Article

Protection and Deprotection of DNA-High-Temperature Stability of Nucleic Acid Barcodes for Polymer Labeling

Authors:
  • Janssen, Johnson & Johnson
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Abstract

Tough to remove this label! When protected within a silica sphere, DNA can withstand high temperatures (up to 200 °C) and aggressive radical conditions. Following deprotection with HF, the DNA can be analyzed by standard biochemical methods. This DNA protection/deprotection scheme is compatible with standard polymer processing and can be used for labeling material of nonbiological origin.

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... A DNA-based nanotracer can be produced by attaching synthetic DNA molecules to the surface of a silica nanoparticle seed and adding a protective outer silica layer, which is used to alleviate the DNA's vulnerability to high reservoir temperatures. Pioneering work by Paunescu et al. (2012) has proven that DNA protected by silica nanoparticles is able to withstand temperature as high as 200°C, and still can be amplified through qPCR (real-time quantitative polymerase chain reaction) after being released into the suspension by dissolving the outer silica layer. Therefore, it should be possible to apply such particles to geothermal tracer testing to investigate the connectivity of fracture networks. ...
... DNA was first adsorbed onto positively charged silica seed particles, after which seed particle growth method was applied to coat the DNA-adsorbed seeds with silica layer, thereby "sandwiching" DNA molecules between inner seed and outer shell ( Figure 2). Synthetic 113-base-pair single stranded DNA (ssDNA) with complementary sequences (Paunescu et al. 2012) purchased from Eurofins Genomics was annealed according to standard annealing procedure to yield double stranded DNA (dsDNA) before being used for encapsulation. ...
... Because both the synthesized silica seeds and DNA molecules carry negative surface charge under experimental conditions, each 1 ml of silica seeds was stirred with 10 µl trimethyl [3-(trimethoxysilyl)propyl]ammonium chloride (TMAPS) at 1400 rpm in a 2-ml micro tube for over 12 h to yield positive surface charge (Paunescu et al. 2012). The particles were Figure 1. ...
Conference Paper
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The objective of our experiments has been to develop and evaluate a uniquely identifiable particle tracer for use in geothermal applications. Following the work of Paunescu et al. (2013), DNA-tagged nanotracers have been made by adsorbing synthetic DNA onto silica nanoparticles which were then coated with silica to protect the DNA. The silica nanoparticles were then evaluated for durability with a controlled heat experiment at 198°C and flowed through packed sand at 25°C, 120°C, and 150°C while monitoring permeability changes. All were subsequently analyzed with SEM imaging.
... As an alternative to PCR-based approaches, here we introduce a direct random access memory approach that retrieves specific files, or arbitrary subsets of files, directly using physical sorting, without a need for amplification, and without any potential for barcodememory crosstalk, while also preserving non-selected files intact by recycling them into the original memory pool. To realize this file system, we first encapsulate DNA-based files physically within discrete, impervious silica capsules 9,23,24 , 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. Downstream file selection may then be optical, physical or biochemical, with sequencing-based read-out following de-encapsulation of the memory DNA from the silica capsule. ...
... While only 20 icon-resolution images were chosen as our image database, representing diverse subject matter including animals, plants, transportation and buildings ( Supplementary Fig. 1), our file system may in principle be scaled to considerably larger sets of images, limited primarily by the cost of DNA synthesis and the need to develop strategies for high-throughput silica encapsulation of distinct file sequences and surface-based DNA labelling for barcoding ( Supplementary Fig. 1). 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 storage 9,23,24 , where external barcodes may be renewed periodically, further protected with secondary encapsulation, or data pools may simply be stored using methods implemented in PCR-based random access, such as dehydrating the data pool and immersing the dried molecular database in oil 21 . Fig. 1 | Write-access-read cycle for a content-addressable molecular file system. ...
... To implement this image database, the images were substituted with black-and-white, 26 × 26 pixel images to minimize synthesis costs, compressed using run-length encoding and converted to DNA (Supplementary Figs. 1 and 2). Following synthesis, bacterial amplification and sequencing validation ( Supplementary Fig. 3), each plasmid DNA was separately encapsulated into silica particles containing a fluorescein dye core and a positively charged surface 23,24 . Because the negatively charged phosphate groups of the DNA interact with positively charged silica particles, plasmid DNA condensed on the silica surface, after which N- (3-(trimethoxysilyl)propyl)-N,N,N-trimethylammonium chloride (TMAPS) was co-condensed with tetraethoxysilane to form an encapsulation shell after four days of incubation at room temperature 9,23 (Fig. 2a), thus forming discrete silica capsules containing the file sequence that encodes for the image file. ...
Article
Full-text available
DNA is an ultrahigh-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and if random access of files within exabyte-to-yottabyte-scale DNA data pools were feasible. Here, we demonstrate a path to overcome the second barrier by encapsulating data-encoding DNA file sequences within impervious silica capsules that are surface labelled with single-stranded DNA barcodes. Barcodes are chosen to represent file metadata, enabling selection of sets of files with Boolean logic directly, without use of amplification. We demonstrate random access of image files from a prototypical 2-kilobyte image database using fluorescence sorting with selection sensitivity of one in 106 files, which thereby enables one in 106N selection capability using N optical channels. Our strategy thereby offers a scalable concept for random access of archival files in large-scale molecular datasets. Silica beads encapsulating DNA information and functionalized with DNA labels create an alternative DNA data storage system, where direct random access and data retrieval are enabled by complementary fluorescent strands that identify beads for separation in fluorescence-activated sorting.
... The long-term structural stability of DNA is integral to all these applications. As DNA is vulnerable to hydrolytic and oxidative damage in aqueous solutions (6)(7)(8)(9), ultralow temperatures are used for long-term storage of DNA. However, not only is refrigeration limited to small number of samples but repeated freeze-thaw of frozen samples can also cause structural damage to the DNA. ...
... However, not only is refrigeration limited to small number of samples but repeated freeze-thaw of frozen samples can also cause structural damage to the DNA. As a result, techniques employing room-temperature storage of DNA is rapidly gaining popularity (8)(9)(10). Following nature's lead, most roomtemperature storage methods employ the strategy of 'anhydrobiosis' or storage under a state of extreme dehydration (9,10). ...
... As a result, techniques employing room-temperature storage of DNA is rapidly gaining popularity (8)(9)(10). Following nature's lead, most roomtemperature storage methods employ the strategy of 'anhydrobiosis' or storage under a state of extreme dehydration (9,10). However, use of artificial agents to induce dehydration severely perturbs the DNA conformation, as water is essential for stabilizing the physiological B-form of double helical DNA. ...
