Magnetically recoverable, thermostable, hydrophobic DNA/silica encapsulates and their application as invisible oil tags

Flow Cytometry Sorting for Random Access in DNA Data Storage: Encapsulation for Enhanced Stability and Sequence Integrity of DNA

As digital data undergo explosive growth, deoxyribonucleic acid (DNA) has emerged as a promising storage medium due to its high density, longevity, and ease of replication, offering vast potential in data storage solutions. This study focuses on the protection and retrieval of data during the DNA storage process, developing a technique that employs flow cytometry sorting (FCS) to segregate multicolored fluorescent DNA microparticles encoded with data and facilitating efficient random access. Moreover, the encapsulated fluorescent DNA microparticles, formed through layer-by-layer self-assembly, preserve structural and sequence integrity even under harsh conditions while also supporting a high-density DNA payload. Experimental results have shown that the encoded data can still be successfully recovered from encapsulated DNA microparticles following de-encapsulation. We also successfully demonstrated the automated encapsulation process of fluorescent DNA microparticles using a microfluidic chip. This research provides an innovative approach to the long-term stability and random readability of DNA data storage.

A strategy to build a library of oil tracers by oleophilic silica-encapsulated DNA nanoparticles

Artificially synthesized DNA is involved in the construction of a library of oil tracers due to their unlimited number and no-biological toxicity. The strategy of the construction is proposed by oleophilic Silica-encapsulated DNA nanoparticles, which offers fresh thinking in developing novel tracers, sensors, and molecular machines in engineering & applied sciences based on artificially synthesized DNA blocks.

Selective ionization of marker molecules in fuels by laser-based ion mobility spectrometry (LIMS)

Careful quality control of complex matrices such as fuels and food is necessary due to the prevalence of counterfeit and pirated goods in global trade. The addition of taggants (indicator substances) to products or their packaging helps to ensure traceability. In order to prevent the mixing of different liquid products, such as different taxed fuels, invisible labelling (marker) can be used to detect illegal activities. This study investigates the qualitative and quantitative analysis of markers in complex fuel matrices using Resonance-Enhanced Multiphoton Ionisation (REMPI) Ion Mobility Spectrometry (IMS). The potential of REMPI as a selective ionisation technique for the detection of markers is highlighted, particularly with respect to minimizing matrix background and the possibility of detection without chromatographic pre-separation. Finding a suitable marker-wavelength combination that provides a suitable marker-to-matrix ratio allows selective ionization of markers while minimising matrix background. Matrix analysis shows that higher excitation wavelengths result in reduced matrix signals, with the low intensities observed at 355 nm for diesel and petrol matrices. Several candidate markers are evaluated based on the criteria of intense signal at 355 nm and non-leachability for the low tax labelling. The analytical performance of selected markers is evaluated, with a focus on the charge transfer reaction (CTR) between markers and matrix components. Our findings demonstrate the potential of REMPI-IMS for marker analysis in fuels without the need for chromatographic pre-separation, providing a promising approach for detecting illegal or fraudulent activities in the supply chain.

Data Storage Using DNA

The exponential growth of global data has outpaced the storage capacities of current technologies, necessitating innovative storage strategies. DNA, as a natural medium for preserving genetic information, has emerged as a highly promising candidate for next-generation storage medium. Storing data in DNA offers several advantages, including ultrahigh physical density and exceptional durability. Facilitated by significant advancements in various technologies, such as DNA synthesis, DNA sequencing, and DNA nanotechnology, remarkable progress has been made in the field of DNA data storage over the past decade. However, several challenges still need to be addressed to realize practical applications of DNA data storage. In this review, the processes and strategies of in vitro DNA data storage are first introduced, highlighting recent advancements. Next, a brief overview of in vivo DNA data storage is provided, with a focus on the various writing strategies developed to date. At last, the challenges encountered in each step of DNA data storage are summarized and promising techniques are discussed that hold great promise in overcoming these obstacles.

Optimized synthesis of polyacrylic acid-coated magnetic nanoparticles for high-efficiency DNA isolation and size selection

Solid-phase reversible immobilization (SPRI) bead technology is widely used in molecular biology for convenient DNA manipulation. However, commercial SPRI bead kits lack cost advantages and flexibility. It is, therefore, necessary to develop new and alternative cost-effective methods of on-par or better quality. Herein, an easy and cost-effective method is proposed for synthesizing polyacrylic acid-coated iron oxide nanoparticles (PAA-IONPs) through in situ polymerization at lab scale for high-efficiency nucleic acid extraction and size selection. A design of experiment (DoE) approach was used to investigate the influence of iron oxide nanoparticles (IONPs), acrylic acid (AA) monomer, and sodium dodecyl sulfate (SDS) surfactant amounts on the sizes and carboxyl group densities of PAA-IONPs. Thorough characterization by thermogravimetric analysis (TGA), attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) and vibrating sample magnetometry (VSM) highlights the importance of a low starting pH achieved by a high ratio of AA/IONPs, to yield the largest sizes (554 nm) and highest carboxyl group densities (2.13 mmol g-1) obtained in this study. An efficient DNA purification strategy is then presented using homemade beads-suspension buffer and optimized bead concentrations (17% PEG 8000, 2.5 M NaCl, and 3 mg mL-1 PAA-IONPs). This method shows comparable performance to the control (AMPure XP beads) for DNA recovery. An adjustable PAA-IONPs DNA purification system was also developed to be used for DNA-size selection at low DNA amounts (50-100 ng) with a high degree of resolution and recovery. In conclusion, this work offers an optimized PAA-IONPs synthesis protocol and a flexible DNA purification approach that will enable researchers to manipulate DNA under various conditions, holding the significant potential to benefit future molecular biology research and diagnostics.

