Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes

A Fluorescent Tile DNA Diagnocode System for In Situ Rapid and Selective Diagnosis of Cytosolic RNA Cancer Markers

Accurate cancer diagnosis often requires extraction and purification of genetic materials from cells, and sophisticated instrumentations that follow. Otherwise in order to directly treat the diagnostic materials to cells, multiple steps to optimize dose concentration and treatment time are necessary due to diversity in cellular behaviors. These processes may offer high precision but hinder fast analysis of cancer, especially in clinical situations that need rapid detection and characterization of cancer. Here we present a novel fluorescent tile DNA nanostructure delivered to cancer cytosol by employing nanoparticle technology. Its structural anisotropicity offers easy manipulation for multifunctionalities, enabling the novel DNA nanostructure to detect intracellular cancer RNA markers with high specificity within 30 minutes post treatment, while the nanoparticle property bypasses the requirement of treatment optimization, effectively reducing the complexity of applying the system for cancer diagnosis. Altogether, the system offers a precise and rapid detection of cancer, suggesting the future use in the clinical fields.

Facets of Nanotechnology as Seen in Food Processing, Packaging, and Preservation Industry

Nanotechnology has proven its competence in almost all possible fields we are aware of. However, today nanotechnology has evolved in true sense by contributing to a very large extent to the food industry. With the growing number of mouths to feed, production of food is not adequate. It has to be preserved in order to reach to the masses on a global scale. Nanotechnology made the idea a reality by increasing the shelf life of different kinds of food materials. It is not an entirely full-proof measure; however it has brought down the extent of wastage of food due to microbial infestation. Not only fresh food but also healthier food is being designed with the help of nano-delivery systems which act as a carrier for the food supplements. There are regulations to follow however as several of them pose serious threats to the wellbeing of the population. In coming days, newer modes of safeguarding food are going to be developed with the help of nanotechnology. In this paper, an overview has been given of the different methods of food processing, packaging, and preservation techniques and the role nanotechnology plays in the food processing, packaging, and preservation industry.

Tuning the Upconversion Luminescence Lifetimes of KYb2 F7 :Ho(3+) Nanocrystals for Optical Multiplexing

Conventional luminescent color coding is limited by spectral overlap and the interference of background fluorescence, thus restricting the number of distinguishable identities that can be used in practice. Here, we demonstrate the possibility of generating diverse time-domain codes, specially designed for a single emission band, using lanthanide-doped upconversion nanocrystals. Based on the knowledge of concentration quenching, the upconversion luminescence kinetics of KYb2 F7 : Ho(3+) nanocrystals can be precisely controlled by modifying the dopant concentration of Ho(3+) ions, resulting in a tunable emission lifetime from 75.8 to 1944.5 μs, which suggests the practicality of these time-domain codes for optical multiplexing.

Self-assembly formed by a short DNA probe pair: Application for highly sensitive mRNA species detection without reverse transcription

We describe a novel technology for detecting nucleic acids: Probe Alteration Link Self-Assembly Reactions (PALSAR). PALSAR comprises DNA self-assembly of pairs of short DNA probes formed by alternate hybridization of three complementary regions in a pair of honeycomb probes (HCPs). Self-assembly occurs at designated salt concentrations and reaction temperatures and requires no enzymes. We prepared pairs of HCPs to detect mRNAs encoded by the GAPDH gene β-actin (BA) gene, CD3D gene, CD4 gene, major vault protein (MV) gene and the signalling lymphocytic activation molecule-associated protein (SAP) gene, and succeeded in quantitatively detecting these mRNAs. PALSAR could detect mRNA directly without synthesizing cDNA. Moreover, multiple mRNAs could be detected simultaneously in a single reaction tube and there was a good correlation between the results obtained PALSAR and those by real-time PCR.

