Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes

Next-generation nanotechnology-integrated biosurfactants: Innovations in biopesticide development for sustainable and modern agriculture

The increasing global demand for eco-friendly agricultural practices necessitates the development of innovative pest management solutions, effectively addressing the environmental and ecological issues associated with traditional chemical pesticides, such as pest resistance, environmental contamination, and non-target organism toxicity. Biosurfactants, biologically derived amphiphilic molecules from microbial and plant sources, offer distinct advantages including biodegradability, excellent surface-active properties, and inherent antimicrobial efficacy, making them as promising candidates for sustainable pest management and control. Concurrently, nanotechnology introduces innovative delivery mechanisms, enhancing biopesticide stability, solubility, and targeted application, significantly minimizing off-target impact and environmental footprint. This review emphasizes recent breakthroughs in integrating biosurfactants with nanotechnological strategies to produce advanced biopesticides. Key advancements include the role of biosurfactants to increase the bioavailability and effectiveness of active ingredients and utilizing nanopesticides for targeted pest control with improved precision. Combining the unique amphiphilic properties of biosurfactants and the precise targeting capabilities of nanocarriers presents substantial improvements in pest management efficacy and aligns closely with Integrated Pest Management (IPM) principles. Despite these promising developments, significant knowledge gaps remain, including understanding the interactions between biosurfactants, nanomaterials, and the environmental matrices, as well as assessing long-term ecological impacts and safety profiles associated with nanopesticide usage. This article outlines critical research areas requiring further exploration to optimize biosurfactant-nanotechnology systems for large-scale agricultural deployment. Addressing these challenges will facilitate broader adoption, ensuring sustainable pest control practices that significantly contribute to global food security and environmental preservation. Integrating biosurfactants with nanotechnology represents a transformative approach in agricultural pest management, offering substantial potential to revolutionize sustainable agriculture through effective, environment-friendly solutions.

Opportunities and Challenges of DNA Materials toward Sustainable Development Goals

Sustainable development represents a significant and pressing challenge confronting the global community at present. A wide variety of macroscopic engineering systems has been developed to promote sustainable development. Recent advancements in DNA materials have showcased their substantial contributions toward achieving sustainable development goals (SDGs). Compared to nonbiological materials, DNA materials possess exceptional properties such as genetic functionality, molecular programmability, recognition capabilities, and biocompatibility. These unique characteristics enable DNA materials to serve as general and versatile substrates beyond their genetic role. Consequently, they can be used to develop DNA-based engineering systems that offer versatile solutions to support sustainable development. In this Perspective, we critically examine the opportunities that DNA-based engineering systems present in contributing to the achievement of the SDGs within various real-world scenarios. We establish direct relationships between DNA-based engineering systems and the SDGs, highlighting their inherent merits in accelerating sustainable development. Furthermore, in order to successfully achieve SDGs, we address the challenges associated with these systems and emphasize the urgent need for developing multifunctional, reliable, biosafe, and intelligent DNA-based engineering systems to overcome these challenges.

Highly spatial-temporal electrochemical profiling of molecules trafficking at a single mitochondrion in one living cell

Simultaneous profiling of multiple molecules trafficking at a single organelle and the surrounding cytosol within a living cell is crucial for elucidating their functions, necessitating advanced techniques that provide high spatial-temporal resolution and molecule specificity. In this study, we present an electrochemical nanodevice based on a θ-nanopipette designed to coanalyze calcium ions (Ca2+) and reactive oxygen species (ROS) at a single mitochondrion and its surrounding cytosol, thereby enhancing our understanding of their trafficking within the signaling pathways of cellular autophagy. Two independent nanosensors integrated within the channels of the θ-nanopipette spatially isolate a single target mitochondrion from the cytosol and simultaneously measure the release of Ca2+ and ROS with high spatial-temporal resolution. Dynamic tracking reveals the direct trafficking of lysosomal Ca2+ to the mitochondrion rather than to the cytosol, which triggers ROS-induced ROS release within the mitochondria. Furthermore, highly temporal and concurrent observations revealed a second burst of Ca2+ in both the mitochondrion and the cytosol, which is not consistent with the change in ROS. These dynamic data elucidate the potential role of a beneficial feedback loop between the Ca2+ signaling pathway and the subsequent generation of mitochondrial ROS in ML-SA-induced autophagy. More importantly, this innovative platform facilitates detailed profiling of the molecular interactions between trafficking molecules within the mitochondria and the adjacent cytosolic environment, which is hardly realized using the current superresolution optical microscopy.

Aptamer-functionalized nucleic acid nanotechnology for biosensing, bioimaging and cancer therapy

Nucleic acids have enabled the fabrication of self-assemblies and dynamic operations. Among different functional nucleic acids, aptamers can specifically bind to a wide range of targets, including proteins, viral antigens, living cells and even tissues, and have thus emerged as molecular recognition tools in molecular medicine. Hence, aptamer-functionalized nucleic acid nanotechnology offers applications of biosensing, bioimaging, and cancer therapy. In this review, after a brief overview of nucleic acid nanotechnology, we focus on the integration of aptamers with nucleic acid nanotechnology, including self-assembly constructions and dynamic molecular manipulations. The emerging applications in molecular medicine are subsequently reviewed with aptamer-based self-assemblies and aptamer-involved dynamic molecular manipulation. For convenience, applications are broadly categorized into biosensing, bioimaging, and cancer therapy. Finally, challenges and potential development of nucleic acid nanotechnology are discussed.

Bead-based spontaneous Raman codes for multiplex immunoassay

In the immunoassay process, for fulfilling the need to identify multiple analytes in a small amount of complex sample matrix, it is desirable to develop highly efficient and specific multiplex suspension array technology. Raman coding strategy offers an attractive solution to code the suspension arrays by simply combing narrow spectral bands with stable signal intensities through solid-phase synthesis on the resin beads. Based on this strategy, we report the bead-based spontaneous Raman codes for multiplex immunoassay. The study resulted in superior selectivity of the Raman-encoded beads for binding with single and multiple analytes, respectively. With the use of mixed types of Raman-encoded immunoassay beads, multiple targets in small amounts of samples were identified rapidly and accurately. By confirming the feasibility of bead-based spontaneous Raman codes for multiplex immunoassay, we anticipate this novel technology to be widely applied in the near future.