DNA Data Storage

The demand for data storage is growing at an unprecedented rate, and current methods are not sufficient to accommodate such rapid growth due to their cost, space requirements, and energy consumption. Therefore, there is a need for a new, long-lasting data storage medium with high capacity, high data density, and high durability against extreme conditions. DNA is one of the most promising next-generation data carriers, with a storage density of 10¹⁹ bits of data per cubic centimeter, and its three-dimensional structure makes it about eight orders of magnitude denser than other storage media. DNA amplification during PCR or replication during cell proliferation enables the quick and inexpensive copying of vast amounts of data. In addition, DNA can possibly endure millions of years if stored in optimal conditions and dehydrated, making it useful for data storage. Numerous space experiments on microorganisms have also proven their extraordinary durability in extreme conditions, which suggests that DNA could be a durable storage medium for data. Despite some remaining challenges, such as the need to refine methods for the fast and error-free synthesis of oligonucleotides, DNA is a promising candidate for future data storage.

Application of CRISPR Cas systems in DNA recorders and writers

The necessity to record and store biological data is increasing in due course of time. However, it is quite difficult to understand biological mechanisms and keep a track of these events in some storage mediums. DNA (deoxyribonucleic acid) is the best candidate for the storage of cellular events in the biological system. It is energy efficient as well as stable at the same time. DNA-based writers and memory devices are continually evolving and finding new avenues in terms of their wide range of applications. Among all the DNA-based storage devices that employ enzymes like recombinases, nucleases, integrases, and polymerases, one of the most popular tools used for these devices is the emerging and versatile CRISPR Cas technology. CRISPR Cas is a prokaryotic immune system that keeps a memory of viral attacks and protects prokaryotes from potential future infections. The main aim of this short review is to study such molecular recorders and writers that employ CRISPR Cas technologies and obtain an in-depth overview of the mechanisms involved and the applications of these molecular devices.

Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications

Synthetic DNA barcodes are double-stranded DNA molecules designed to carry recoverable information, information that can be used to represent and track objects and organisms. DNA barcodes offer robust, sensitive detection using standard amplification and sequencing techniques. While numerous research groups have promoted DNA as an information storage medium, less attention has been devoted to the design of economical, scalable DNA barcode libraries. Here, we present an alternative modular approach to sequence design. Barcode sequences were constructed from smaller, interchangeable blocks, allowing for the combinatorial assembly of numerous distinct tags. We demonstrated the design and construction of first-generation (N = 256) and second-generation (N = 512) modular barcode libraries, from fewer than 50 total single-stranded oligonucleotides for each library. To avoid contamination during experimental validation, a liquid-handling robot was employed for oligonucleotide mixing. Generating barcode sequences in-house reduces dependency upon external entities for unique tag generation, increasing flexibility in barcode generation and deployment. Next generation sequencing (NGS) detection of 256 different samples in parallel highlights the multiplexing afforded by the modular barcode design coupled with high-throughput sequencing. Deletion variant analysis of the first-generation library informed sequence design for enhancing barcode assembly specificity in the second-generation library.

An Accurate and Rapid Way for Identifying Food Geographical Origin and Authenticity: Editable DNA-Traceable Barcode

DNA offers significant advantages in information density, durability, and replication efficiency compared with information labeling solutions using electronic, magnetic, or optical devices. Synthetic DNA containing specific information via gene editing techniques is a promising identifying approach. We developed a new traceability approach to convert traditional digitized information into DNA sequence information. We used encapsulation to make it stable for storage and to enable reading and detection by DNA sequencing and PCR-capillary electrophoresis (PCR-CE). The synthesized fragment consisted of a short fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene from the Holothuria fuscogilva (ID: LC593268.1), inserted geographical origin information (18 bp), and authenticity information from Citrus sinensis (20 bp). The obtained DNA-traceable barcodes were cloned into vector PMD19-T. Sanger sequencing of the DNA-traceable barcode vector was 100% accurate and provided a complete readout of the traceability information. Using selected recognition primers CAI-B, DNA-traceable barcodes were identified rapidly by PCR amplification. We encapsulated the DNA-traceable barcodes into amorphous silica spheres and improved the encapsulation procedure to ensure the durability of the DNA-traceable barcodes. To demonstrate the applicability of DNA-traceable barcodes as product labels, we selected Citrus sinensis as an example. We found that the recovered and purified DNA-traceable barcode can be analyzed by standard techniques (PCR-CE for DNA-traceable barcode identification and DNA sequencing for readout). This study provides an accurate and rapid approach to identifying and certifying products' authenticity and traceability.