Article
Full-text available
The functional B-conformation of DNA succumbs to the A-form at low water activity. Methods for room temperature DNA storage that rely upon 'anhydrobiosis', thus, often encounter the loss of DNA activity due to the B→A-DNA transition. Here, we show that ionic liquids, an emerging class of green solvents, can induce conformational transitions in DNA and even rescue the dehydrated DNA in the functional B-form. CD spectroscopic analyses not only reveal rapid transition of A-DNA in 78% ethanol medium to B-conformation in presence of ILs, but also the high resistance of IL-bound B-form to transit to A-DNA under dehydration. Molecular dynamics simulations show the unique ability of ILs to disrupt Na+ ion condensation and form 'IL spine' in DNA minor groove to drive the A→B transition. Implications of these findings range from the plausible use of ILs as novel anhydrobiotic DNA storage medium to a switch for modulating DNA conformational transitions.
... Considering all conditions mentioned above, a currently feasible solution for DNA database preservation is to encapsulate the DNA in a dehydrated state ( Figure 5A) (116,179,180). Paunescu et al. (180) reported the preservation of DNA by adsorption on the surface of submicronsized silica particles modified with positive-charged ammonium groups and subsequently depositing a silica layer on it. ...
... Considering all conditions mentioned above, a currently feasible solution for DNA database preservation is to encapsulate the DNA in a dehydrated state ( Figure 5A) (116,179,180). Paunescu et al. (180) reported the preservation of DNA by adsorption on the surface of submicronsized silica particles modified with positive-charged ammonium groups and subsequently depositing a silica layer on it. The encapsulation of the silica layer prevented the DNA from damages under high temperature, ROS, and UV irradiation. ...
Article
Full-text available
Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.
... To prepare 3D-printing filaments, we mixed the SPED capsules with dissolved PCL and extruded the mix into a 2.85 mm filament compatible with desktop 3D printers. Notably, the filament contained SPED beads in a concentration of 100 mg kg −1 (100 ppm), which did not create any detectable changes to the mechanical properties, weight or color of the filament 13 . The DNA loading within SPED was 2 mg of DNA per gram of SPED beads, which translates to a DNA concentration of 0.2 mg kg −1 (0.2 ppm) of the PCL filament ( Fig. 1b and Supplementary Note 3), well below the concentration Letters Nature BiotechNology of DNA in biological organisms compared with their body weight (~1,000 ppm in Escherichia coli). ...
... The results also indicate that it is possible to use elevated temperatures for short cycle times during polymer processing, while suffering some losses of DNA 13 , which could be compensated by loading more DNA into the polymer preforms. Such temperatures will allow the use of DoT for selected polymer injection molding processes, ...
Data
SI video of A DNA-of-things storage architecture to create materials with embedded memory
... To prepare 3D-printing filaments, we mixed the SPED capsules with dissolved PCL and extruded the mix into a 2.85 mm filament compatible with desktop 3D printers. Notably, the filament contained SPED beads in a concentration of 100 mg kg −1 (100 ppm), which did not create any detectable changes to the mechanical properties, weight or color of the filament 13 . The DNA loading within SPED was 2 mg of DNA per gram of SPED beads, which translates to a DNA concentration of 0.2 mg kg −1 (0.2 ppm) of the PCL filament ( Fig. 1b and Supplementary Note 3), well below the concentration Letters Nature BiotechNology of DNA in biological organisms compared with their body weight (~1,000 ppm in Escherichia coli). ...
... The results also indicate that it is possible to use elevated temperatures for short cycle times during polymer processing, while suffering some losses of DNA 13 , which could be compensated by loading more DNA into the polymer preforms. Such temperatures will allow the use of DoT for selected polymer injection molding processes, ...
Article
Full-text available
DNA storage offers substantial information density1,2,3,4,5,6,7 and exceptional half-life³. We devised a ‘DNA-of-things’ (DoT) storage architecture to produce materials with immutable memory. In a DoT framework, DNA molecules record the data, and these molecules are then encapsulated in nanometer silica beads⁸, which are fused into various materials that are used to print or cast objects in any shape. First, we applied DoT to three-dimensionally print a Stanford Bunny⁹ that contained a 45 kB digital DNA blueprint for its synthesis. We synthesized five generations of the bunny, each from the memory of the previous generation without additional DNA synthesis or degradation of information. To test the scalability of DoT, we stored a 1.4 MB video in DNA in plexiglass spectacle lenses and retrieved it by excising a tiny piece of the plexiglass and sequencing the embedded DNA. DoT could be applied to store electronic health records in medical implants, to hide data in everyday objects (steganography) and to manufacture objects containing their own blueprint. It may also facilitate the development of self-replicating machines.
... Ways to extend the lifespan of DNA are therefore required. There are three primary categories of strategies to preserve DNA data for a long period of time: robust chemical preservation [219][220][221][222][223], dry-state room temperature storage [224][225][226][227][228][229] and in-vivo preservation [230][231][232][233][234][235][236][237][238]. While cryptopreservation of DNA is cumbersome and costly, room temperature storage is a good option. ...
... Spatial isolation between storage containers enables the physical storage of information that share the same addressing scheme. The most commonly used method of robust chemical preservation is the encapsulation of DNA with silica [219][220][221]. It was recently proposed that DNA could be stored in any shape by the application of the encapsulated DNA to 3D-printing technology [220]. ...
... Considering all conditions mentioned above, a currently feasible solution for DNA database preservation is to encapsulate the DNA in a dehydrated state ( Figure 5A) (116,179,180). Paunescu et al. (180) reported the preservation of DNA by adsorption on the surface of submicronsized silica particles modified with positive-charged ammonium groups and subsequently depositing a silica layer on it. ...
... Considering all conditions mentioned above, a currently feasible solution for DNA database preservation is to encapsulate the DNA in a dehydrated state ( Figure 5A) (116,179,180). Paunescu et al. (180) reported the preservation of DNA by adsorption on the surface of submicronsized silica particles modified with positive-charged ammonium groups and subsequently depositing a silica layer on it. The encapsulation of the silica layer prevented the DNA from damages under high temperature, ROS, and UV irradiation. ...