Temperature-Invariant Aqueous Microgels as Hosts for Biomacromolecules

Immobilization of enzymes on solid supports has been widely used to improve enzyme recycling, enzyme stability, and performance. We are interested in using aqueous microgels (colloidal hydrogels) as carriers for enzymes used in high-temperature reactions. These microgels should maintain their volume and colloidal stability in aqueous media up to 100 °C to serve as thermo-stable supports for enzymes. For this purpose, we prepared poly(N-hydroxyethyl acrylamide) (PHEAA) microgels via a two-step synthesis. First, we used precipitation polymerization in water to synthesize colloidal poly(diethylene glycol-ethyl ether acrylate) (PDEGAC) particles as a precursor. PDEGAC forms solvent swollen microgels in organic solvents such as methanol and dioxane and in water at temperatures below 15 °C. In the second step, these PDEGAC particles were transformed to PHEAA microgels through aminolysis in dioxane with ethanolamine and a small amount of ethylenediamine. Dynamic laser scattering studies confirmed that the colloidal stability of microgels was maintained during the aminolysis in dioxane and subsequent transfer to water. Characterization of the PHEAA microgels indicated about 9 mol % of primary amino groups. These provide functionality for bioconjugation. As proof-of-concept experiments, we attached the enzyme horseradish peroxidase (HRP) to these aqueous microgels through (i) N-(3-(dimethylamino)propyl)-N'-ethylcarbodiimide hydrochloride (EDC) coupling to the carboxylated microgels or (ii) bis-aryl hydrazone (BAH) coupling to microgels functionalized with 6-hydrazinonicotinate acetone (PHEAA-HyNic). Our results showed that HRP maintained its catalytic activity after covalent attachment (87% for EDC coupling, 96% for BAH coupling). The microgel enhanced the stability of the enzyme to thermal denaturation. For example, the residual activity of the microgel-supported enzyme was 76% after 330 min of annealing at 50 °C, compared to only 20% for the free enzyme under these conditions. PHEAA microgels in water show great promise as hosts for enzymatic reaction, especially at elevated temperatures.

Post-Translational Modification of Bionanoparticles as a Modular Platform for Biosensor Assembly

Context driven biosensor assembly with modular targeting and detection moieties is gaining significant attentions. Although protein-based nanoparticles have emerged as an excellent platform for biosensor assembly, current strategies of decorating bionanoparticles with targeting and detection moieties often suffer from unfavorable spacing and orientation as well as bionanoparticle aggregation. Herein, we report a highly modular post-translational modification approach for biosensor assembly based on sortase A-mediated ligation. This approach enables the simultaneous modifications of the Bacillus stearothermophilus E2 nanoparticles with different functional moieties for antibody, enzyme, DNA aptamer, and dye decoration. The resulting easy-purification platform offers a high degree of targeting and detection modularity with signal amplification. This flexibility is demonstrated for the detection of both immobilized antigens and cancer cells.

Lab on a single microbead: an ultrasensitive detection strategy enabling microRNA analysis at the single-molecule level

A single microbead-based sensing platform has been developed, which enables the detection of microRNA at the single-molecule level.

Detection of a single nucleic acid molecule is of great significance for both fundamental biochemistry studies and clinical diagnostics. By using microRNA (miRNA) as a model target, herein, we have developed a single-microbead-based sensing (SMBS) platform, which simply enables the detection of miRNA at the single-molecule level. In this strategy, an isothermal exponential amplification reaction (EXPAR) is rationally designed towards specific miRNAs and all products of the EXPAR are integrated onto a single microbead for signal amplification and fluorescence enrichment. This pushes the detection of miRNAs down to 1 aM in a 5 μL sample, corresponding to 3 copies of the miRNA molecule. This new strategy also affords high selectivity and it is capable of distinguishing among homologous miRNA family members even with a single-base difference. Due to its ultrahigh sensitivity and selectivity, the proposed SMBS platform has been successfully applied to the detection of miRNA extracted from a single cell.

Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection

Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and "point of care" platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields.

Molecular approaches to recognize relevant and emerging infectious diseases in animals

Since the introduction of the first molecular tests, there has been a continuous effort to develop new and improved assays for rapid and efficient detection of infectious agents. This has been motivated by a need for improved sensitivity as well as results that can be easily communicated. The experiences and knowledge gained at the World Organisation for Animal Health (OIE) Collaborating Centre for Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden, will here be used to provide an overview of the different molecular approaches that can be used to diagnose and identify relevant and emerging infectious diseases in animals.

The effect of temperature on electrochemically driven denaturation monitored by SERS

Scanning the electrochemical potential negative results in the gradual denaturation of dsDNA immobilised at a nanostructure gold electrode, the DNA melting is monitored by SERS. We demonstrate the effect of the experimental temperature on the electrochemically driven melting (E-melting) by carrying out experiments between 10 and 28 °C using two DNA duplexes (20 and 21 base pairs). Significant temperature dependence for both the melting potentials, Em, and the steepness of the melting curves was found over the range 10 to 18 °C. Above 18 °C the results were found to be independent of temperature. The relative temperature insensitivity of the melting potentials above 18 °C is advantageous for the application of the electrochemically driven melting technique because precise temperature control is not necessary for measurements that are carried out around room temperature. Conversely temperature dependence below 18 °C offers a way to improve discrimination for highly similar DNA sequences.