Mosquito tagging using DNA-barcoded nanoporous protein microcrystals

Conventional mosquito marking technology for mark-release-recapture (MRR) is quite limited in terms of information capacity and efficacy. To overcome both challenges, we have engineered, lab-tested, and field-evaluated a new class of marker particles, in which synthetic, short DNA oligonucleotides (DNA barcodes) are adsorbed and protected within tough, crosslinked porous protein microcrystals. Mosquitoes self-mark through ingestion of microcrystals in their larval habitat. Barcoded microcrystals persist trans-stadially through mosquito development if ingested by larvae, do not significantly affect adult mosquito survivorship, and individual barcoded mosquitoes are detectable in pools of up to at least 20 mosquitoes. We have also demonstrated crystal persistence following adult mosquito ingestion. Barcode sequences can be recovered by qPCR and next-generation sequencing (NGS) without detectable amplification of native mosquito DNA. These DNA-laden protein microcrystals have the potential to radically increase the amount of information obtained from future MRR studies compared to previous studies employing conventional mosquito marking materials.

Preservation and Encryption in DNA Digital Data Storage

The exponential growth of the total amount of global data presents a huge challenge to mainstream storage media. The emergence of molecular digital storage inspires the development of the new-generation higher-density digital data storage. In particular, DNA with high storage density, reproducibility, and long recoverable lifetime behaves the ideal representative of molecular digital storage media. With the development of DNA synthesis and sequencing technologies and the reduction of cost, DNA digital storage has attracted more and more attention and achieved significant breakthroughs. Herein, this Review briefly describes the workflow of DNA storage, and highlights the storage step of DNA digital data storage. Then, according to different information storage forms, the current DNA information encryption methods are emphatically expounded. Finally, the brief perspectives on the current challenges and optimizing proposals in DNA information preservation and encryption are presented.

Optically Sensitive and Magnetically Identifiable Supraparticles as Indicators of Surface Abrasion

Identifying and ensuring the integrity of products plays an important role in today's globalized world. Miniaturized information taggants in the packaging surface are therefore required to monitor the product itself instead of applying external labels. Ideally, multiple types of information are stored in such additives. In this work, micrometer-sized core-shell particles (supraparticles) were developed to provide material surfaces with both an identifier and a surface abrasion indication functionality. The core of the supraparticles contains iron oxide nanoparticles that allow identification of the surface with a spectral magnetic code resolved by magnetic particle spectroscopy. The fluorescent silica nanoparticles in the supraparticle shell can be abraded by mechanical stress and resolved by fluorescence spectroscopy. This provides information about the mechanical integrity of the system. The application as surfaces, that contain several types of information in one supraparticle, was demonstrated here by incorporating such bifunctional supraparticles as additives in a surface coating.

Integrating DNA Encapsulates and Digital Microfluidics for Automated Data Storage in DNA

Using DNA as a durable, high-density storage medium with eternal format relevance can address a future data storage deficiency. The proposed storage format incorporates dehydrated particle spots on glass, at a theoretical capacity of more than 20 TB per spot, which can be efficiently retrieved without significant loss of DNA. The authors measure the rapid decay of dried DNA at room temperature and present the synthesis of encapsulated DNA in silica nanoparticles as a possible solution. In this form, the protected DNA can be readily applied to digital microfluidics (DMF) used to handle retrieval operations amenable to full automation. A storage architecture is demonstrated, which can increase the storage capacity of today's archival storage systems by more than three orders of magnitude: A DNA library containing 7373 unique sequences is encapsulated and stored under accelerated aging conditions (4 days at 70 °C, 50% RH) corresponding to 116 years at room temperature and the stored information is successfully recovered.

Colorful Luminescent Magnetic Supraparticles: Expanding the Applicability, Information Capacity, and Security of Micrometer-Scaled Identification Taggants by Dual-Spectral Encoding

(Sub)micrometer-scaled identification (ID) taggants enable direct identification of arbitrary goods, thereby opening up application fields based on the possibility of tracking, tracing, and anti-counterfeiting. Due to their small dimensions, these taggants can equip in principle even the smallest subcomponents or raw materials with information. To achieve the demanded applicability, the mostly used optically encoded ID taggants must be further improved. Here, micrometer-scaled supraparticles with spectrally encoded luminescent and magnetically encoded signal characteristics are reported. They are produced in a readily customizable bottom-up fabrication procedure that enables precise adjustment of luminescent and magnetic properties on multiple hierarchy levels. The incorporation of commonly used magnetic nanoparticles and fluorescent dyes, respectively, into polymer nanocomposite particles, establishes a convenient toolbox of magnetic and luminescent building blocks. The subsequent assembly of selected building blocks in the desired ratios into supraparticles grants for all the flexibility to freely adjust both signal characteristics. The obtained spectrally resolved visible luminescent and invisible magnetic ID signatures are complementary in nature, thus expanding applicability and information security compared to recently reported optical- or magnetic-encoded taggants. Additionally, the introduced ID taggant supraparticles can significantly enhance the coding capacity. Therefore, the introduced supraparticles are considered as next-generation ID taggants.