Article
Soft actuators with perception capability are essential for robots to intelligently interact with humans and the environment. However, existing perceptive soft actuators require complex integration and coupling between the discrete functional units to achieve autonomy. Here, we report entirely soft actuators with embodied sensing, actuation, and control at the single-unit level. This is achieved by synergistically harnessing the mechanosensing and electrothermal properties of liquid metal (LM) to actuate the thermally responsive liquid crystal elastomer (LCE). We create multifunctional LM circuits on the LCE surface using a simple and facile methodology based on magnetic printing. The fluidic LM circuit can not only be utilized as a conformable resistive heater but also as a sensory skin to perceive its own deformation. Moreover, the rational design of the LM circuits makes it possible to achieve biomimetic autonomous actuation in response to mechanical stimuli such as pressure or strain. In addition, the intrinsic stretchability of LM allows us to create 3D spring-like actuators via a simple prestretch step, and complex helical motions can be obtained upon mechanical stimulation. This work provides a unique and simple design for autonomous soft robotics with embodied intelligence.
... Besides the fragmentation mechanisms of DNA in liquid solution available in the literature, Karni et al. (2013) pointed out that DNA may possess better heat stability at dry conditions with degradation starting at 130 °C. This may be an explanation of why DNA embedded within silica nanoparticles was able to withstand heat treatment better than unprotected DNA (Paunescu et al. 2013, Zhang et al. 2016, because separating DNA from water reduces the chance of hydrolysis. ...
Conference Paper
Full-text available
Tracer testing in fractured reservoirs has long been limited by the availability of unique and unambiguous tracers. In this study, we introduce the concept of using thermophilic microorganisms and DNA barcoding techniques for fractured reservoir characterization. On the one hand, thermophilic microorganisms have the potential of thriving in the extreme environment of geothermal and oil reservoirs. On the other hand, even if the microbes lose the basic functions of life after passing through the subsurface, their genetic information may still be retrieved and identified using modern sequencing technologies. In addition, because microorganisms are able to replicate themselves given appropriate nutrients and growing conditions, they are also a cost-effective solution for potential up-scaled field tracer testing applications. Heating experiments were conducted to examine the possibility of short-fragment identification of archaeal genomic DNA after prolonged heat treatment. The results show that it is feasible to still identify a short region of genomic DNA even after prolonged heat treatment, and a short region within a long genomic DNA appears to be more robust than a similar-length shortstranded DNA. We therefore conclude that the concept of using thermophilic microorganisms combined with DNA barcoding techniques to perform unambiguous reservoir tracer analysis shows good promise. To avoid confusion with the indigenous microbes in a reservoir, either exogenous microbes or engineered microbes containing artificial barcodes may be used.
... Advanced anticounterfeit technologies tend to focus on medicines at the dosage level, which means that a security measure is integrated directly into the product itself so that each product can be independently verified and traced. 4,5 Interestingly, multiple fluorescent color materials have received increasing attention due to their ability to read stored information under external stimuli. 6−8 To this end, the authors chose edible and digestible silk protein as the coding material, which could be recombined with fluorescent proteins (eCFP, eGFP, and mKate2) by the piggyBac transposase method. ...
... An ideal tagging and tracing technology protecting against adulteration should be imperceptible within the material matrix and should not alter the properties of the product. Some existing tagging technologies include isotopic tracers, 4 fluorescent labels, 5 polypeptides, 6 and nucleic acids. 7 Since many products are a combination of different materials, detailed quantification of the material composition is an important factor to ensure a specific quality. ...
Article
For many manufacturing processes correct mixing compositions are crucial to guarantee product quality. However, analysis of mixing ratios based from component balances can be challenging and require extensive infrastructure. DNA barcodes have been previously proposed as low-cost markers for product authenticity, and we show here that the quantification of such barcodes via quantitative real time polymerase chain reaction (PCR) enables the determination of mixing ratios in a range of liquid and polymeric products. To enable distribution of the DNA within the various matrixes, the biochemical is encapsulated in silica nanoparticles and distributed within the matrix of the raw material. If both raw materials of a two-component mixture contain such barcodes, the composition of the mixture can be determined from the relative concentration of the barcodes via multiplex PCR reactions, irrespective of the sampling volume and for a wide range of initial barcode concentrations (10 ppm - 10 ppb). As an application example we use the barcodes to determine the mixing ratios of cross-linked and multi component polysilicon products.
... much less susceptible to such damage. For example, the addition of silica has been shown to act as an ideal material for encapsulation and provide exceptional barrier properties (Paunescu et al., 2013(Paunescu et al., , 2016. Adding such silica-encapsulated DNA to milk before manufacturing cheese resulted in the barcode maintaining its integrity during the manufacturing process (Bloch et al., 2014). ...
Article
The licensed pharmaceutical industry and regulators use many approaches to control counterfeiting, but it remains a very difficult task to differentiate between counterfeit and real products. Moreover, there is a lack of techniques available for providing a batch specific molecular bar code for tablets that has the required traceability, specificity and sensitivity to be fit for purpose. The aim of this study was to evaluate DNA molecular tags as a potential anti-counterfeiting technology in tablets. Lactose tablets (400 mg) were used as a model to investigate incorporation DNA molecular tag into a solid dosage form: DNA authentication was carried out on an Applied DNA SigNify® qPCR instrument. Tablet batches were subjected to accelerated stability conditions (40 °C and 75% RH) for up to 6 months. All batches passed the monograph specifications of the British Pharmacopoeia (hardness, friability and mass uniformity) throughout the storage period. In all of recovery plots, the number of cycles required for DNA detection (Cq values) increased as a function of storage time, which indicated a reduction in tag levels, but it should be noted for all storage experiments the tag was clearly detected. It would appear that DNA molecular tags could feasibly be applied within the pharmaceutical development cycle when a new solid dosage form is brought to the market so as to mitigate the risk and dangers of counterfeiting.
... The major downside of DNA as a tracer is its limited environmental stability-the biopolymer is prone to chemical decay in the presence of metal ions, 10 non-neutral pH, 1 strong microbial activity, 11 elevated temperature, 12 and even sunlight. 13, 14 Halter and Zahn, for example, found that DNA has a half-life of only roughly 2 days in soil. ...
Article
DNA is often used as a tracer in both environmental fluid flow characterization and in material tracking to avoid counterfeiting and ensure transparency in product value chains. The main drawback of DNA as a tracer is its limited stability, making quantitative analysis difficult. Here we study length‐dependent DNA decay at elevated temperatures and under sunlight by quantitative PCR and show that the stability of randomly generated DNA sequences is inversely proportional to the sequence length. By quantifying the remaining DNA length distribution, we present a method to determine the extent of decay and to account for it. We propose a correction factor based on the ratio of measured concentrations of two different length sequences. Multiplying the measured DNA concentration by this length‐dependent correction factor enables precise DNA tracer quantification, even if the DNA molecules have undergone more than 100‐fold degradation. This article is protected by copyright. All rights reserved.