Polymerase-Based Signal Delay for Temporally Regulating DNA Involved Reactions, Programming Dynamic Molecular Systems, and Biomimetic Sensing

Complex temporal molecular signals play a pivotal role in the intricate biological pathways of living organisms, and cells exhibit the ability to transmit and receive information by intricately managing the temporal dynamics of their signaling molecules. Although biomimetic molecular networks are successfully engineered outside of cells, the capacity to precisely manipulate temporal behaviors remains limited. In this study, the catalysis activity of isothermal DNA polymerase (DNAP) through combined use of molecular dynamics simulation analysis and fluorescence assays is first characterized. DNAP-driven delay in signal strand release ranged from 100 to 102 min, which is achieved through new strategies including the introduction of primer overhangs, utilization of inhibitory reagents, and alteration of DNA template lengths. The results provide a deeper insight into the underlying mechanisms of temporal control DNAP-mediated primer extension and DNA strand displacement reactions. Then, the regulated DNAP catalysis reactions are applied in temporal modulation of downstream DNA-involved reactions, the establishment of dynamic molecular signals, and the generation of barcodes for multiplexed detection of target genes. The utility of DNAP-based signal delay as a dynamic DNA nanotechnology extends beyond theoretical concepts and achieves practical applications in the fields of cell-free synthetic biology and bionic sensing.

Self-assembled methodologies for the construction of DNA nanostructures and biological applications

Over the past decades, deoxyribonucleic acid (DNA), as a versatile building block, has been widely employed to construct functionalized nanostructures. Among the diverse types of materials, DNA related nanostructures have gained growing attention due to their intrinsic programmability, favorable biocompatibility, and strong molecular recognition capability. The conventional construction strategy for building DNA structures is based on Watson-Crick base-pairing rules, which are mainly driven by the hydrogen bonding of bases. However, hydrogen bonding-based DNA nanostructures cannot meet the requirements of specific morphology and multifunctionality. Currently, various functional elements have been introduced to expand the synthetic methodologies for constructing the DNA hybrid nanostructures, including small molecules, peptide polymers, organic ligands and transition metal ions. Besides, the potential applications for these DNA hybrid nanostructures have also been explored. It has been demonstrated that DNA hybrid structures with various properties can be extensively applied in the fields of magnetic resonance, luminescence imaging, biomedical detection, and drug delivery systems. In this review, we highlight the pioneering contributions to the methodologies of DNA-based nanostructure assembly. Furthermore, the recent advances in drug delivery systems and biomedical diagnosis based on DNA hybrid nanostructures are briefly summarized.

A light-efficient and versatile multiplexing method for snapshot spectral imaging

The study of rapid and stochastic events that involve multiple species, such as chemical reactions and plasma dynamics, requires means to capture multispectral information in two dimensions at both high temporal- and spatial resolution. Commercially available cameras that provide high temporal resolution are based on either signal intensification or rapid data acquisition. Intensified cameras provide extremely short acquisition times using intensification by means of micro channel plates, but the conversion between electrons and photons makes these cameras inherently monochrome. In contrast, high-speed cameras can achieve color-sensitivity through integrated Bayer filters but suffer from a reduced light collection efficiency and a fixed spectral composition. In this article we present a non-integrated optical arrangement for instantaneous multispectral imaging based on FRAME image multiplexing. By spectrally separating the signal using lossless dichroic mirrors, a 16-fold increase in light-collection efficiency is gained (compared to past solutions), resulting in an equivalent increase in temporal resolution. This improvement provides new avenues for multispectral imaging of rapid events. We demonstrate the system's versatility and suitability for studies of such processes by applying it for (i) temperature mapping using a high-resolution CCD camera, (ii) high-speed videography up to 10 kHz at four spectral channels and (iii) dual-species visualization in a plasma discharge using an intensified sCMOS camera.

Label-Free Field Effect Transistors (FETs) for Fabrication of Point-of-Care (POC) Biomedical Detection Probes

Field effect transistors (FETs)-based detection probes are powerful platforms for quantification in biological media due to their sensitivity, ease of miniaturization, and ability to function in biological media. Especially, FET-based platforms have been utilized as promising probes for label-free detections with the potential for use in real-time monitoring. The integration of new materials in the FET-based probe enhances the analytical performance of the developed probes by increasing the active surface area, rejecting interfering agents, and providing the possibility for surface modification. Furthermore, the use of new materials eliminates the need for traditional labeling techniques, providing rapid and cost-effective detection of biological analytes. This review discusses the application of materials in the development of FET-based label-free systems for point-of-care (POC) analysis of different biomedical analytes from 2018 to 2024. The mechanism of action of the reported probes is discussed, as well as their pros and cons were also investigated. Also, the possible challenges and potential for the fabrication of commercial devices or methods for use in clinics were discussed.

Sensing, Imaging, and Therapeutic Strategies Endowing by Conjugate Polymers for Precision Medicine

Conjugated polymers (CPs) have promising applications in biomedical fields, such as disease monitoring, real-time imaging diagnosis, and disease treatment. As a promising luminescent material with tunable emission, high brightness and excellent stability, CPs are widely used as fluorescent probes in biological detection and imaging. Rational molecular design and structural optimization have broadened absorption/emission range of CPs, which are more conductive for disease diagnosis and precision therapy. This review provides a comprehensive overview of recent advances in the application of CPs, aiming to elucidate their structural and functional relationships. The fluorescence properties of CPs and the mechanism of detection signal amplification are first discussed, followed by an elucidation of their emerging applications in biological detection. Subsequently, CPs-based imaging systems and therapeutic strategies are illustrated systematically. Finally, recent advancements in utilizing CPs as electroactive materials for bioelectronic devices are also investigated. Moreover, the challenges and outlooks of CPs for precision medicine are discussed. Through this systematic review, it is hoped to highlight the frontier progress of CPs and promote new breakthroughs in fundamental research and clinical transformation.