Spray-Drying and Atomic Layer Deposition: Complementary Tools toward Fully Orthogonal Control of Bulk Composition and Surface Identity of Multifunctional Supraparticles

Spray-drying is a scalable process enabling one to assemble freely chosen nanoparticles into supraparticles. Atomic layer deposition (ALD) allows for controlled thin film deposition of a vast variety of materials including exotic ones that can hardly be synthesized by wet chemical methods. The properties of coated supraparticles are defined not only by the nanoparticle material chosen and the nanostructure adjusted during spray-drying but also by surface functionalities modified by ALD, if ALD is capable of modifying not only the outer surfaces but also surfaces buried inside the porous supraparticle. Simultaneously, surface accessibility in the porous supraparticles must be ensured to make use of all functionalized surfaces. In this work, iron oxide supraparticles are utilized as a model substrate as their magnetic properties enable the use of advanced magnetic characterization methods. Detailed information about the structural evolution upon individual ALD cycles of aluminium oxide, zinc oxide and titanium dioxide are thereby revealed and confirmed by gas sorption analyses. This demonstrates a powerful and versatile approach to freely designing the functionality of future materials by combination of spray-drying and ALD.

Scalable Nucleic Acid Storage and Retrieval Using Barcoded Microcapsules

Rapid advances in nucleic acid sequencing and synthesis technologies have spurred a major need to collect, store, and sequence the DNA and RNA from viral, bacterial, and mammalian sources and organisms. However, current approaches to storing nucleic acids rely on a low-temperature environment and require robotics for access, posing challenges for scalable and low-cost nucleic acid storage. Here, we present an alternative method for storing nucleic acids, termed Preservation and Access of Nucleic aciDs using barcOded micRocApsules (PANDORA). Nucleic acids spanning kilobases to gigabases and from different sources, including animals, bacteria, and viruses, are encapsulated into silica microcapsules to protect them from environmental denaturants at room temperature. Molecular barcodes attached to each microcapsule enable sample pooling and subsequent identification and retrieval using fluorescence-activated sorting. We demonstrate quantitative storage and rapid access to targeted nucleic acids from a pool emulating standard retrieval operations implemented in conventional storage systems, including recovery of 100,000-200,000 samples and Boolean logic selection using four unique barcodes. Quantitative polymerase chain reaction and short-read sequencing of the retrieved samples validated the sorting experiments and the integrity of the released nucleic acids. Our proposed approach offers a scalable long-term, room-temperature storage and retrieval of nucleic acids with high sample fidelity.

Transport of silica encapsulated DNA microparticles in controlled instantaneous injection open channel experiments

Surface water tracing is a widely used technique to investigate in-stream mass transport including contaminant migration. Recently, a microparticle tracer was developed with unique synthetic DNA encapsulated in an environmentally-friendly silica coating (Si-DNA microparticle). Previous tracing applications of such tracers reported detection and quantification, but a massive loss of tracer mass. However, the transport behavior of these DNA-tagged microparticle tracers has not been rigorously quantified and compared with that of solute tracers. Therefore, we compared the transport behavior of Si-DNA microparticles to the behavior of solute NaCl in 6 different, environmentally representative water types using breakthrough curves (BTCs), obtained from laboratory open channel injection experiments, whereby no Si-DNA microparticle tracer mass was lost. Hereafter, we modelled the BTCs using a 1-D advection-dispersion model with one transient storage zone (OTIS) by calibrating the hydrodynamic dispersion coefficient D and a storage zone exchange rate coefficient. We concluded that the transport behavior of Si-DNA microparticles resembled that of NaCl in surface-water relevant conditions, evidenced by BTCs with a similar range of D; however, the Si-DNA microparticle had a more erratic BTC than its solute counterpart, whereby the scatter increased as a function of water quality complexity. The overall larger confidence interval of D_Si-DNA was attributed to the discrete nature of colloidal particles with a certain particle size distribution and possibly minor shear-induced aggregations. This research established a solid methodological foundation for field application of Si-DNA microparticles in surface water tracing, providing insight in transport behavior of equivalent sized and mass particles in rivers.

The untapped potential of magnetic nanoparticles for forensic investigations: A comprehensive review

With a growing interest in precise and sensitive diagnosis for criminal investigations, nanoparticles (NPs) have intrigued scientific minds working in the field of forensic science due to their exceptional properties. Magnetic nanoparticles (MNPs) have emerged as a powerful tool for improving forensic analysis due to their super magnetic behavior combined with smaller dimensions. MNP-based applications can benefit criminologists to solve criminal mysteries with greater precision and pace. This review highlights the different types of MNP-based applications and their developmental and implicational aspects of forensic science. It also renders insight into the future prospects of a splendid blend of nanotechnology and forensic science, leading to a better scientific analysis.

A Single Magnetic Particle with Nearly Unlimited Encoding Options

Communicating objects are demanded for product security and the concepts of a circular economy or the Internet of Nano Things. Smart additives in the form of particles can be the key to equip objects with the desired materials intelligence as their miniaturized size improves applicability and security. Beyond their proposed identification by optical signals, magnetic signals deriving from magnetic particles can hypothetically be used for identification but are to date only resolved roughly. Herein, a magnetic particle-based toolbox is reported, that provides more than 77 billion (77 × 10⁹ ) different magnetic codes, adjustable in one single particle, that can be read out unambiguously, easily, and quickly. The key towards achieving the vast code variety is a hierarchical supraparticle design that is inspired by music: similarly to how the line-up variation of a musical ensemble yields distinguishable overtones, the variation of the supraparticle composition alters their magnetic overtones. By minimizing magnetic interactions, customizable signals are spectrally decoded by the simple method of magnetic particle spectroscopy. A large number of chemically adjustable magnetic codes and the possibility of their remote, contactless detection from within materials is a breakthrough for unexploited labeling applications and pave the way towards materials intelligence.