Simultaneous and sensitive detection of dual DNA targets via quantum dot-assembled amplification labels

We describe a signal amplification assay for the simultaneous detection of HIV-1 and HIV-2 via a quantum dot (QD) layer-by-layer assembled polystyrene microsphere (PS) composite in a homogeneous format. The crucial point of this composite is the core-shell system. PS is utilized as the core and QDs as the shell. Based on the high affinity of streptavidin and biotin, QDs are assembled layer-by-layer on the surface of the PS as amplification labels. Biotinylated reporter probe is combined with the PS-QDs conjugate and then hybridized with target DNA immobilized on the surface of a 96-well plate. Using this approach, each target DNA corresponds to a large number of QDs and the fluorescence signal is greatly enhanced. Two QD colors (605 and 655 nm) are used to detect dual-target DNAs simultaneously. Taking advantage of the enzyme-free reaction and high sensitivity, this PS-QD-based sensor can be used in simple 'mix and detection' assays. Our results show that this technology has potential application in rapid point-of-care testing, gene expression studies, high-throughput screening and clinical diagnostics.

Nanostructured sensor based on carbon nanotubes and clavanin A for bacterial detection

Unusual methods for specific detection of pathogenic bacteria are becoming key points for control and identification of problems related to health and (bio)safety. In this context, this work aims to propose a new approach for the development of nanostructured biosensors based on carbon nanotubes (CNTs) and antimicrobial peptides for bacterial detection. Firstly, the antimicrobial peptide clavanin A (ClavA) was chemically immobilized on CNTs and surface-immobilized ClavA was used to detect Klebsiella pneumoniae, Enterococcus faecalis, Escherichia coli and Bacillus subtilis in a direct assay format. We used electrochemical impedance spectroscopy technique to evaluate the effectiveness and sensitivity of the ClavA-based biosensors by measuring the modifications in their electrochemical responses before and after incubation in presence of different bacteria concentrations. The biosensor was able to discriminate between bacteria concentrations in the 10(2)-10(6)CFU mL(-1) range. Atomic force microscopy analysis confirmed the biosensor functionality for bacterial recognition. This new sensor system was capable of differentiating between Gram-positive and Gram-negative bacteria, since ClavA showed different affinities toward the pathogenic bacteria species.

Single-layer transition metal dichalcogenide nanosheet-based nanosensors for rapid, sensitive, and multiplexed detection of DNA

Single-layer transition metal dichalcogenide nanosheets, including MoS2, TiS2, and TaS2, are used as novel sensing platforms for sensitive and selective detection of DNA, based on their high fluorescence-quenching ability and different affinities toward single-stranded DNA and double-stranded DNA. Importantly, for the first time, a single-layer TaS2 nanosheet-based multiplexed DNA sensor is also developed.

Evaluation of the formation of a junctional DNA nanostructure through annealing curve analysis

During the self-assembly of different numbers of oligonucleotides comprising junctional DNA nanostructures, a change in environmental variables (e.g., temperature or salt concentration) has a substantial influence on the final products. Further, distinctive annealing temperatures of oligonucleotides are observed depending on the state of hybridization. Here, we present an evaluation of the annealing characteristics of oligonucleotides for the formation of a simple junctional DNA nanostructure using an annealing curve analysis. This method may be useful for analyzing the formation of complex junctional DNA nanostructures.

Microfluidic synthesis of barcode particles for multiplex assays

The increasing use of high-throughput assays in biomedical applications, including drug discovery and clinical diagnostics, demands effective strategies for multiplexing. One promising strategy is the use of barcode particles that encode information about their specific compositions and enable simple identification. Various encoding mechanisms, including spectroscopic, graphical, electronic, and physical encoding, have been proposed for the provision of sufficient identification codes for the barcode particles. These particles are synthesized in various ways. Microfluidics is an effective approach that has created exciting avenues of scientific research in barcode particle synthesis. The resultant particles have found important application in the detection of multiple biological species as they have properties of high flexibility, fast reaction times, less reagent consumption, and good repeatability. In this paper, research progress in the microfluidic synthesis of barcode particles for multiplex assays is discussed. After introducing the general developing strategies of the barcode particles, the focus is on studies of microfluidics, including their design, fabrication, and application in the generation of barcode particles. Applications of the achieved barcode particles in multiplex assays will be described and emphasized. The prospects for future development of these barcode particles are also presented.

An in situ assembly of a DNA–streptavidin dendrimer nanostructure: a new amplified quartz crystal microbalance platform for nucleic acid sensing

A target-triggered in situ assembly of a DNA–streptavidin dendrimer nanostructure was developed to create a facile platform for nucleic acid sensing.