SeParate: multiway fluorescence-activated droplet sorting based on integration of serial and parallel triaging concepts

Fluorescence-activated droplet sorting (FADS) has emerged as a versatile high-throughput sorting tool that is, unlike most fluorescence-activated cell sorting (FACS) platforms, capable of sorting droplet-compartmentalized cells, cell secretions, entire enzymatic reactions and more. Recently, multiplex FADS platforms have been developed for the sorting of multi-fluorophore populations towards different outlets in addition to the standard, more commonly used, 2-way FADS platform. These multiplex FADS platforms consist of either multiple 2-way junctions one after the other (i.e. serial sorters) or of one junction sorting droplets in more than 2 outlets (i.e. parallel sorters). In this work, we present SeParate, a novel platform based on integrating s̲e̲rial and p̲a̲r̲allel sorting principles for accura̲t̲e̲ multiplex droplet sorting that is able to mitigate limitations of current multiplex sorters. We show the SeParate platform and its capability in highly accurate 4-way sorting of a multi-fluorophore population into four subpopulations with the potential to expand to more. More specifically, the SeParate platform was thoroughly validated using mixed populations of fluorescent beads and picoinjected droplets, yielding sorting accuracies up to 100% and 99.9%, respectively. Finally, transfected HEK-293T cells were sorted employing two different optical setups, resulting in an accuracy up to 99.5%. SeParate's high accuracy for a diverse set of samples, including highly variable biological specimens, together with its scalability beyond the demonstrated 4-way sorting, warrants a broad applicability for multi-fluorophore studies in life sciences, environmental sciences and others.

Encoding fluorescence intensity with tetrahedron DNA nanostructure based FRET effect for bio-detection

Biocoding technology constructed by readable tags with distinct signatures is a brand-new bioanalysis method to realize multiplexed identification and bio-information decoding. In this study, a novel fluorescence intensity coding technology termed Tetra-FICT was reported based on tetrahedron DNA nanostructure (TDN) carrier and Főrster Resonance Energy Transfer (FRET) effect. By modulating numbers and distances of Cy3 and Cy5 at four vertexes of TDN, different fluorescence intensities of twenty-six samples were produced at ∼565.0 nm (FICy3) and ∼665.0 nm (FICy5) by detecting fluorescence spectra. By developing an error correction mechanism, eleven codes were established based on divided intensity ranges of the final FICy3 together with FICy5 (Final-FICy3&FICy5). These resulting codes were used to construct barcode probes, with three miRNA biomarkers (miRNA-210, miRNA-199a and miRNA-21) as cases for multiplexed bio-assay. The high specificity and sensitivity were also demonstrated for the detection of miRNA-210. Overall, the proposed Tetra-FICT enriched the toolbox of fluorescence coding, which could be applied to multiplexing biomarkers detection.

DNA and Nanomaterials: A Functional Combination for DNA Sensing

Recent decades have experienced tough situations due to the lack of reliable diagnostic facilities. The most recent cases occurred during the pandemic, where researchers observed the lack of diagnostic facilities with precision. Microorganisms and viral disease's ability to escape diagnosis has been a global challenge. DNA always has been a unique moiety with a strong and precise base-paired structure. DNA in human and foreign particles makes identification possible through base pairing. Since then, researchers have focused heavily on designing diagnostic assays targeting DNA in particular. Moreover, DNA nanotechnology has contributed vastly to designing composite nanomaterials by combining DNA/nucleic acids with functional nanomaterials and inorganic nanoparticles exploiting their physicochemical properties. These nanomaterials often exhibit unique or enhanced properties due to the synergistic activity of the many components. The capabilities of DNA and additional nanomaterials have shown the combination of robust and advanced tailoring of biosensors. Preceding findings state that the conventional strategies have exhibited certain limitations such as a low range of target detection, less biodegradability, subordinate half-life, and high susceptibility to microenvironments; however, a DNA-nanomaterial-based biosensor has overcome these limitations meaningfully. Additionally, the unique properties of nucleic acids have been studied extensively due to their high signal conduction abilities. Here, we review recent studies on DNA-nanomaterial-based biosensors, their mechanism of action, and improved/updated strategies in vivo and in situ. Furthermore, this review highlights the recent methodologies on DNA utilization to exploit the interfacial properties of nanomaterials in DNA sensing. Lastly, the review concludes with the limitations/challenges and future directions.

Rational design of genotyping nanodevice for HPV subtype distinction

There are more than 200 subtypes of human papillomavirus (HPV), and high-risk HPVs are a leading cause of cervical cancer. Identifying the genotypes of HPV is significant for clinical diagnosis and cancer control. Herein, we used programmable and modified DNA as the backbone to construct fluorescent genotyping nanodevice for HPV subtype distinction. In our strategy, the dye-labeled single-stranded recognize-DNA (R-DNA) was hybridized with Black Hole Quencher (BHQ) labeled single-stranded link-DNA (L-DNA) to form three functionalized DNA (RL-DNA). Through the extension of polycytosine (poly-C) in L-DNA, three RL-DNAs can be more firmly adsorbed on graphene oxide to construct reliable genotyping nanodevice. The genotyping nanodevice had low background noise since the dual energy transfer, including Förster resonance energy transfer (FRET) from dye to BHQ and the resonance energy transfer (RET) from dye to graphene oxide. Meanwhile, the programmability of DNA allows the proposed strategy to simultaneously and selectively distinguish several HPV subtypes in solution using DNA labeled with different dyes. To demonstrate clinical potential, we show multiplexed assay of HPV subtypes in cervical scrapes, and it has been successfully applied in HPV-DNA analysis in cervical scrapes samples. The genotyping nanodevice could be developed for simultaneous and multiplex analysis of several oligonucleotides in a homogeneous solution by adjusting the recognition sequence, demonstrating its potential application in the rapid screening of multiple biomarkers.

Micro- and nanosystems for the detection of hemorrhagic fever viruses

Hemorrhagic fever viruses (HFVs) are virulent pathogens that can cause severe and often fatal illnesses in humans. Timely and accurate detection of HFVs is critical for effective disease management and prevention. In recent years, micro- and nano-technologies have emerged as promising approaches for the detection of HFVs. This paper provides an overview of the current state-of-the-art systems for micro- and nano-scale approaches to detect HFVs. It covers various aspects of these technologies, including the principles behind their sensing assays, as well as the different types of diagnostic strategies that have been developed. This paper also explores future possibilities of employing micro- and nano-systems for the development of HFV diagnostic tools that meet the practical demands of clinical settings.