The Effect of pH and Viscosity on Magnetophoretic Separation of Iron Oxide Nanoparticles

Magnetic nanoparticles (MNPs) are used for magnetophoresis-based separation processes in various biomedical and engineering applications. Essential requirements are the colloidal stability of the MNPs and the ability to be separated even in low magnetic field gradients. Bare iron oxide nanoparticles (BIONs) with a diameter of 9.2 nm are synthesized via coprecipitation, exhibiting a high saturation magnetization of 70.84 Am2 kg−1 and no remanence. In our study, zeta potential, dynamic light scattering (DLS), and sedimentation analysis show that the aggregation behavior of BIONs is influenced by pH and viscosity. Small aggregate clusters are formed with either low or high pH values or increased viscosity. Regarding magnetophoresis-based separation, a higher viscosity leads to lower magnetophoretic velocities, similar to how small aggregates do. Additionally, cooperative magnetophoresis, the joint motion of strongly interacting particles, affects the separation of the BIONs, too. Our study emphasizes the effect of pH and viscosity on the physicochemical characteristics of MNPs, resulting in different aggregation behavior. Particularly, for high viscous working media in downstream processing and medicine, respectively, the viscosity should be taken into account, as it will affect particle migration.

Application of DNA sequences in anti-counterfeiting: Current progress and challenges

Counterfeiting has never been more challenging than during the COVID-19 pandemic as counterfeit test kits and therapeutics have been discovered in the market. Current anti-counterfeiting labels have weaknesses: they can either be duplicated easily, are expensive or ill-suited for the existing complex supply chains. While RFID tags provide for an excellent alternative to current anti-counterfeiting methods, they can prove to be expensive and other routes involving nanomaterials can be difficult to encrypt. A DNA based anticounterfeiting system has significant advantages such as relative ease of synthesis and vast data storage abilities, along with great potential in encryption. Although DNA is equipped with such beneficial properties, major challenges that limit its real-world anti-counterfeiting applications include protection in harsh environments, rapid inexpensive sequence determination, and its attachment to products. This review elaborates the current progress of DNA based anti-counterfeiting systems and identifies technological gaps that need to be filled for its practical application. Progress made on addressing the primary challenges associated with the use of DNA, and potential solutions are discussed.

Preservation of DNA for data storage

The preservation of DNA has attracted significant interest of scientists in diverse research fields from ancient biological remains to the information field. In light of the different DNA safekeeping requirements (e.g., storage time, storage conditions) in these disparate fields, scientists have proposed distinct methods to maintain the DNA integrity. Specifically, DNA data storage is an emerging research, which means that the binary digital information is converted to the sequences of nucleotides leading to dense and durable data storage in the form of synthesized DNA. The intact preservation of DNA plays a significant role because it is closely related to data integrity. This review discusses DNA preservation methods, aiming to confirm an appropriate one for synthetic oligonucleotides in DNA data storage. First, we analyze the impact factors of the DNA long-term storage, including the intrinsic stability of DNA, environmental factors, and storage methods. Then, the benefits and disadvantages of diverse conservation approaches (e.g., encapsulation-free, chemical encapsulation) are discussed. Finally, we provide advice for storing non-genetic information in DNA in vitro. We expect these preservation suggestions to promote further research that may extend the DNA storage time.

The bibliography includes 99 references.

Magnetic Nanoparticles to Unique DNA Tracers: Effect of Functionalization on Physico-chemical Properties

To monitor and manage hydrological systems such as brooks, streams, rivers, the use of tracers is a well-established process. Limited number of potential tracers such as salts, isotopes and dyes, make study of hydrological processes a challenge. Traditional tracers find limited use due to lack of multiplexed, multipoint tracing and background noise, among others. In this regard, DNA based tracers possess remarkable advantages including, environmentally friendly, stability, and high sensitivity in addition to showing great potential in the synthesis of ideally unlimited number of unique tracers capable of multipoint tracing. To prevent unintentional losses in the environment during application and easy recovery for analysis, we hereby report DNA encapsulation in silica containing magnetic cores (iron oxide) of two different shapes-spheres and cubes. The iron oxide nanoparticles having size range 10-20 nm, have been synthesized using co-precipitation of iron salts or thermal decomposition of iron oleate precursor in the presence of oleic acid or sodium oleate. Physico-chemical properties such as size, zeta potential, magnetism etc. of the iron oxide nanoparticles have been optimized using different ligands for effective binding of dsDNA, followed by silanization. We report for the first time the effect of surface coating on the magnetic properties of the iron oxide nanoparticles at each stage of functionalization, culminating in silica shells. Efficiency of encapsulation of three different dsDNA molecules has been studied using quantitative polymerase chain reaction (qPCR). Our results show that our DNA based magnetic tracers are excellent candidates for hydrological monitoring with easy recoverability and high signal amplification.

Novel Modalities in DNA Data Storage

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.