Ultrasensitive electrochemical detection of dual DNA targets based on G-quadruplex-mediated amplification

Dual DNA targets were ligated to a long strand containing a G-quadruplex forming sequence and detected on a capture probe modified electrode.

Surface-enhanced Raman spectroscopy for DNA detection by the self-assembly of Ag nanoparticles onto Ag nanoparticle–graphene oxide nanocomposites

A novel surface-enhanced Raman scattering (SERS) sensing system which operates by the self-assembly of Ag nanoparticles (AgNPs) onto the nanocomposite of AgNPs and graphene oxide (AgNP–GO) in the presence of two complementary DNAs has been developed.

Integrating dye-intercalated DNA dendrimers with electrospun nanofibers: a new fluorescent sensing platform for nucleic acids, proteins, and cells

A fluorescent dye-intercalated DNA dendrimer probe was integrated with electrospun nanofibers to create an amplified sensing platform for disease-related species.

A programmable Y-shaped junction scaffold-mediated modular and cascade amplification strategy for the one-step, isothermal and ultrasensitive detection of target DNA

A programmable Y-shaped junction probe-mediated modular and cascade amplification strategy was proposed for the one-pot, isothermal and ultrasensitive detection of target DNA.

Barcoded microchips for biomolecular assays

Multiplexed assay of analytes is of great importance for clinical diagnostics and other analytical applications. Barcode-based bioassays with the ability to encode and decode may realize this goal in a straightforward and consistent manner. We present here a microfluidic barcoded chip containing several sets of microchannels with different widths, imitating the commonly used barcode. A single barcoded microchip can carry out tens of individual protein/nucleic acid assays (encode) and immediately yield all assay results by a portable barcode reader or a smartphone (decode). The applicability of a barcoded microchip is demonstrated by human immunodeficiency virus (HIV) immunoassays for simultaneous detection of three targets (anti-gp41 antibody, anti-gp120 antibody, and anti-gp36 antibody) from six human serum samples. We can also determine seven pathogen-specific oligonucleotides by a single chip containing both positive and negative controls.

Isothermal amplified detection of DNA and RNA

This review highlights various methods that can be used for a sensitive detection of nucleic acids without using thermal cycling procedures, as is done in PCR or LCR. Topics included are nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), loop-mediated amplification (LAMP), Invader assay, rolling circle amplification (RCA), signal mediated amplification of RNA technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), nicking endonuclease signal amplification (NESA) and nicking endonuclease assisted nanoparticle activation (NENNA), exonuclease-aided target recycling, Junction or Y-probes, split DNAZyme and deoxyribozyme amplification strategies, template-directed chemical reactions that lead to amplified signals, non-covalent DNA catalytic reactions, hybridization chain reactions (HCR) and detection via the self-assembly of DNA probes to give supramolecular structures. The majority of these isothermal amplification methods can detect DNA or RNA in complex biological matrices and have great potential for use at point-of-care.

SERS nanosensors and nanoreporters: golden opportunities in biomedical applications

This article provides an overview of recent developments and applications of surface-enhanced Raman scattering (SERS) nanosensors and nanoreporters in our laboratory for use in biochemical monitoring, medical diagnostics, and therapy. The design and fabrication of different types of plasmonics-active nanostructures are discussed. The SERS nanosensors can be used in various applications including pH sensing, protein detection, and gene diagnostics. For DNA detection the 'Molecular Sentinel' nanoprobe can be used as a homogenous bioassay in solution or on a chip platform. Gold nanostars provide an excellent multi-modality theranostic platform, combining Raman and SERS with two-photon luminescence (TPL) imaging as well as photodynamic therapy (PDT), and photothermal therapy (PTT). Plasmonics-enhanced and optically modulated delivery of nanostars into brain tumor in live animals was demonstrated; photothermal treatment of tumor vasculature may induce inflammasome activation, thus increasing the permeability of the blood brain-tumor barrier. The imaging method using TPL of gold nanostars provides an unprecedented spatial selectivity for enhanced targeted nanostar delivery to cortical tumor tissue. A quintuple-modality nanoreporter based on gold nanostars for SERS, TPL, magnetic resonance imaging (MRI), computed tomography (CT), and PTT has recently been developed. The possibility of combining spectral selectivity and high sensitivity of the SERS process with the inherent molecular specificity of bioreceptor-based nanoprobes provides a unique multiplex and selective diagnostic modality. Several examples of optical detection using SERS in combination with other detection and treatment modalities are discussed to illustrate the usefulness and potential of SERS nanosensors and nanoreporters for medical applications.