Absolute Quantification of Serum Exosomes in Patients with an SERS-Lateral Flow Strip Biosensor for Noninvasive Clinical Cancer Diagnosis

Exosomes (exos) widely existing in body fluids show great potential for noninvasive cancer diagnosis. Quantitative analysis of exos is traditionally performed by targeting specific exosomal surface proteins, but it is often imprecise due to the common expression of exosomal proteins and subtle expression differences between different cancer subtypes. Herein, we report quantitative surface-enhanced Raman spectroscopy (SERS) of serum exos through a combination of a paper-based lateral flow strip (LFS) biosensor with multivariate spectral unmixing analysis rather than simply quantifying exosomal proteins. Our SERS-LFS biosensor enables absolute quantification of two different serum exos with a limit of detection down to ∼106 particles/mL for both exos. We further exemplify the application of this strategy in quantitative dual-plex detection of serum exos from breast cancer patients. We find that human epidermal growth factor receptor 2+ (HER2+) and luminal A breast cancer patients undergoing no surgery are enriched in serum exos derived from SKBR-3 cells and MCF-7 cells (denoted as SKBR and MCF exos), respectively. The surgical treatment of these breast cancer patients accompanies an obvious decrease of either SKBR or MCF exos in the serum. These results suggest the great potential of the combination of the SERS-LFS biosensor and multivariate spectral unmixing for breast cancer subtyping and therapeutic surveillance with the powerful quantitative capability of exos in clinical samples.

Staphylococcus aureus Detection in Milk Using a Thickness Shear Mode Acoustic Aptasensor with an Antifouling Probe Linker

Contamination of food by pathogens can pose a serious risk to health. Therefore, monitoring for the presence of pathogens is critical to identify and regulate microbiological contamination of food. In this work, an aptasensor based on a thickness shear mode acoustic method (TSM) with dissipation monitoring was developed to detect and quantify Staphylococcus aureus directly in whole UHT cow's milk. The frequency variation and dissipation data demonstrated the correct immobilization of the components. The analysis of viscoelastic properties suggests that DNA aptamers bind to the surface in a non-dense manner, which favors the binding with bacteria. The aptasensor demonstrated high sensitivity and was able to detect S. aureus in milk with a 33 CFU/mL limit of detection. Analysis was successful in milk due to the sensor's antifouling properties, which is based on 3-dithiothreitol propanoic acid (DTT_COOH) antifouling thiol linker. Compared to bare and modified (dithiothreitol (DTT), 11-mercaptoundecanoic acid (MUA), and 1-undecanethiol (UDT)) quartz crystals, the sensitivity of the sensor's antifouling in milk improved by about 82-96%. The excellent sensitivity and ability to detect and quantify S. aureus in whole UHT cow's milk demonstrates that the system is applicable for rapid and efficient analysis of milk safety.

Orthometric multicolor encoded hybridization chain reaction amplifiers for multiplexed microRNA profiling in living cells

Multiplexed microRNA (miRNA) profiling of more than four types in living cells is challenging due to fluorescent spectral overlap, representing a significant limitation in studying the complex interactions related to the occurrence and development of diseases. Herein, we report a multiplexed fluorescent imaging strategy based on an orthometric multicolor encoded hybridization chain reaction amplifier named multi-HCR. The targeting miRNA can trigger this multi-HCR strategy due to the specific sequence recognition, and then its self-assembly to amplify the programmability signals. We take the four-colored chain amplifiers, showing that the multi-HCR can form 15 combinations simultaneously. In a living process of hypoxia-induced apoptosis and autophagy under complicated mitochondria and endoplasmic reticulum stress, the multi-HCR demonstrates excellent performance in detecting eight different miRNA changes. The multi-HCR provides a robust strategy for simultaneously profiling multiplexed miRNA biomarkers in studying complicated cellular processes.

Microcavity- and Microlaser-Based Optical Barcoding: A Review of Encoding Techniques and Applications

Optical microbarcodes have recently received a great deal of interest because of their suitability for a wide range of applications, such as multiplexed assays, cell tagging and tracking, anticounterfeiting, and product labeling. Spectral barcodes are especially promising because they are robust and have a simple readout. In addition, microcavity- and microlaser-based barcodes have very narrow spectra and therefore have the potential to generate millions of unique barcodes. This review begins with a discussion of the different types of barcodes and then focuses specifically on microcavity-based barcodes. While almost any kind of optical microcavity can be used for barcoding, currently whispering-gallery microcavities (in the form of spheres and disks), nanowire lasers, Fabry-Pérot lasers, random lasers, and distributed feedback lasers are the most frequently employed for this purpose. In microcavity-based barcodes, the information is encoded in various ways in the properties of the emitted light, most frequently in the spectrum. The barcode is dependent on the properties of the microcavity, such as the size, shape, and the gain materials. Various applications of these barcodes, including cell tracking, anticounterfeiting, and product labeling are described. Finally, the future prospects for microcavity- and microlaser-based barcodes are discussed.

DNA Nanoclusters Combined with One-Shot Radiotherapy Augment Cancer Immunotherapy Efficiency

Immunotherapy shows immense promise for improving cancer treatment. Combining immunotherapy with radiotherapy provides a conspicuous advantage due to its enhanced abscopal effect. However, established immune tolerance mechanisms in the tumor microenvironment can hamper the generation of a sufficient abscopal effect. Herein, a type of DNA nanocluster (DNAnc) that is self-assembled by a CpG-ODNs-loaded Y-shaped double-stranded DNA vector based on the unique complementary base-pairing rules is designed. The unique structure of DNAnc makes it load more than ≈8125.5 ± 822.5 copies of CpG ODNs within one single nanostructure, which effectively increases resistance to nuclease degradation and elevates the efficiency of repolarizing macrophages to an M1-like phenotype. Mechanistic studies reveal that more DNAncs are endocytosed by macrophages in the cancer tissue and repolarized macrophages to elicit a robust abscopal effect with the accumulation of macrophages induced by radiotherapy, generating potent, long-term, and durable antitumor immunity for the inhibition of tumor metastasis and the prevention of tumor recurrence, which provides a novel strategy to boost cancer immunotherapy.