DNA nanostructures as templates for biomineralization

Nature uses extracellular matrix scaffolds to organize biominerals into hierarchical structures over various length scales. This has inspired the design of biomimetic mineralization scaffolds, with DNA nanostructures being among the most promising. DNA nanotechnology makes use of molecular recognition to controllably give 1D, 2D and 3D nanostructures. The control we have over these structures makes them attractive templates for the synthesis of mineralized tissues, such as bones and teeth. In this Review, we first summarize recent work on the crystallization processes and structural features of biominerals on the nanoscale. We then describe self-assembled DNA nanostructures and come to the intersection of these two themes: recent applications of DNA templates in nanoscale biomineralization, a crucial process to regenerate mineralized tissues.

Effect of Iron Oxide Nanoparticles on the Properties of Water-Based Drilling Fluids

In recent years, several studies have indicated the impact of nanoparticles (NPs) on various properties (such as viscosity and fluid loss) of conventional drilling fluids. Our previous study with commercial iron oxide NPs indicated the potential of using NPs to improve the properties of a laboratory bentonite-based drilling fluid without barite. In the present work, iron oxide NPs have been synthesized using the co-precipitation method. The effect of these hydrophilic NPs has been evaluated in bentonite and KCl-based drilling fluids. Rheological properties at different temperatures, viscoelastic properties, lubricity, and filtrate loss were measured to study the effect of NPs on the base fluid. Also, elemental analysis of the filtrate and microscale analysis of the filter cake was performed. Results for bentonite-based fluid showed that 0.019 wt% (0.1 g) of NPs reduced the coefficient of friction by 47%, and 0.0095 wt% (0.05 g) of NPs reduced the fluid loss by 20%. Moreover, for KCl-based fluids, 0.019 wt% (0.1 g) of additive reduced the coefficient of friction by 45%, while higher concentration of 0.038 wt% (0.2 g) of NPs shows 14% reduction in the filtrate loss. Microscale analysis shows that presence of NPs in the cake structure produces a more compact and less porous structure. This study indicates that very small concentration of NPs can provide better performance for the drilling fluids. Additionally, results from this work indicate the ability of NPs to fine-tune the properties of drilling fluids.

Accelerated non-crosslinking assembly of DNA-functionalized nanoparticles in alcoholic solvents: for application in the identification of clear liquors

Colorimetric detection of various target molecules in aqueous solutions based on the non-crosslinking assembly of DNA-functionalized Au nanoparticles (DNA-AuNPs) has been well established in recent years. The extension of DNA-AuNPs to other solvents remains much less explored, despite the practical importance of detection in non-aqueous solutions, such as those containing an organic ingredient that is required or not removable in many contexts. However, the general consideration that DNA is easily denatured and precipitated in organic solvents has been hampering the use of DNA-AuNPs in low polar solvents. Herein, we report a more rapid non-crosslinking assembly of double-stranded (ds) DNA-AuNPs in alcoholic solvents than in aqueous solvents. When the concentration of ethanol in the disperse medium is increased from 0% to 20% (v/v), the rate of non-crosslinking assembly is distinctly increased by a factor of 5-6, whereas the rate is sharply decreased when the ethanol concentration is further increased to 40%. This biphasic kinetics trend could be attributed to the competitive balance between the enhanced intermolecular attraction between dsDNAs and the increased propensity for melting of dsDNA. Rapid naked-eye identification of clear liquors that are encoded by oligonucleotide additives has also been demonstrated by using the alcoholic non-crosslinking assembly of dsDNA-AuNPs as a proof-of-concept.

DNA assembly for nanopore data storage readout

Synthetic DNA is becoming an attractive substrate for digital data storage due to its density, durability, and relevance in biological research. A major challenge in making DNA data storage a reality is that reading DNA back into data using sequencing by synthesis remains a laborious, slow and expensive process. Here, we demonstrate successful decoding of 1.67 megabytes of information stored in short fragments of synthetic DNA using a portable nanopore sequencing platform. We design and validate an assembly strategy for DNA storage that drastically increases the throughput of nanopore sequencing. Importantly, this assembly strategy is generalizable to any application that requires nanopore sequencing of small DNA amplicons.

Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter

The emergence of high-throughput DNA sequencing technologies sparked a 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 parallel DNA sequencing have since motivated its use as a broad-spectrum molecular counter. A key aspect of extrapolating DNA sequencing to non-traditional applications is the need to append nucleic-acid barcodes to entities of interest. In this review, we describe the chemical and biochemical approaches that have enabled nucleic-acid barcoding of proteinaceous and non-proteinaceous materials and provide examples of downstream technologies that have been made possible by DNA-encoded molecules. As commercially available high-throughput sequencers were first released less than 15 years ago, we believe related applications will continue to mature and close by proposing new frontiers to support this assertion.

Tomographic Reservoir Imaging with DNA-Labeled Silica Nanotracers: The First Field Validation

This study presents the first field validation of using DNA-labeled silica nanoparticles as tracers to image subsurface reservoirs by travel time based tomography. During a field campaign in Switzerland, we performed short-pulse tracer tests under a forced hydraulic head gradient to conduct a multisource-multireceiver tracer test and tomographic inversion, determining the two-dimensional hydraulic conductivity field between two vertical wells. Together with three traditional solute dye tracers, we injected spherical silica nanotracers, encoded with synthetic DNA molecules, which are protected by a silica layer against damage due to chemicals, microorganisms, and enzymes. Temporal moment analyses of the recorded tracer concentration breakthrough curves (BTCs) indicate higher mass recovery, less mean residence time, and smaller dispersion of the DNA-labeled nanotracers, compared to solute dye tracers. Importantly, travel time based tomography, using nanotracer BTCs, yields a satisfactory hydraulic conductivity tomogram, validated by the dye tracer results and previous field investigations. These advantages of DNA-labeled nanotracers, in comparison to traditional solute dye tracers, make them well-suited for tomographic reservoir characterizations in fields such as hydrogeology, petroleum engineering, and geothermal energy, particularly with respect to resolving preferential flow paths or the heterogeneity of contact surfaces or by enabling source zone characterizations of dense nonaqueous phase liquids.