Assembly of barcode-like nucleic acid nanostructures

Barcode-like (BC) nanopatterns from programmed self-assembly of nucleic acids (DNA and RNA) are reported. BC nanostructures are generated by the introduction of open spaces at selected sites to an otherwise closely packed, plain, rectangle nucleic acid nanostructure. This strategy is applied to nanostructures assembled from both origami approach and single stranded tile approach.

Near-infrared-emitting two-dimensional codes based on lattice-strained core/(doped) shell quantum dots with long fluorescence lifetime

Lattice-strained CdTe/CdS:Cu quantum dots (QDs) with a widely tunable near-infrared (NIR) fluorescence emission spectrum (700-910 nm) and long lifetime (up to 1 μs) are synthesized. Based on the multiemission and multi-lifetime of the well-defined QDs, NIR-emitting two-dimensional (2D) codes are achieved by embedding as-prepared QDs into agarose beads. This provides a new strategy for fluorescent 2D codes.

DNA Barcoding on Bacteria: A Review

Bacteria are omnipotent and they can be found everywhere. The study of bacterial pathogens has been happening from olden days to prevent epidemics, food spoilage, losses in agricultural production, and loss of lives. Modern techniques in DNA based species identification are considered. So, there is a need to acquire simple and quick identification technique. Hence, this review article covers the efficacy of DNA barcoding of bacteria. Routine DNA barcoding involves the production of PCR amplicons from particular regions to sequence them and these sequence data are used to identify or “barcode” that organism to make a distinction from other species.

Highly sensitive fluorescence detection of target DNA by coupling exonuclease-assisted cascade target recycling and DNAzyme amplification

Because of the intrinsic importance of nucleic acid as bio-targets, the simple and sensitive detection of nucleic acid is very essential for biological studies and medical diagnostics. Herein, a simple, isothermal and highly sensitive fluorescence detection of target DNA was developed with the combination of exonuclease III (Exo III)-assisted cascade target recycling and DNAzyme amplification. A hairpin DNA probe was designed, which contained the 3'-protruding DNA fragment as target recognition unit, the caged DNA fragment in the stem region as target analogue, and the caged 8-17 DNAzyme sequence in the loop region as signal response unit. Upon sensing of target DNA, the 3'-strand of hairpin DNA probe could be stepwise removed by Exo III, accompanied by the releasing of target DNA and autonomous generation of new target analogues for the successive hybridization and cleavage process. Simultaneously, the 8-17 DNAzyme unit could be exponentially released from this hairpin DNA probe and activated for the cyclic cleavage toward the ribonucleotide-containing molecular beacon substrate, inducing a remarkable fluorescence signal amplification for target detection. A low detection limit of 20 fM with an excellent selectivity toward target DNA could be achieved. The developed cascade amplification strategy may be further extended for the detection of a wide spectrum of analytes including protein and biological small molecules by combining DNA aptamer technology.

Multiplexed detection of various breast cancer cells by perfluorocarbon/quantum dot nanoemulsions conjugated with antibodies

The effective targeting of cancer cell surface antigens is an attractive approach in cancer diagnosis and therapy. Multifunctional nanoprobes with cell-targeting specificity are likely to find important applications in bioanalysis, biomedicine, and clinical diagnosis. In this study, we have fabricated biocompatible perfluorocan/quantum dot nanoemulsions as bimodal imaging nanoprobes for the targeting of breast cancer cells. Perfluorocarbon/quantum dot nanoemulsions conjugated with monoclonal antibodies, as a type of bimodal imaging nanoprobe based on 19 F-MR and optical imaging, have been synthesized and applied for targeted imaging of three different breast cancer cells (SKBR3, MCF-7, MDA-MB 468), respectively. We have shown that the cancer-detection capabilities of antibody-conjugated PFC/QDs nanoemulsions could be successfully applied to target of various breast cancer cells. These modified PFC/QDs nanoemulsions were shown to target the cancer cell surface receptors specially. Conjugation of ligands to nanoemulsions targeting over-expressed cell surface receptors is a promising approach for targeted imaging to tumor cells. We further propose that the PFC/QDs nanoemulsions could be used in targeted imaging of breast cancer cells.

Biomolecule-to-fluorescent-color encoder: modulation of fluorescence emission via DNA structural changes

A biomolecule-to-fluorescent-color (B/F) encoder for optical readout of biomolecular information is proposed. In the B/F encoder, a set of fluorescence wavelengths and their intensity levels are used for coding of a biomolecular signal. A hybridization chain reaction of hairpin DNAs labeled with fluorescent reporters was performed to generate the fluorescence color codes. The fluorescence is modulated via fluorescence resonance energy transfer, which is controlled by DNA structural changes. The results demonstrate that fluorescent color codes can be configured based on two wavelengths and five intensities using the B/F encoder, and the assigned codes can be retrieved via fluorescence measurements.