... We include the discussion of molecular taggants to emphasize the role of chemical information in PUF keys, despite the fact that they are clonable. Molecular taggants include DNA 24,25,[89][90][91][92][93][94][95][96][97] , peptides 26,98,99 , polymers 100 and phase-change eutectic alloys 101,102 . Although the readout of these taggants is presently both invasive and time-consuming (for example, sequencing, mass spectrometric or calorimetric analysis). ...
Article
The counterfeiting of goods has important economic implications and is also a threat to health and security. Incorporating anti-counterfeiting tags with physical unclonable functions (PUFs) into products is a promising solution for their authentication. PUFs are unique random physical patterns of taggants that cannot be copied and must be fabricated by a stochastic process that affords a large number of robust PUF tags. A PUF tag has a physical pattern that, if read with an appropriate analytical tool, can be recorded and stored. The PUF tag is then the ‘key’, whereas the stored pattern is the ‘lock’. This combination forms PUF keys that provide unbreakable encryption and combat counterfeiting. The stochastic assembly of physical patterns made from taggants exhibiting particular molecular properties is thus an excellent approach to designing new PUF keys.
... Melting temperature (Tm) is often used to characterize stability. Thermodynamic calculations are widely used to predict Tm of oligonucleotides [1,2]. However,Tm values calculated using standard entropy and enthalpy changes do not always provide an adequate description of the experiment. ...
Article
The stability of double-stranded DNA (dsDNA) was assessed on the basis of unwinding force measurement. Unwinding force was measured directly with a quartz crystal microbalance (QCM). The amplitude of its surface oscillations was controlled by supplying variable alternate voltage. Under smoothly increasing amplitude of QCM surface oscillations, dsDNA fixed on QCM surface through one of its ends got unwound. This procedure allows reliable measurement of rupture force as small as 5-10 pN. It was demonstrated that oscillations of the surface, with dsDNA bound through one of its ends to this surface, at a frequency of 14 MHz, cause helix unwinding to form two complementary parts due to viscous forces of the liquid medium. Unwinding starts at the upper end. This was proven using oligonucleotide duplexes containing mismatches in different positions. For duplexes containing complementary 20 base pairs, the helix unwinding force is equal to 30-40 pN, which is in agreement with the data obtained by means of atomic-force microscopy (AFM) for the case of unzipping mode. Graphical Abstract Rupture force depending on mismatch position in dsDNA.
... Indeed, such polymers could be easily blended, adsorbed or covalentlyattached to aw ide range of organic or inorganic materials. Some examples of such molecular barcodes have already been reported using DNA, [9] although these developments should not be confused with the unrelated field of DNA barcoding,w hich deals with species detection in biology. Synthetic sequence-coded polymers could be an interesting alternative to DNAf or anti-counterfeit materials. ...
Article
A 2D approach was studied for the design of polymer-based molecular barcodes. Uniform oligo(alkoxyamine amide)s, containing a monomer-coded binary message, were synthesized by orthogonal solid-phase chemistry. Sets of oligomers with different chain-lengths were prepared. The physical mixture of these uniform oligomers leads to an intentional dispersity (1st dimension fingerprint), which is measured by electrospray mass spectrometry. Furthermore, the monomer sequence of each component of the mass distribution can be analyzed by tandem mass spectrometry (2nd dimension sequencing). By summing the sequence information of all components, a binary message can be read. A 4-bytes extended ASCII-coded message was written on a set of six uniform oligomers. Alternatively, a 3-bytes sequence was written on a set of five oligomers. In both cases, the coded binary information was recovered.
... 12 Among the large selection of anti-counterfeiting technology currently available, molecular tags such as DNA and peptides present an interesting option. [13][14][15][16] Their dened sequence acts as a molecular barcode and can be used in trace amounts to label and protect pharmaceuticals. However, these forensic methods are oen susceptible to chemical and thermal degradation and must be identied through sequencing and mass spectrometry, which require specialized equipment and are typically not possible for the average consumer. ...
Article
Full-text available
A new concept for difficult-to-replicate security inks for use in advanced anti-counterfeiting applications is presented. Inks fabricated from a mixture of photoactive dyes result in a unique fluorescent color upon irradiation that differs from the starting fluorescence. The dyes are substituted 9,9′-dianthryl sulfoxides that undergo photochemical extrusion of a sulfoxide moiety (SO) to produce emissive red, blue, and green emitters. The resulting emissive feature has specific Commission international de l'éclairage (CIE) coordinates that are used for authentication. Additionally, the temporal evolution of the fluorescence can be monitored, introducing a dynamic nature to these security features. The three compounds show different rates of photoconversion dependent on the irradiation wavelength, allowing selective wavelengths for activation to be used for additional security. CIE coordinates can be extracted from patches containing the three compounds using an inexpensive, commercially available smartphone application (app) and compared against a known value to confirm the validity of the method.
... Although reservoir conditions such as high temperature may be harsh for the DNA molecules, it is possible to protect the DNA using synthetic "fossils" by first attaching DNA onto silica nanoparticles and then adding a protective silica layer to the particles. Pioneering work of Paunescu et al. (2012) has shown that DNA protected by silica nanoparticles is able to withstand temperature as high as 200 °C, and can still be amplified and quantified through qPCR (real-time quantitative polymerase chain reaction) after being released into solution by dissolving the silica outer layer. Therefore, such DNA-embedded silica nanoparticles could conceivably be applied in geothermal fields for reservoir characterization. ...
Conference Paper
Full-text available
The objective of this study was to develop and evaluate a type of uniquely identifiable nanoparticle tracer to map fracture networks without ambiguity. DNA-tagged nanotracers were synthesized by first adsorbing synthetic DNA molecules onto the surface of plain silica nanoparticles of around 140 nm diameter, and then coating the particles with a silica outer layer to protect the DNA from harsh environmental conditions. Heating and flow experiments were conducted to evaluate the durability of silica as a protective material for DNA molecules. DNA-embedded silica nanoparticles were injected through packed sand at various temperatures and analyzed in the effluent in order to test whether the DNA-silica nanotracer could flow successfully through porous medium while maintaining the integrity of the DNA. This paper summarizes the advantages and limitations of DNA-embedded silica nanoparticles as reservoir tracers, and discusses possible approaches to adjust the DNA-silica nanotracer to achieve more favorable properties for fractured reservoir analysis.