Silica-Encapsulated DNA-Based Tracers for Aquifer Characterization

Environmental tracing is a direct way to characterize aquifers, evaluate the solute transfer parameter in underground reservoirs, and track contamination. By performing multitracer tests, and translating the tracer breakthrough times into tomographic maps, key parameters such as a reservoir's effective porosity and permeability field may be obtained. DNA, with its modular design, allows the generation of a virtually unlimited number of distinguishable tracers. To overcome the insufficient DNA stability due to microbial activity, heat, and chemical stress, we present a method to encapsulated DNA into silica with control over the particle size. The reliability of DNA quantification is improved by the sample preservation with NaN₃ and particle redispersion strategies. In both sand column and unconsolidated aquifer experiments, DNA-based particle tracers exhibited slightly earlier and sharper breakthrough than the traditional solute tracer uranine. The reason behind this observation is the size exclusion effect, whereby larger tracer particles are excluded from small pores, and are therefore transported with higher average velocity, which is pore size-dependent. Identical surface properties, and thus flow behavior, makes the new material an attractive tracer to characterize sandy groundwater reservoirs or to track multiple sources of contaminants with high spatial resolution.

Magnetic nano fluids for isolation of genomic DNA and total RNA from various prokaryote and eukaryote cells

The correct isolation of nucleic acid from various cells is an important preliminary step before many biochemical and diagnostic processes such as cloning, sequencing, replication, hybridization, and complementary DNA (cDNA) synthesis. In this study, the coated magnetic nanoparticles (MNFs) with Tween 20 and oleic acid because of paramagnetic and bio-compatibility properties used in the extractions of genomic DNA (gDNA) and total RNA from prokaryote and eukaryote cells. The amount and accuracy of gDNA and total RNA extracted were proved via agarose gel electrophoresis, digestion and polymerase chain reaction (PCR) techniques. According to UV-Vis spectrophotometry data and gDNA and ribosomal RNA (rRNA) bands observed on the agarose gel, the results showed that extraction of this nano-kit can be comparable with the existing methods used to purifying nucleic acids such as purification based on the use of Cetyltrimethylammonium bromide (CTAB) and phenol-chloroform methods. Characterization of the particles defines them to be ~34.85 nm in diameter and exhibiting high saturation magnetization (28 emu/g). Elimination of hazardous reagents such as phenol and chloroform from extraction solutions, the replacement for inorganic coating such as silica with organic oil, and reduction of reaction time are some advantages of this method. Therefore, according to the challenges in the nucleic acid purification pathway, the use of these kits can be remarkable.

Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications

BACKGROUND

Biosafety is a key aspect in the international Genetically Engineered Machine (iGEM) competition, which offers student teams an amazing opportunity to pursue their own research projects in the field of Synthetic Biology. iGEM projects often involve the creation of genetically engineered bacterial strains. To minimize the risks associated with bacterial release, a variety of biosafety systems were constructed, either to prevent survival of bacteria outside the lab or to hinder horizontal or vertical gene transfer.

MAIN BODY

Physical containment methods such as bioreactors or microencapsulation are considered the first safety level. Additionally, various systems involving auxotrophies for both natural and synthetic compounds have been utilized by iGEM teams in recent years. Combinatorial systems comprising multiple auxotrophies have been shown to reduced escape frequencies below the detection limit. Furthermore, a number of natural toxin-antitoxin systems can be deployed to kill cells under certain conditions. Additionally, parts of naturally occurring toxin-antitoxin systems can be used for the construction of 'kill switches' controlled by synthetic regulatory modules, allowing control of cell survival. Kill switches prevent cell survival but do not completely degrade nucleic acids. To avoid horizontal gene transfer, multiple mechanisms to cleave nucleic acids can be employed, resulting in 'self-destruction' of cells. Changes in light or temperature conditions are powerful regulators of gene expression and could serve as triggers for kill switches or self-destruction systems. Xenobiology-based containment uses applications of Xeno-DNA, recoded codons and non-canonical amino acids to nullify the genetic information of constructed cells for wild type organisms. A 'minimal genome' approach brings the opportunity to reduce the genome of a cell to only genes necessary for survival under lab conditions. Such cells are unlikely to survive in the natural environment and are thus considered safe hosts. If suitable for the desired application, a shift to cell-free systems based on Xeno-DNA may represent the ultimate biosafety system.

CONCLUSION

Here we describe different containment approaches in synthetic biology, ranging from auxotrophies to minimal genomes, which can be combined to significantly improve reliability. Since the iGEM competition greatly increases the number of people involved in synthetic biology, we will focus especially on biosafety systems developed and applied in the context of the iGEM competition.