Assembly of multiple DNA components through target binding toward homogeneous, isothermally amplified, and specific detection of proteins

We describe a strategy of utilizing specific target binding to trigger assembly of three DNA components that are otherwise unable to spontaneously assemble with one another. This binding-induced DNA assembly forms a three-arm DNA junction, subsequently initiating nicking endonuclease-assisted isothermal fluorescence signal amplification. Real-time monitoring of fluorescence enables amplified detection of specific protein targets. The implementation of the strategy necessitates the simultaneous binding of a single target molecule with two affinity ligands each conjugated to a DNA motif. Simple alternation of affinity ligands enables different protein targets to induce the formation of the DNA junction and subsequent isothermal amplification. The use of the strategy allowed us to develop a sensitive assay for proteins with three appealing features: homogeneous analysis without the need for separation, isothermal amplification, and high specificity. Streptavidin was chosen as an initial target to establish and optimize the assay. Sensitivity of protein detection was improved by 1000-fold upon the application of isothermal amplification. A limit of detection of 10 pM was achieved for detection of prostate-specific antigen in buffer and diluted serum. The combination of its three appealing features makes the assay attractive for potential applications in molecular diagnosis, point-of-care testing, and on-site analysis.

Acoustic detection of DNA conformation in genetic assays combined with PCR

Application of PCR to multiplexing assays is not trivial; it requires multiple fluorescent labels for amplicon detection and sophisticated software for data interpretation. Alternative PCR-free methods exploiting new concepts in nanotechnology exhibit high sensitivities but require multiple labeling and/or amplification steps. Here, we propose to simplify the problem of simultaneous analysis of multiple targets in genetic assays by detecting directly the conformation, rather than mass, of target amplicons produced in the same PCR reaction. The new methodology exploits acoustic wave devices which are shown to be able to characterize in a fully quantitative manner multiple double stranded DNAs of various lengths. The generic nature of the combined acoustic/PCR platform is shown using real samples and, specifically, during the detection of SNP genotyping in Anopheles gambiae and gene expression quantification in treated mice. The method possesses significant advantages to TaqMan assay and real-time PCR regarding multiplexing capability, speed, simplicity and cost.

DNA materials: bridging nanotechnology and biotechnology

CONSPECTUS: In recent decades, DNA has taken on an assortment of diverse roles, not only as the central genetic molecule in biological systems but also as a generic material for nanoscale engineering. DNA possesses many exceptional properties, including its biological function, biocompatibility, molecular recognition ability, and nanoscale controllability. Taking advantage of these unique attributes, a variety of DNA materials have been created with properties derived both from the biological functions and from the structural characteristics of DNA molecules. These novel DNA materials provide a natural bridge between nanotechnology and biotechnology, leading to far-ranging real-world applications. In this Account, we describe our work on the design and construction of DNA materials. Based on the role of DNA in the construction, we categorize DNA materials into two classes: substrate and linker. As a substrate, DNA interfaces with enzymes in biochemical reactions, making use of molecular biology's "enzymatic toolkit". For example, employing DNA as a substrate, we utilized enzymatic ligation to prepare the first bulk hydrogel made entirely of DNA. Using this DNA hydrogel as a structural scaffold, we created a protein-producing DNA hydrogel via linking plasmid DNA onto the hydrogel matrix through enzymatic ligation. Furthermore, to fully make use of the advantages of both DNA materials and polymerase chain reaction (PCR), we prepared thermostable branched DNA that could remain intact even under denaturing conditions, allowing for their use as modular primers for PCR. Moreover, via enzymatic polymerization, we have recently constructed a physical DNA hydrogel with unique internal structure and mechanical properties. As a linker, we have used DNA to interface with other functional moieties, including gold nanoparticles, clay minerals, proteins, and lipids, allowing for hybrid materials with unique properties for desired applications. For example, we recently designed a DNA-protein conjugate as a universal adapter for protein detection. We further demonstrate a diverse assortment of applications for these DNA materials including diagnostics, protein production, controlled drug release systems, the exploration of life evolution, and plasmonics. Although DNA has shown great potential as both substrate and linker in the construction of DNA materials, it is still in the initial stages of becoming a well-established and widely used material. Important challenges include the ease of design and fabrication, scaling-up, and minimizing cost. We envision that DNA materials will continue to bridge the gap between nanotechnology and biotechnology and will ultimately be employed for many real-world applications.