Nanoparticle applications in food - a review

The use of nanotechnology in the food industry raises uncertainty in many respects. For years, achievements of nanotechnology have been applied mainly in biomedicine and computer science, but recently it has also been used in the food industry. Due to the extremely small (nano) scale, the properties and behavior of nanomaterials may differ from their macroscopic counterparts. They can be used as biosensors to detect reagents or microorganisms, monitor bacterial growth conditions, increase food durability e.g. when placed in food packaging, reducing the amount of certain ingredients without changing the consistency of the product (research on fat substitutes is underway), improve the taste of food, make some nutrients get better absorbed by the body, etc. There are companies on the market that are already introducing nanoparticles into the economy to improve their functionality, e.g. baby feeding bottles. This review focuses on the use of nanoparticles in the food industry, both organic (chitosan, cellulose, proteins) and inorganic (silver, iron, zinc oxide, titanium oxide, etc.). The use of nanomaterials in food production requires compliance with all legal requirements regarding the safety and quantity of nano-processed food products described in this review. In the future, new methods of testing nanoparticles should be developed that would ensure the effectiveness of compounds subjected to, for example, nano-encapsulation, i.e. whether the encapsulation process had a positive impact on the specific properties of these compounds. Nanotechnology has revolutionized our approach towards food engineering (from production to processing), food storage and the creation of new materials and products, and the search for new product applications.

DNA Droplets: Intelligent, Dynamic Fluid

Breathtaking advances in DNA nanotechnology have established DNA as a promising biomaterial for the fabrication of programmable higher-order nano/microstructures. In the context of developing artificial cells and tissues, DNA droplets have emerged as a powerful platform for creating intelligent, dynamic cell-like machinery. DNA droplets are a microscale membrane-free coacervate of DNA formed through phase separation. This new type of DNA system couples dynamic fluid-like property with long-established DNA programmability. This hybrid nature offers an advantageous route to facile and robust control over the structures, functions, and behaviors of DNA droplets. This review begins by describing programmable DNA condensation, commenting on the physical properties and fabrication strategies of DNA hydrogels and droplets. By presenting an overview of the development pathways leading to DNA droplets, it is shown that DNA technology has evolved from static, rigid systems to soft, dynamic systems. Next, the basic characteristics of DNA droplets are described as intelligent, dynamic fluid by showcasing the latest examples highlighting their distinctive features related to sequence-specific interactions and programmable mechanical properties. Finally, this review discusses the potential and challenges of numerical modeling able to connect a robust link between individual sequences and macroscopic mechanical properties of DNA droplets.

Hierarchical DNA branch assembly-encoded fluorescent nanoladders for single-cell transcripts imaging

Spatial visualization of single-cell transcripts is limited by signal specificity and multiplexing. Here, we report hierarchical DNA branch assembly-encoded fluorescent nanoladders, which achieve denoised and highly multiplexed signal amplification for single-molecule transcript imaging. This method first offers independent RNA-primed rolling circle amplification without nonspecific amplification based on circular DNAzyme. It then executes programmable DNA branch assembly on these amplicons to encode virtual signals for visualizing numbers of targets by FISH. In theory, more virtual signals can be encoded via the increase of detection spectral channels and repeats of the same sequences on barcode. Our method almost eliminates nonspecific amplification in fixed cells (reducing nonspecific spots of single cells from 16 to nearly zero), and achieves simultaneous quantitation of nine transcripts by using only two detection spectral channels. We demonstrate accurate RNA profiling in different cancer cells, and reveal diverse localization patterns for spatial regulation of transcripts.

Detection of Trace Amounts of Water in Organic Solvents by DNA-Based Nanomechanical Sensors

The detection of trace amounts of water in organic solvents is of great importance in the field of chemistry and in the industry. Karl Fischer titration is known as a classic method and is widely used for detecting trace amounts of water; however, it has some limitations in terms of rapid and direct detection because of its time-consuming sample preparation and specific equipment requirements. Here, we found that a DNA-based nanomechanical sensor exhibits high sensitivity and selectivity to water vapor, leading to the detection and quantification of trace amounts of water in organic solvents as low as 12 ppm in THF, with a ppb level of LoD through their vapors. Since the present method is simple and rapid, it can be an alternative technique to the conventional Karl Fischer titration.

Application of nanotechnology in food: processing, preservation, packaging and safety assessment

Even though nanotechnology is extensively applied in agriculture, biochemistry, medicine and many other sectors, it is a developing field that conforms to new and more complex applications in food systems as compared to other technologies. It offers a viable strategy for integrating cutting-edge technology into a wide range of operations related to the production, development, fabrication, packaging, storage and distribution of food. The most fundamentally sophisticated technology in nano-based food science, nanoparticles deal with a wide range of nanostructured materials and nano methods, including nanofood, nanotubes, nanocomposites, nano packaging, nanocapsules, nanosensors, liposomes, nanoemulsions, polymeric nanoparticles and nanoencapsulation. This method is developed to increase food solubility and shelf life, availability of bioactive chemical, the protection of food constituents, nutritional supplementation, fortification and food or constituent delivery. Additionally, it serves as an antibacterial agent by generating reactive oxygen species (ROS) which cause bacterial DNA damage, protein denaturation and cell damage. Although the use of nanotechnology in food applications is advancing, there are certain negative or dangerous effects on health related to the toxicity and dangers of ingesting nanoparticles in food. The use of nanotechnology in the food industry, notably in processing, preservation and packaging, with its promising future, was addressed in this study. The toxicity of nanoparticles in food as well as its development in food safety assessments with certain areas of concern were also reviewed.