... Indeed, such polymers could be easily blended, adsorbed or covalentlyattached to a wide range of organic or inorganic materials. Some examples of such molecular barcodes have already been reported using DNA, [9] although these developments should not be confused with the unrelated field of DNA barcoding, which deals with species detection in biology. Synthetic sequence-coded polymers could be an interesting alternative to DNA for anti-counterfeit materials. ...
Article
A 2D approach was studied for the design of polymer-based molecular barcodes. Uniform oligo(alkoxyamine amide)s, containing a monomer-coded binary message, were synthesized by orthogonal solid-phase chemistry. Sets of oligomers with different chain-lengths were prepared. The physical mixture of these uniform oligomers leads to an intentional dispersity (1st dimension fingerprint), which is measured by electrospray mass spectrometry. Furthermore, the monomer sequence of each component of the mass distribution can be analyzed by tandem mass spectrometry (2nd dimension sequencing). By summing the sequence information of all components, a binary message can be read. A 4-bytes extended ASCII-coded message was written on a set of six uniform oligomers. Alternatively, a 3-bytes sequence was written on a set of five oligomers. In both cases, the coded binary information was recovered.
... In addition, the previous study reported that mushroom DNA was significantly degraded when dried at temperatures above 80 • C (Wang, Liu, & Xu, 2017). Moreover, a study showed that DNA loses remarkably at 120 • C or higher (Paunescu, Fuhrer, & Grass, 2013), accompanied with the oxidation and deamination of purine bases. The polycyclic aromatic hydrocarbons or heterocyclic amines produced by roasting can bind to the C8, N6, N2 and N7 of purine bases (Lukin & de los Santos, 2006), thus reducing the detectable content of guanine and adenine after acidolysis. ...
Article
Full-text available
Lentinus edodes (LE) is very popular in the world and also considered as high purine food. However, few focuses on purine types and its change during food processing. Here, we first compared 3 drying techniques, including roast-drying, freeze-drying, sun-drying on purine contents of LE by using acidolysis and HPLC. It showed that adenine decreased significantly after roast-drying (120 ℃), which may be caused by thermal damage of DNA. Total purine decreased significantly after freeze-drying, while roast-dried and sun-dried LE remained unchanged. The effect of moist heat (boiling) on LE purine were also evaluated. Total purine increased due to xanthine increasement (331.72 ± 50.07%). And purine contents transferred into boiled liquid was higher than that in boiled solid. Compared with sun-dry and roast-dry processing, freeze-drying could notably affect the purine release from LE and decrease purine contents. Therefore, freeze-drying is recommended for process techniques for hyperuricemia and gouts populations.
... The sequencing process can be scaled up or down as desired to accommodate for various sizes of random numbers synthesized and results in a digital file of DNA nucleotides, which can then be encoded into bits. By encapsulating the DNA using silica particles 5,64 , is it also possible to keep the random number in a physical form, completely air-gapped, as a source of entropy that can be stable for millennia. ...
Article
Full-text available
Synthetic DNA is a growing alternative to electronic-based technologies in fields such as data storage, product tagging, or signal processing. Its value lies in its characteristic attributes, namely Watson-Crick base pairing, array synthesis, sequencing, toehold displacement and polymerase chain reaction (PCR) capabilities. In this review, we provide an overview of the most prevalent applications of synthetic DNA that could shape the future of information technology. We emphasize the reasons why the biomolecule can be a valuable alternative for conventional electronic-based media, and give insights on where the DNA-analog technology stands with respect to its electronic counterparts.
... 50 In short, negatively charged short-sequence dsDNA is adsorbed onto positively charged SiO 2 particles because of electrostatic interactions. The exposed DNA layer is covered by an additional layer of SiO 2 through Stober synthesis, which is enough to protect the DNA from external factors such as high temperature 51 and chemical stress, 25 as shown by exposing the particles to reactive oxygen species (ROS) ( Table 2). In addition, free DNA and encapsulated DNA were subjected to diluted household bleach. ...
Article
Full-text available
Environmental tracers are chemical species that move with a fluid and allow us to understand its origin and material transport properties. DNA-based materials have been proposed and used for tracing due to their potential for multitracing with high specificity and sensitivity. For large-scale applications of this new material it is of interest to understand its impact on the environment. We therefore assessed the ecotoxicity of sub-micron silica particles with and without encapsulated DNA in the context of surface and underground tracing of natural waterflows using standard ecotoxicity assays according to ISO standards. Acute toxicity tests were performed with Daphnia magna (48 h), showing no effect on mobility at tracer concentrations below 300 ppm. Chronic ecotoxicological potential was tested with Raphidocelis subcapitata (green algae) (72 h) and Ceriodaphnia species (7 d) with no effect observed at realistic exposure scenario concentrations for both silica particles with and without encapsulated DNA. These results suggest that large-scale environmental tracing with DNA-tagged silica particles in the given exposure scenarios has a low impact on aquatic species with low trophic levels such as select algae and planktonic crustaceans.
... Undoubtedly, the information-storing l-DNAs are still susceptible to physical stress and chemical degradation 53 , and future studies to better understand the environmental processing and degradation of mirror-image molecules under various temperature, humidity and pH conditions, as well as their potential interactions with natural biology systems should be carried out. Incorporation into other DNA-protecting storage architectures may help further improve their stability in practical settings 54,55 . Conversely, given their unique ability to evade biodegradation, l-DNAs may become an excellent model system for studying DNA stability under physical stress and chemical degradation. ...
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Traditional storage methods have limitations and concerns regarding capacity, decay, and sustainability. These drawbacks can be mitigated by developing long‐term digital information storage systems using deoxyribonucleic acid (DNA), which are often referred to as DNA‐based data storage. These advanced technologies for storing big data are emulated by DNA synthesis, DNA sequencing, and encoding and decoding algorithms that can pack information into DNA, extreme durability, environmental sustainability, energy conservation, and eternal relevance, and at higher density than the conventional systems. This field has arisen to become a hot topic for researchers in the past decade, with significant breakthroughs in its course. This review provides a comprehensive overview of the latest advances in in vivo DNA digital storage and in vitro DNA digital storage with novel modalities, preservation techniques, applications, and practical and technical issues. Also summarize the field of in vivo molecular writing mode that records and stores data within cells' genomes, which lie at the growing intersection of biocomputing and biotechnology. The field of storing information in organic matters has recently emerged as a novel class of potential future data storage medium. In this review, mainly aim to provide a comprehensive understanding of future data storage applications. Recent advances have witnessed an extensive significant breakthrough in the field, which enable startups to capitalize and bring DNA data storage into daily life via alliance of multidisciplinary research.