Nanotechnology in agri-food production: an overview

Nanotechnology is one of the most important tools in modern agriculture, and agri-food nanotechnology is anticipated to become a driving economic force in the near future. Agri-food themes focus on sustainability and protection of agriculturally produced foods, including crops for human consumption and animal feeding. Nanotechnology provides new agrochemical agents and new delivery mechanisms to improve crop productivity, and it promises to reduce pesticide use. Nanotechnology can boost agricultural production, and its applications include: 1) nanoformulations of agrochemicals for applying pesticides and fertilizers for crop improvement; 2) the application of nanosensors/nanobiosensors in crop protection for the identification of diseases and residues of agrochemicals; 3) nanodevices for the genetic manipulation of plants; 4) plant disease diagnostics; 5) animal health, animal breeding, poultry production; and 6) postharvest management. Precision farming techniques could be used to further improve crop yields but not damage soil and water, reduce nitrogen loss due to leaching and emissions, as well as enhance nutrients long-term incorporation by soil microorganisms. Nanotechnology uses include nanoparticle-mediated gene or DNA transfer in plants for the development of insect-resistant varieties, food processing and storage, nanofeed additives, and increased product shelf life. Nanotechnology promises to accelerate the development of biomass-to-fuels production technologies. Experts feel that the potential benefits of nanotechnology for agriculture, food, fisheries, and aquaculture need to be balanced against concerns for the soil, water, and environment and the occupational health of workers. Raising awareness of nanotechnology in the agri-food sector, including feed and food ingredients, intelligent packaging and quick-detection systems, is one of the keys to influencing consumer acceptance. On the basis of only a handful of toxicological studies, concerns have arisen regarding the safety of nanomaterials, and researchers and companies will need to prove that these nanotechnologies do not have more of a negative impact on the environment.

A new building block for DNA network formation by self-assembly and polymerase chain reaction

The predictability of DNA self-assembly is exploited in many nanotechnological approaches. Inspired by naturally existing self-assembled DNA architectures, branched DNA has been developed that allows self-assembly to predesigned architectures with dimensions on the nanometer scale. DNA is an attractive material for generation of nanostructures due to a plethora of enzymes which modify DNA with high accuracy, providing a toolbox for many different manipulations to construct nanometer scaled objects. We present a straightforward synthesis of a rigid DNA branching building block successfully used for the generation of DNA networks by self-assembly and network formation by enzymatic DNA synthesis. The Y-shaped 3-armed DNA construct, bearing 3 primer strands is accepted by Taq DNA polymerase. The enzyme uses each arm as primer strand and incorporates the branched construct into large assemblies during PCR. The networks were investigated by agarose gel electrophoresis, atomic force microscopy, dynamic light scattering, and electron paramagnetic resonance spectroscopy. The findings indicate that rather rigid DNA networks were formed. This presents a new bottom-up approach for DNA material formation and might find applications like in the generation of functional hydrogels.

Graphene-coated surface plasmon resonance interfaces for studying the interactions between bacteria and surfaces

A variety of physical and chemical parameters are of importance for adhesion of bacteria to surfaces. In the colonization of mammalian organisms for example, bacterial fimbriae and their adhesins not only seek particular glycan sequences exposed on diverse epithelial linings, they also enable the bacteria to overcome electrostatic repulsion exerted by their selected surfaces. In this work, we present a new technique based on simplified model systems for studying the adhesion strength of different Escherichia coli strains. For this purpose, gold-based surface plasmon resonance (SPR) interfaces were coated with thin films of reduced graphene oxide (rGO) through electrophoretic deposition. The rGO matrix was post-modified with polyethyleneimine (PEI), poly(sodium 4-styrenesulfonate) (PSS), mannose, and lactose through π-stacking and/or electrostatic interactions by simple immersion of the SPR interface into their respective aqueous solutions. The adhesion behaviors of one uropathogenic and two enterotoxigenic Escherichia coli clinical isolates, that each express structurally characterized fimbrial adhesins, were investigated. It was found that the UTI89 cystitis isolate that carries the mannose-binding FimH adhesin was most attracted to the PEI- and mannose-modified surfaces, whereas the att25 diarrhoeal strain with the N-acetylglucosamine-specific F17a-G adhesin disintegrated the lactose-modified rGO. The highly virulent 107/86 strain interacted strongly with the PSS-modified graphene oxide, in agreement with the polybasic surroundings of the ABH blood group-binding site of the FedF adhesin, and showed a linear SPR response in a concentration range between 1 × 10(2) and 1 × 10(9) cfu/mL.