A highly sensitive bio-barcode immunoassay for multi-residue detection of organophosphate pesticides based on fluorescence anti-quenching

Balancing the risks and benefits of organophosphate pesticides (OPs) on human and environmental health relies partly on their accurate measurement. A highly sensitive fluorescence anti-quenching multi-residue bio-barcode immunoassay was developed to detect OPs (triazophos, parathion, and chlorpyrifos) in apples, turnips, cabbages, and rice. Gold nanoparticles were functionalized with monoclonal antibodies against the tested OPs. DNA oligonucleotides were complementarily hybridized with an RNA fluorescent label for signal amplification. The detection signals were generated by DNA-RNA hybridization and ribonuclease H dissociation of the fluorophore. The resulting fluorescence signal enables multiplexed quantification of triazophos, parathion, and chlorpyrifos residues over the concentration range of 0.01-25, 0.01-50, and 0.1-50 ng/mL with limits of detection of 0.014, 0.011, and 0.126 ng/mL, respectively. The mean recovery ranged between 80.3% and 110.8% with relative standard deviations of 7.3%-17.6%, which correlate well with results obtained by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The proposed bio-barcode immunoassay is stable, reproducible and reliable, and is able to detect low residual levels of multi-residue OPs in agricultural products.

The Pivotal Role of Quantum Dots-Based Biomarkers Integrated with Ultra-Sensitive Probes for Multiplex Detection of Human Viral Infections

The spread of viral diseases has caused global concern in recent years. Detecting viral infections has become challenging in medical research due to their high infectivity and mutation. A rapid and accurate detection method in biomedical and healthcare segments is essential for the effective treatment of pathogenic viruses and early detection of these viruses. Biosensors are used worldwide to detect viral infections associated with the molecular detection of biomarkers. Thus, detecting viruses based on quantum dots biomarkers is inexpensive and has great potential. To detect the ultrasensitive biomarkers of viral infections, QDs appear to be a promising option as biological probes, while physiological components have been used directly to detect multiple biomarkers simultaneously. The simultaneous measurement of numerous clinical parameters of the same sample volume is possible through multiplex detection of human viral infections, which reduces the time and cost required to record any data point. The purpose of this paper is to review recent studies on the effectiveness of the quantum dot as a detection tool for human pandemic viruses. In this review study, different types of quantum dots and their valuable properties in the structure of biomarkers were investigated. Finally, a vision for recent advances in quantum dot-based biomarkers was presented, whereby they can be integrated into super-sensitive probes for the multiplex detection of human viral infections.

Nanotechnology Approaches for Rapid Detection and Theranostics of Antimicrobial Resistant Bacterial Infections

As declared by WHO, antimicrobial resistance (AMR) is a high priority issue with a pressing need to develop impactful technologies to curb it. The rampant and inappropriate use of antibiotics due to the lack of adequate and timely diagnosis is a leading cause behind AMR evolution. Unfortunately, populations with poor economic status and those residing in densely populated areas are the most affected ones, frequently leading to emergence of AMR pathogens. Classical approaches for AMR diagnostics like phenotypic methods, biochemical assays, and molecular techniques are cumbersome and resource-intensive and involve a long turnaround time to yield confirmatory results. In contrast, recent emergence of nanotechnology-assisted approaches helps to overcome challenges in classical approaches and offer simpler, more sensitive, faster, and more affordable solutions for AMR diagnostics. Nanomaterial platforms (metallic, quantum-dot, carbon-based, upconversion, etc.), nanoparticle-based rapid point-of-care platforms, nano-biosensors (optical, mechanical, electrochemical), microfluidic-assisted devices, and importantly, nanotheranostic devices for diagnostics with treatment of AMR infections are examples of rapidly growing nanotechnology approaches used for AMR management. This review comprehensively summarizes the past 10 years of research progress on nanotechnology approaches for AMR diagnostics and for estimating antimicrobial susceptibility against commonly used antibiotics. This review also highlights several bottlenecks in nanotechnology approaches that need to be addressed prior to considering their translation to clinics.

Aptamers for Viral Detection and Inhibition

Recent times have experienced more than ever the impact of viral infections in humans. Viral infections are known to cause diseases not only in humans but also in plants and animals. Here, we have compiled the literature review of aptamers selected and used for detection and inhibition of viral infections in all three categories: humans, animals, and plants. This review gives an in-depth introduction to aptamers, different types of aptamer selection (SELEX) methodologies, the benefits of using aptamers over commonly used antibody-based strategies, and the structural and functional mechanism of aptasensors for viral detection and therapy. The review is organized based on the different characterization and read-out tools used to detect virus-aptasensor interactions with a detailed index of existing virus-targeting aptamers. Along with addressing recent developments, we also discuss a way forward with aptamers for DNA nanotechnology-based detection and treatment of viral diseases. Overall, this review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics and treatment.

Single-particle combinatorial multiplexed liposome fusion mediated by DNA

Combinatorial high-throughput methodologies are central for both screening and discovery in synthetic biochemistry and biomedical sciences. They are, however, often reliant on large-scale analyses and thus limited by a long running time and excessive materials cost. We here present a single-particle combinatorial multiplexed liposome fusion mediated by DNA for parallelized multistep and non-deterministic fusion of individual subattolitre nanocontainers. We observed directly the efficient (>93%) and leakage free stochastic fusion sequences for arrays of surface-tethered target liposomes with six freely diffusing populations of cargo liposomes, each functionalized with individual lipidated single-stranded DNA and fluorescently barcoded by a distinct ratio of chromophores. The stochastic fusion resulted in a distinct permutation of fusion sequences for each autonomous nanocontainer. Real-time total internal reflection imaging allowed the direct observation of >16,000 fusions and 566 distinct fusion sequences accurately classified using machine learning. The high-density arrays of surface-tethered target nanocontainers (~42,000 containers per mm²) offers entire combinatorial multiplex screens using only picograms of material.

Recent Advances in Surface Plasmon Resonance Sensors for Sensitive Optical Detection of Pathogens

The advancement of science and technology has led to the recent development of highly sensitive pathogen biosensing techniques. The effective treatment of pathogen infections requires sensing technologies to not only be sensitive but also render results in real-time. This review thus summarises the recent advances in optical surface plasmon resonance (SPR) sensor technology, which possesses the aforementioned advantages. Specifically, this technology allows for the detection of specific pathogens by applying nano-sized materials. This review focuses on various nanomaterials that are used to ensure the performance and high selectivity of SPR sensors. This review will undoubtedly accelerate the development of optical biosensing technology, thus allowing for real-time diagnosis and the timely delivery of appropriate treatments as well as preventing the spread of highly contagious pathogens.