Supraparticles: Functionality from Uniform Structural Motifs

Under the right process conditions, nanoparticles can cluster together to form defined, dispersed structures, which can be termed supraparticles. Controlling the size, shape, and morphology of such entities is a central step in various fields of science and technology, ranging from colloid chemistry and soft matter physics to powder technology and pharmaceutical and food sciences. These diverse scientific communities have been investigating formation processes and structure/property relations of such supraparticles under completely different boundary conditions. On the fundamental side, the field is driven by the desire to gain maximum control of the assembly structures using very defined and tailored colloidal building blocks, whereas more applied disciplines focus on optimizing the functional properties from rather ill-defined starting materials. With this review article, we aim to provide a connecting perspective by outlining fundamental principles that govern the formation and functionality of supraparticles. We discuss the formation of supraparticles as a result of colloidal properties interplaying with external process parameters. We then outline how the structure of the supraparticles gives rise to diverse functional properties. They can be a result of the structure itself (emergent properties), of the colocalization of different, functional building blocks, or of coupling between individual particles in close proximity. Taken together, we aim to establish structure-property and process-structure relationships that provide unifying guidelines for the rational design of functional supraparticles with optimized properties. Finally, we aspire to connect the different disciplines by providing a categorized overview of the existing, diverging nomenclature of seemingly similar supraparticle structures.

Critical review of the safety assessment of titanium dioxide additives in food

Nanomaterial engineering provides an important technological advance that offers substantial benefits for applications not only in the production and processing, but also in the packaging and storage of food. An expanding commercialization of nanomaterials as part of the modern diet will substantially increase their oral intake worldwide. While the risk of particle inhalation received much attention, gaps of knowledge exist regarding possible adverse health effects due to gastrointestinal exposure. This problem is highlighted by pigment-grade titanium dioxide (TiO2), which confers a white color and increased opacity with an optimal particle diameter of 200-300 nm. However, size distribution analyses showed that batches of food-grade TiO2 always comprise a nano-sized fraction as inevitable byproduct of the manufacturing processes. Submicron-sized TiO2 particles, in Europe listed as E 171, are widely used as a food additive although the relevant risk assessment has never been satisfactorily completed. For example, it is not possible to derive a safe daily intake of TiO2 from the available long-term feeding studies in rodents. Also, the use of TiO2 particles in the food sector leads to highest exposures in children, but only few studies address the vulnerability of this particular age group. Extrapolation of animal studies to humans is also problematic due to knowledge gaps as to local gastrointestinal effects of TiO2 particles, primarily on the mucosa and the gut-associated lymphoid system. Tissue distributions after oral administration of TiO2 differ from other exposure routes, thus limiting the relevance of data obtained from inhalation or parenteral injections. Such difficulties and uncertainties emerging in the retrospective assessment of TiO2 particles exemplify the need for a fit-to-purpose data requirement for the future evaluation of novel nano-sized or submicron-sized particles added deliberately to food.

A DNA Tracer System for Hydrological Environment Investigations

To monitor and manage hydrological pollution effectively, tracing sources of pollutants is of great importance and also is in urgent need. A variety of tracers have been developed such as isotopes, silica, bromide, and dyes; however, practical limitations of these traditional tracers still exist such as lack of multiplexed, multipoint tracing and interference of background noise. To overcome these limitations, a new tracing system based on DNA nanomaterials, namely DNA tracer, has already been developed. DNA tracers possess remarkable advantages including sufficient species, specificity, environmental friendly, stable migration, and high sensitivity as well as allowing for multipoints tracing. In this review article, we introduce the molecular design, synthesis, protection and signal readout strategies of DNA tracers, compare the advantages and disadvantages of DNA tracer with traditional tracers, and summarize the-state-of-art applications in hydrological environment investigations. In the end, we provide our perspective on the future development of DNA tracers.

Fluorescent and magnetic anti-counterfeiting realized by biocompatible multifunctional silicon nanoshuttle-based security ink

Herein, we present the first example of a silicon nanoshuttle-based security ink simultaneously featuring attractive optical and magnetic properties, suitable for fluorescent and magnetic anti-counterfeiting and encryption. Significantly, the information can be dual-encrypted through multi-color fluorescence and longitudinal (T₁)/transverse (T₂) relaxation contrast by using the silicon nanoshuttle-based security ink. We further demonstrate the feasibility of this high-performance ink for practical application in banknote anti-counterfeiting.

Decoding DNA labels by melting curve analysis using real-time PCR

Synthetic DNA has been used as an authentication code for a diverse number of applications. However, existing decoding approaches are based on either DNA sequencing or the determination of DNA length variations. Here, we present a simple alternative protocol for labeling different objects using a small number of short DNA sequences that differ in their melting points. Code amplification and decoding can be done in two steps using quantitative PCR (qPCR). To obtain a DNA barcode with high complexity, we defined 8 template groups, each having 4 different DNA templates, yielding 158 (>2.5 billion) combinations of different individual melting temperature (Tm) values and corresponding ID codes. The reproducibility and specificity of the decoding was confirmed by using the most complex template mixture, which had 32 different products in 8 groups with different Tm values. The industrial applicability of our protocol was also demonstrated by labeling a drone with an oil-based paint containing a predefined DNA code, which was then successfully decoded. The method presented here consists of a simple code system based on a small number of synthetic DNA sequences and a cost-effective, rapid decoding protocol using a few qPCR reactions, enabling a wide range of authentication applications.