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Sequence‐defined oligourethanes were tested as in vivo taggants for implants identification. The oligomers were prepared via an orthogonal solid‐phase iterative approach and thus contained a coded monomer sequence that can be unequivocally identified by tandem mass spectrometry (MS/MS). In order to simplify the use of these taggants, automated synthesis and sequencing protocols were developped in this work. Before testing them in vivo, cytotoxicity assays were performed and indicated an excellent cytocompatibility. The oligomers were then included in small amount (1 wt%) in square centimeter crosslinked poly(vinyl alcohol) (PVA) model films, which were intramuscularly‐ and subcutaneously‐implanted in the abdomen of rats. After one week, one month and three months of in vivo implantation, the PVA films were explanted. The rat tissues exposed to the implants did not exhibit any adverse reactions, thus suggesting that the taggants are not harmful and probably not leaching out from the films; the latter aspect being confirmed by in vitro studies in physiological conditions. Furthermore, the explanted films were immersed in methanol, as a solvent for oligourethanes, and the liquid extract was analyzed by mass spectrometry. In all cases, the oligourethane taggant was detected and its sequence was identified by MS/MS.
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The emergence of high-throughput DNA sequencing technologies sparked an immediate revolution in the field of genomics that has rippled into many branches of the life and physical sciences. The remarkable sensitivity, specificity, throughput, and multiplexing capacity that are inherent to massively parallel DNA sequencing have since motivated its use as a broad-spectrum molecular counter in small molecule and peptide-based inhibitor discovery, high-throughput biochemistry, protein and cellular detection and diagnostics, and even materials science. A key aspect of extrapolating DNA sequencing to 'non-traditional' applications is the underlying need to append nucleic acid barcodes to entities of interest. In this review, we describe the chemical and biochemical approaches that have enabled facile nucleic acid barcoding of proteinaceous and non-proteinaceous materials, and provide exciting examples of downstream technologies that have been made possible by DNA-encoded molecules. Considering that commercially available high-throughput sequencers were first released less than 15 years ago, we believe related applications will continue to mature for years to come, and close by proposing potential new frontiers to support this assertion.
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The field of storing information in DNA has expanded exponentially. Most common modalities involve encoding information from bits into synthesized nucleotides, storage in liquid or dry media, and decoding via sequencing. However, limitations to this paradigm include the cost of DNA synthesis and sequencing, along with low throughput. Further unresolved questions include the appropriate media of storage and the scalability of such approaches for commercial viability. In this review, we examine various storage modalities involving the use of DNA from a systems-level perspective. We compare novel methods that draw inspiration from molecular biology techniques that have been devised to overcome the difficulties posed by standard workflows and conceptualize potential applications that can arise from these advances.
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Barcode technology can deliver batched information for patient healthcare. For clinical examinations, barcodes serve as reporters for labeling multiple targets, and meanwhile, facilitate improved sensitivity and specificity, thus enabling barcode as a promising alternative to traditional labels for biomarker identification and signal amplification. However, faced with the stringent claims of point-of-care (POC) bioassays, efforts are needed to advance current technologies toward rapidity, robustness, affordability, and user-friendliness. In the past decades, chemists have succeeded in delicate fabrication of the barcode libraries for encoding. Nevertheless, the decoding technologies remain poorly discussed, especially simplified decoding strategies for POC bioassays. Recent emergence of portable cartridges and miniaturized signal-recording devices has brought a promise to merge barcodes-assisted bioassay with POC testing (POCT). This review provides a comprehensive summary on barcode encoding and decoding, with emphasis on their potential use in POCT, facilitated by improved manufacturing and portable devices. Future directions of barcoded bioassays for POCT and current challenges are also presented. We anticipate that this review will be beneficial to promoting barcodes toward broad applications.
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In this paper the practical density of long‐term DNA storage is increased. Specifically, the DNA weight loading of silica sphere DNA storage is increased to 3.4 wt%, a ten‐fold increase compared to the previous state‐of‐the‐art. By applying a Layer‐by‐Layer (LbL) design with alternating layers of DNA and a polycationic molecule, namely polyethyleneimine (PEI), another dimension to DNA surface binding onto magnetic nanoparticles is added. A protective silica layer is grown on top of the multilayered nanoparticles to shield the DNA from external sources of damage. Accelerated aging experiments of the nanoparticles and the subsequent quantification of DNA stability via qPCR show a significantly lower degradation rate compared to unprotected DNA. The novel material is compared to previous DNA storage technologies, outperforming those in DNA storage density as well as stability. Finally, the storage of an 83 kB digital file in DNA through a successful readout of a 4991 oligonucleotide pool is demonstrated from particle encapsulation, through accelerated aging, to sequencing.
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DNA outperforms most conventional storage media in terms of information retention time, physical density, and volumetric coding capacity. Advances in synthesis and sequencing technologies have enabled implementations of large synthetic DNA databases with impressive storage capacity and reliable data recovery. Several robust DNA storage architectures featuring random access, error correction, and content-rewritability have been constructed with potential for scalability and cost reduction. We survey these recent achievements and discuss alternative routes for overcoming the hurdles of engineering practical DNA storage systems. We also review recent exciting work on in vivo DNA memory including intracellular recorders constructed by programmable genome editing tools. Besides information storage, DNA could serve as a versatile molecular computing substrate. We highlight several state-of-the-art DNA computing techniques such as strand displacement, localized hybridization chain reactions, and enzymatic reaction networks. We summarize how these simple primitives have facilitated rational designs and implementations of in vitro DNA reaction networks that emulate digital/analog circuits, artificial neural networks, or non-linear dynamic systems. We envision these modular primitives could be strategically adapted for sophisticated database operations and massively parallel computations on DNA databases. We also highlight in vivo DNA computing modules such as CRISPR logic gates for building scalable genetic circuits in living cells. To conclude, we discuss various implications and challenges of DNA-based storage and computing, and we particularly encourage innovative work on bridging these two areas of research to further explore molecular parallelism and near-data processing. Such integrated molecular systems could lead to far-reaching applications in biocomputing, security, and medicine.