Smart Nucleic Acid Hydrogels with High Stimuli-Responsiveness in Biomedical Fields

Due to their hydrophilic, biocompatible and adjustability properties, hydrogels have received a lot of attention. The introduction of nucleic acids has made hydrogels highly stimuli-responsiveness and they have become a new generation of intelligent biomaterials. In this review, the development and utilization of smart nucleic acid hydrogels (NAHs) with a high stimulation responsiveness were elaborated systematically. We discussed NAHs with a high stimuli-responsiveness, including pure NAHs and hybrid NAHs. In particular, four stimulation factors of NAHs were described in details, including pH, ions, small molecular substances, and temperature. The research progress of nucleic acid hydrogels in biomedical applications in recent years is comprehensively discussed. Finally, the opportunities and challenges facing the future development of nucleic acid hydrogels are also discussed.

Multiplexed structured illumination super-resolution imaging with lifetime-engineered upconversion nanoparticles

The emerging optical multiplexing within nanoscale shows super-capacity in encoding information by using lifetime fingerprints from luminescent nanoparticles. However, the optical diffraction limit compromises the decoding accuracy and throughput of the nanoparticles during conventional widefield imaging. This, in turn, challenges the quality of nanoparticles to afford the modulated excitation condition and further retain the multiplexed optical fingerprints for super-resolution multiplexing. Here we report a tailor-made multiplexed super-resolution imaging method using the lifetime-engineered upconversion nanoparticles. We demonstrate that the nanoparticles are bright, uniform, and stable under structured illumination, which supports a lateral resolution of 185 nm, less than 1/4th of the excitation wavelength. We further develop a deep learning algorithm to coordinate with super-resolution images for more accurate decoding compared to a numeric algorithm. We demonstrate a three-channel super-resolution imaging based optical multiplexing with decoding accuracies above 93% for each channel and larger than 60% accuracy for potential seven-channel multiplexing. The improved resolution provides high throughput by resolving the particles within the diffraction-limited spots, which enables higher multiplexing capacity in space. This lifetime multiplexing super-resolution method opens a new horizon for handling the growing amount of information content, disease source, and security risk in modern society.

A multiplexed circulating tumor DNA detection platform engineered from 3D-coded interlocked DNA rings

Circulating tumor DNA (ctDNA) is a critical biomarker not only important for the early detection of tumors but also invaluable for personalized treatments. Currently ctDNA detection relies on sequencing. Here, a platform termed three-dimensional-coded interlocked DNA rings (3D-coded ID rings) was created for multiplexed ctDNA identification. The ID rings provide a ctDNA recognition ring that is physically interlocked with a reporter ring. The specific binding of ctDNA to the recognition ring initiates target-responsive cutting via a restriction endonuclease; the cutting then triggers rolling circle amplification on the reporter ring. The signals are further integrated with internal 3D codes for multiplexed readouts. ctDNAs from non-invasive clinical specimens including plasma, feces, and urine were detected and validated at a sensitivity much higher than those obtained through sequencing. This 3D-coded ID ring platform can detect any multiple DNA fragments simultaneously without sequencing. We envision that our platform will facilitate the implementation of future personalized/precision medicine.

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A platform termed 3D-coded ID rings was created for multiplexed ctDNA detection.

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This platform was integrated with two schemes: the ID ring scheme and the 3D-coded scheme.

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The platform could achieve multiplexed detection with detection limit of 500 copies per million in non-invasive specimens.

Concepts and Application of DNA Origami and DNA Self-Assembly: A Systematic Review

With the arrival of the post-Moore Era, the development of traditional silicon-based computers has reached the limit, and it is urgent to develop new computing technology to meet the needs of science and life. DNA computing has become an essential branch and research hotspot of new computer technology because of its powerful parallel computing capability and excellent data storage capability. Due to good biocompatibility and programmability properties, DNA molecules have been widely used to construct novel self-assembled structures. In this review, DNA origami is briefly introduced firstly. Then, the applications of DNA self-assembly in material physics, biogenetics, medicine, and other fields are described in detail, which will aid the development of DNA computational model in the future.

Droplet microfluidic generation of a million optical microparticle barcodes

Micron-scale barcode particles enable labelling of small objects. Here, we demonstrate high-throughput barcode fabrication inside a microfluidic chip that can embed multiple, dye-doped high quality-factor whispering gallery mode cavities inside aqueous droplets at kilohertz rates. These droplets are then cured to form polyacrylamide hydrogel beads as small as 30 μm in diameter. Optical resonance spectra of the embedded cavities provide the hydrogels with unique barcodes with their diversity combinatorically scaled with the number of embedded cavities. Using 3 cavities per hydrogel, we obtain approximately one million uniquely identifiable, optically readable barcode microparticles.

Monochromatic Fluorescent Barcodes Hierarchically Assembled from Modular DNA Origami Nanorods

With the rapid advancement of fluorescence microscopy, there is a growing interest in the multiplexed detection and identification of various bioanalytes (e.g., nucleic acids and proteins) for efficient sample processing and analysis. We introduce in this work a simple and robust method to provide combinations for micrometer-scale fluorescent DNA barcodes of hierarchically assembled DNA origami superstructures for multiplexed molecular probing. In addition to optically resolvable dots, we placed fluorescent loci on adjacent origami within the diffraction limit of each other, rendering them as unresolvable bars of measurable lengths. We created a basic set of barcodes and trained a machine learning algorithm to process and identify individual barcodes from raw images with high accuracy. Moreover, we demonstrated that the number of combinations can be increased exponentially by generating longer barcodes, by controlling the number of incorporated fluorophores to create multiple levels of fluorescence intensity, and by employing super-resolution imaging. To showcase the readiness of the barcodes for applications, we used our barcodes to capture and identify target nucleic acid sequences and for simultaneous multiplexed characterization of binding kinetics of several orthogonal complementary nucleic acids.