Highly enhanced optical properties of indocyanine green/perfluorocarbon nanoemulsions for efficient lymph node mapping using near-infrared and magnetic resonance imaging

The near-infrared (NIR) fluorescence probe has better tissue penetration and lower autofluorescence. Indocyanine green (ICG) is an NIR organic dye for extensive biological application, and it has been clinically approved for human medical imaging and diagnosis. However, application of this dye is limited by its numerous disadvantageous properties in aqueous solution, including its concentration-dependent aggregation, poor aqueous stability in vitro, and low quantum yield. Its use in molecular imaging probes is limited because it loses fluorescence after binding to nonspecific plasma proteins, leading to rapid elimination from the body with a half-life of 2 - 4 min. In this study, the multifunctional perfluorocarbon (PFC)/ICG nanoemulsions were investigated with the aim of overcoming these limitations. The PFC/ICG nanoemulsions as a new type of delivery vehicle for contrast agents have both NIR optical imaging and ¹⁹ F-MR imaging moieties. These nanoemulsions exhibited less aggregation, increased fluorescence intensity, long-term stability, and physicochemical stability against external light and temperature compared to free aqueous ICG. Also, the PFC/ICG bimodal nanoemulsions allow excellent detection of lymph nodes in vivo through NIR optical imaging and ¹⁹ F-MR imaging. This result showed the suitability of the proposed nanoemulsions for non-invasive lymph node mapping as they enable long-time detection of lymph nodes.

Multiplex detection of disease biomarkers using SERS molecular sentinel-on-chip

Developing techniques for multiplex detection of disease biomarkers is important for clinical diagnosis. In this work, we have demonstrated for the first time the feasibility of multiplex detection of genetic disease biomarkers using the surface-enhanced Raman scattering (SERS)-based molecular sentinel-on-chip (MSC) diagnostic technology. The molecular sentinel (MS) sensing mechanism is based upon the decrease of SERS intensity when Raman labels tagged at 3'-ends of MS nanoprobes are physically displaced from the nanowave chip's surface upon DNA hybridization. The use of bimetallic layer (silver and gold) for the nanowave fabrication was investigated. SERS measurements were performed immediately following a single hybridization reaction between the target single-stranded DNA sequences and the complementary MS nanoprobes immobilized on the nanowave chip without requiring target labeling (i.e., label-free), secondary hybridization, or post-hybridization washing, thus shortening the assay time and reducing cost. Two nucleic acid transcripts, interferon alpha-inducible protein 27 and interferon-induced protein 44-like, are used as model systems for the multiplex detection concept demonstration. These two genes are well known for their critical role in host immune response to viral infection and can be used as molecular signature for viral infection diagnosis. The results indicate the potential of the MSC technology for nucleic acid biomarker multiplex detection.

Functional DNA nanostructures for theranostic applications

There has been tremendous interest in constructing nanostructures by exploiting the unparalleled ability of DNA molecules in self-assembly. We have seen the appearance of many fantastic, "art-like" DNA nanostructures in one, two, or three dimensions during the last two decades. More recently, much attention has been directed to the use of these elegant nanoobjects for applications in a wide range of areas. Among them, diagnosis and therapy (i.e., theranostics) are of particular interest given the biological nature of DNA. One of the major barricades for the biosensor design lies in the restricted target accessibility at the solid-water interface. DNA nanotechnology provides a convenient approach to well control the biomolecule-confined surface to increase the ability of molecular recognition at the biosensing interface. For example, tetrahedral DNA nanostructures with thiol modifications can be self-assembled at the gold surface with high reproducibility. Since DNA tetrahedra are highly rigid and well-defined structures with atomic precision and versatile functionality, they provide scaffolds for anchoring of a variety of biomolecular probes (DNA, aptamers, peptides, and proteins) for biosensing. Significantly, this DNA nanostructure-based biosensing platform greatly increases target accessibility and improves the sensitivity for various types of molecular targets (DNA, RNA, proteins, and small molecules) by several orders of magnitude. In an alternative approach, DNA nanostructures provide a framework for the development of dynamic nanosensors that can function inside the cell. DNA tetrahedra are found to be facilely cell permeable and can sense and image specific molecules in cells. More importantly, these DNA nanostructures can be efficient drug delivery nanocarriers. Since they are DNA molecules by themselves, they have shown excellent cellular biocompatibility with minimal cytotoxicity. As an example, DNA tetrahedra tailored with CpG oligonucleotide drugs have shown greatly improved immunostimulatory effects that makes them a highly promising nanomedicine. By taking them together, we believe these functionalized DNA nanostructures can be a type of intelligent theranostic nanodevice for simultaneous sensing, diagnosis, and therapy inside the cell.