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DNA is a biological polymer that encodes and stores genetic information in all living organism. Particularly, the precise nucleobase pairing inside DNA is exploited for the self-assembling of nanostructures with defined size, shape and functionality. These DNA nanostructures are known as framework nucleic acids (FNAs) for their skeleton-like features. Recently, FNAs have been explored in various fields ranging from physics, chemistry to biology. In this review, we mainly focus on the recent progress of FNAs in a pharmaceutical perspective. We summarize the advantages and applications of FNAs for drug discovery, drug delivery and drug analysis. We further discuss the drawbacks of FNAs and provide an outlook on the pharmaceutical research direction of FNAs in the future.
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DNA, a biological macromolecule, is a naturally evolved information material. From the structural point of view, an individual DNA strand can be considered as a chain of data with its bases working as single units. For decades, due to the high biochemical stability, large information storage capacity, and high recognition specificity, DNA has been recognized as an attractive material for information processing. Especially, the chemical synthesis strategies and DNA sequencing techniques have been rapidly developed recently, further enabling encoding information with synthetic DNA molecules. Herein, recent progresses are summarized on information processing based on synthetic DNA molecules from three aspects including information storage, computation, and encryption, and proposed the challenges and future development directions. Information processing with synthetic DNA molecules is among the most promising ways to next‐generation information science. The biocompatibility, high density, chain structure, and hybridization specificity enable synthetic DNA attractive material for encoding arbitrary information in vitro and in vivo. In this review, recent strategies are systematically summarized for information processing based on synthetic DNA molecules.
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The design of synthetic polymers with controlled monomer sequences is an important emerging trend in polymer science. This new field of research is bio‐inspired by sequence‐defined biopolymers such as proteins and nucleic acids. The chemical synthesis of nonnatural sequence‐controlled polymers (SCPs) has been described in several reviews. However, there is currently little information about the properties and applications of these polymers. In this context, the aim of this article is to give a comprehensive view on these aspects. After a general introduction and a short section about the synthesis of SCPs, the physicochemical properties of these synthetic macromolecules are described in detail. For instance, emphasis is put on the bulk and solution self‐assembly of SCPs. In the last part of this article, potential applications are reviewed and discussed. Overall, SCPs, which are more time‐consuming to synthesize than regular commodity polymers, are not meant to be used in high‐scale applications but more in specialty technologies with high‐added value. For instance, application areas such as data storage, anti‐counterfeiting technologies, catalysis, and photovoltaics are described in this article.
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Chapter
In the living cell, DNA functions as a principal informational molecule: it holds a linear array of heritable genetic information and it is the storehouse of this information. And while in nature DNA encodes proteins, the current ability to readily generate sufficiently long stretches of synthetic DNAs can be used for encrypting in DNA sequences some secret messages and for encoding and storing in DNA the large amounts of digital data, or even for tagging (or marking) and tracing various objects and materials with the coded DNA labels. To practically do so, we also need the ability to selectively amplify tiny amounts of DNA carrying an encoded or encrypted message or a label, and to read the DNA sequence in order to retrieve the DNA message (or DNA label). Fortunately, all this can now be done automatically by special machines.
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The globalization of drug trade leads to the expansion of pharmaceutical counterfeiting. The immense threat of low quality drugs to millions of patients is considered to be an under‐addressed global health challenge. Analytical authentication technologies are the most effective methods to identify active pharmaceutical ingredients and impurities. However, most of these analytical testing techniques are expensive and need skilled personnel. To combat counterfeiting of drugs, the package of an increasing number of drugs is being protected through advanced package labeling technologies. Though, package labeling is only effective if the drugs are not repackaged. Therefore “in‐drug labeling,” instead of “drug package labeling,” may become powerful tools to protect drugs. This review aims to overview how advanced micro‐ and nanomaterials might become interesting markers for the labeling of tablets and capsules. Clearly, how well such identifiers can be integrated into “solid drugs” without compromising drug safety and efficacy remains a challenge. Also, incorporation of tags has so far only been reported for the protection of solid drug dosage forms. No doubts that in‐drug labeling technologies for “liquid drugs,” like injectables which contain expensive peptides, monoclonal antibodies, vaccines, dermal fillers, could help to protect them from counterfeiting as well. The immense threat of low‐quality drugs to millions of patients is considered to be an under‐addressed global health challenge. In addition to analytical authentication technologies, “in‐drug labeling,” including printing or encrypting, as well as microscopic, nanoscopic, and molecular tags, may become powerful tools to protect drugs from counterfeiting.
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DNA origami technique has emerged as one of the most versatile bottom-up nanofabrication methods due to its ability to construct well-defined complex three-dimensional nanostructures and guide assembly of functional nanoscale objects with unprecedented precision, high yields and controlled stoichiometry. Nonetheless, limited compatibility with biologically relevant fluids and typical solvents utilized in nanofabrication often restricts applications of DNA origami-based assemblies and devices. Here we present an approach for coating DNA origami structures with silica. By careful adjustment of experiment parameters, we achieved reproduci-ble growth of ultrathin silica shell in solution without agglomeration or deformation of DNA origami structures. The silica coated structures are stable in water and exhibit an increased resistivity to nuclease-mediated degradation. In addition, the coated struc-tures preserve their structural integrity in polar organic solvents. We anticipate that our results will aid further advancement of DNA origami techniques as nanofabrication method.
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Recent years have witnessed the exponential growth of information, calling for the development of new storage media. DNA provides an attractive alternative for data storage due to its high physical density, reproducibility and excellent durability that have been tested by nature. Rapid progress has been made during the last decade by exploiting artificially designed DNA materials for data storage. In this Review, we summarize recent advances of DNA‐based encoding, writing, storage, retrieving, reading and decoding for data storage. In addition to encoding with nucleic acid sequences, different forms of data storage strategies using DNA nanostructures are also highlighted. We also discuss in vivo DNA data storage, especially with the use of CRISPR‐Cas systems. The challenges and opportunities for the development and application of DNA‐based data storage are presented. This article is protected by copyright. All rights reserved.
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DNA computing is a discipline that aims at harnessing individual molecules at the nanoscopic level for computational purposes. Computation with DNA molecules possesses an inherent interest for researchers in computers and biology. Given its vast parallelism and high-density storage, DNA computing approaches are employed to solve many combinatorial problems. However, the exponential scaling of the solution space prevents applying an exhaustive search method to problem instances of realistic size, and therefore artificial intelligence models are used in designing methods that are more efficient. DNA has also been explored as an excellent material and a fundamental building block for building large-scale nanostructures, constructing individual nanomechanical devices, and performing computations. Molecular-scale autonomous programmable computers are demonstrated allowing both input and output information to be in molecular form. This paper presents a review of recent advances in DNA computing and presents major achievements and challenges for researchers in the foreseeable future.