Optical Fingerprint Classification of Single Upconversion Nanoparticles by Deep Learning

Highly controlled synthesis of upconversion nanoparticles (UCNPs) can be achieved in the heterogeneous design, so that a library of optical properties can be arbitrarily produced by depositing multiple lanthanide ions. Such a control offers the potential in creating nanoscale barcodes carrying high-capacity information. With the increasing creation of optical information, it poses more challenges in decoding them in an accurate, high-throughput, and speedy fashion. Here, we reported that the deep-learning approach can recognize the complexity of the optical fingerprints from different UCNPs. Under a wide-field microscope, the lifetime profiles of hundreds of single nanoparticles can be collected at once, which offers a sufficient amount of data to develop deep-learning algorithms. We demonstrated that high accuracies of over 90% can be achieved in classifying 14 kinds of UCNPs. This work suggests new opportunities in handling the diverse properties of nanoscale optical barcodes toward the establishment of vast luminescent information carriers.

Direct SARS-CoV-2 Nucleic Acid Detection by Y-Shaped DNA Dual-Probe Transistor Assay

Rapid screening of infected individuals from a large population is an effective means in epidemiology, especially to contain outbreaks such as COVID-19. The gold standard assays for COVID-19 diagnostics are mainly based on the reverse transcription polymerase chain reaction, which mismatches the requirements for wide-population screening due to time-consuming nucleic acid extraction and amplification procedures. Here, we report a direct nucleic acid assay by using a graphene field-effect transistor (g-FET) with Y-shaped DNA dual probes (Y-dual probes). The assay relies on Y-dual probes modified on g-FET simultaneously targeting ORF1ab and N genes of SARS-CoV-2 nucleic acid, enabling high a recognition ratio and a limit of detection (0.03 copy μL-1) 1-2 orders of magnitude lower than existing nucleic acid assays. The assay realizes the fastest nucleic acid testing (∼1 min) and achieves direct 5-in-1 pooled testing for the first time. Owing to its rapid, ultrasensitive, easily operated features as well as capability in pooled testing, it holds great promise as a comprehensive tool for population-wide screening of COVID-19 and other epidemics.

Nanoparticle Superlattices through Template-Encoded DNA Dendrimers

The chemical interactions that lead to the emergence of hierarchical structures are often highly complex and difficult to program. Herein, the synthesis of a series of superlattices based upon 30 different structurally reconfigurable DNA dendrimers is reported, each of which presents a well-defined number of single-stranded oligonucleotides (i.e., sticky ends) on its surface. Such building blocks assemble with complementary DNA-functionalized gold nanoparticles (AuNPs) to yield five distinct crystal structures, depending upon choice of dendrimer and defined by phase symmetry. These DNA dendrimers can associate to form micelle-dendrimers, whereby the extent of association can be modulated based upon surfactant concentration and dendrimer length to produce a low-symmetry Ti5Ga4-type phase that has yet to be reported in the field of colloidal crystal engineering. Taken together, colloidal crystals that feature three different types of particle bonding interactions-template-dendron, dendrimer-dendrimer, and DNA-modified AuNP-dendrimer-are reported, illustrating how sequence-defined recognition and dynamic association can be combined to yield complex hierarchical materials.

Snapshot multicolor fluorescence imaging using double multiplexing of excitation and emission on a single detector

Fluorescence-based multispectral imaging of rapidly moving or dynamic samples requires both fast two-dimensional data acquisition as well as sufficient spectral sensitivity for species separation. As the number of fluorophores in the experiment increases, meeting both these requirements becomes technically challenging. Although several solutions for fast imaging of multiple fluorophores exist, they all have one main restriction; they rely solely on spectrally resolving either the excitation- or the emission characteristics of the fluorophores. This inability directly limits how many fluorophores existing methods can simultaneously distinguish. Here we present a snapshot multispectral imaging approach that not only senses the excitation and emission characteristics of the probed fluorophores but also all cross term combinations of excitation and emission. To the best of the authors’ knowledge, this is the only snapshot multispectral imaging method that has this ability, allowing us to even sense and differentiate between light of equal wavelengths emitted from the same fluorescing species but where the signal components stem from different excitation sources. The current implementation of the technique allows us to simultaneously gather 24 different spectral images on a single detector, from which we demonstrate the ability to visualize and distinguish up to nine fluorophores within the visible wavelength range.

Preselectable Optical Fingerprints of Heterogeneous Upconversion Nanoparticles

The control in optical uniformity of single nanoparticles and tuning their diversity in multiple dimensions, dot to dot, holds the key to unlocking nanoscale applications. Here we report that the entire lifetime profile of the single upconversion nanoparticle (τ² profile) can be resolved by confocal, wide-field, and super-resolution microscopy techniques. The advances in both spatial and temporal resolutions push the limit of optical multiplexing from microscale to nanoscale. We further demonstrate that the time-domain optical fingerprints can be created by utilizing nanophotonic upconversion schemes, including interfacial energy migration, concentration dependency, energy transfer, and isolation of surface quenchers. We exemplify that three multiple dimensions, including the excitation wavelength, emission color, and τ² profile, can be built into the nanoscale derivative τ²-dots. Creating a vast library of individually preselectable nanotags opens up a new horizon for diverse applications, spanning from sub-diffraction-limit data storage to high-throughput single-molecule digital assays and super-resolution imaging.

DNA Studies: Latest Spectroscopic and Structural Approaches

This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.

Greatly Enhanced Single Particle Fluorescence Detection Using High Refractive Index Liquid-Core Waveguides

High sensitivity and easy integration with microfabrication techniques has made silicon photonics one of the leading technologies used to build biosensors for diagnostic applications. Here we introduce a new silicon dioxide based optofluidic platform having a planar solid-core (SC) waveguide orthogonally intersecting a liquid-core (LC) waveguide with high refractive index ZnI2 salt solution as core. This enables both more uniform collection of particle fluorescence by the core mode and its propagation to an off-chip detector. This approach results in ultra-high sensitivity performance, demonstrated by achieving 8X enhancement in signal-to-noise ratio, a 45x increase in detection efficiency, and a 100x lower detection limit of 80 aM of fluorescent nanobeads. This represents a key step towards an ultrasensitive biosensor system for analyzing pathogens at clinical concentrations.