Cited by 111 publications

References 25 publications

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

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

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

Taggant materials in forensic science: A review

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