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Many synthetic polycationic vectors for non-viral gene delivery show high efficiency in vitro, but their usually excessive charge density makes them toxic for in vivo applications. Here we describe the synthesis of a series of high molecular weight terpolymers with low charge density, and show that they exhibit efficient gene delivery, some surpassing the efficiency of the commercial transfection reagents Polyethylenimine and Lipofectamine 2000. The terpolymers were synthesized via enzyme-catalyzed copolymerization of lactone with dialkyl diester and amino diol, and their hydrophobicity adjusted by varying the lactone content and by selecting a lactone comonomer of specific ring size. Targeted delivery of the pro-apoptotic TRAIL gene to tumour xenografts by one of the terpolymers results in significant inhibition of tumour growth, with minimal toxicity both in vitro and in vivo. Our findings suggest that the gene delivery ability of the terpolymers stems from their high molecular weight and increased hydrophobicity, which compensates for their low charge density.
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Traceability is the ability to maintain the identification of animal, or animal products, all along the production chain. It represents an essential tool to safeguard public and animal health and to valorize typical production systems. European food legislation is particularly strict and traceability systems, based on product labeling, have become mandatory in all European countries. However, the implementation of this system does not ensure consumers against fraud. Paper documents can be counterfeit so researchers have focused on the study of genetic traceability systems based on products identification through DNA analysis. In fact DNA is inalterable, detectable in every cell, resistant to heat treatments, and allows for individual, breed or species identification. Even if results are promising, these techniques are too expensive to be converted in routine tests but they could be a trusted tool for verification of suspected fraud. The present review proposes a synthesis of the major advances made in individual, breed, and species genetic identification in the last years, focusing on advantages and disadvantages and on their real future applications for animal productions.
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DNA molecules have been used to build a variety of nanoscale structures and devices over the past 30 years, and potential applications have begun to emerge. But the development of more advanced structures and applications will require a number of issues to be addressed, the most significant of which are the high cost of DNA and the high error rate of self-assembly. Here we examine the technical challenges in the field of structural DNA nanotechnology and outline some of the promising applications that could be developed if these hurdles can be overcome. In particular, we highlight the potential use of DNA nanostructures in molecular and cellular biophysics, as biomimetic systems, in energy transfer and photonics, and in diagnostics and therapeutics for human health.
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The application of nanotechnology in the field of drug delivery has attracted much attention in the latest decades. Recent breakthroughs on the morphology control and surface functionalization of inorganic-based delivery vehicles, such as mesoporous silica nanoparticles (MSNs), have brought new possibilities to this burgeoning area of research. The ability to functionalize the surface of mesoporous-silica-based nanocarriers with stimuli-responsive groups, nanoparticles, polymers, and proteins that work as caps and gatekeepers for controlled release of various cargos is just one of the exciting results reported in the literature that highlights MSNs as a promising platform for various biotechnological and biomedical applications. This review focuses on the most recent progresses in the application of MSNs for intracellular drug delivery. The latest research on the pathways of entry into live mammalian and plant cells together with intracellular trafficking are described. One of the main areas of interest in this field is the development of site-specific drug delivery vehicles; the contribution of MSNs toward this topic is also summarized. In addition, the current research progress on the biocompatibility of this material in vitro and in vivo is discussed. Finally, the latest breakthroughs for intracellular controlled drug release using stimuli-responsive mesoporous-silica-based systems are described.
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Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.
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We reported before that silica hollow spheres (microcapsules) are prepared by interfacial reaction method that W/O emulsion with the aqueous solution of sodium silicate and n-hexane solution of Tween 80 and Span 80 is combined with another aqueous solution of silica precipitant such as NH(4)HCO(3) and NH(4)Cl. This procedure using W/O/W emulsion fabricates the hollow structures of silica particles directly, and additional steps such as the removal of core parts, that are often essential for the preparation of hollow particles via core-shell materials, are not required. When biomacromolecules such as protein and nucleic acid are mixed in the aqueous solution of sodium silicate, these macromolecules can be encapsulated into the microcapsules. We succeeded the direct encapsulation of bovine serum albumin (BSA) and duplex DNA. Most of encapsulated BSA and DNA cannot be released from the microcapsules without the destruction of microcapsule shell. These microcapsule materials encapsulating biomacromolecules will be applied to biotechnologies such as immobilized enzyme and so on.
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Structural DNA Nanotechnology uses unusual DNA motifs to build target shapes and arrangements. These unusual motifs are generated by reciprocal exchange of DNA backbones, leading to branched systems with many strands and multiple helical domains. The motifs may be combined by sticky ended cohesion, involving hydrogen bonding or covalent interactions. Other forms of cohesion involve edge-sharing or paranemic interactions of double helices. A large number of individual species have been developed by this approach, including polyhedral catenanes, a variety of single-stranded knots, and Borromean rings. In addition to these static species, DNA-based nanomechanical devices have been produced that are ultimately targeted to lead to nanorobotics. Many of the key goals of structural DNA nanotechnology entail the use of periodic arrays. A variety of 2D DNA arrays have been produced with tunable features, such as patterns and cavities. DNA molecules have be used successfully in DNA-based computation as molecular representations of Wang tiles, whose self-assembly can be programmed to perform a calculation. About 4 years ago, on the fiftieth anniversary of the double helix, the area appeared to be at the cusp of a truly exciting explosion of applications; this was a correct assessment, and much progress has been made in the intervening period.
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In this review, we highlight the recent research developments of a series of surface-functionalized mesoporous silica nanoparticle (MSN) materials as efficient drug delivery carriers. The synthesis of this type of MSN materials is described along with the current methods for controlling the structural properties and chemical functionalization for biotechnological and biomedical applications. We summarized the advantages of using MSN for several drug delivery applications. The recent investigations of the biocompatibility of MSN in vitro are discussed. We also describe the exciting progress on using MSN to penetrate various cell membranes in animal and plant cells. The novel concept of gatekeeping is introduced and applied to the design of a variety of stimuli-responsive nanodevices. We envision that these MSN-based systems have a great potential for a variety of drug delivery applications, such as the site-specific delivery and intracellular controlled release of drugs, genes, and other therapeutic agents.