Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes

Dendrimers and DNA: combinations of two special topologies for nanomaterials and biology

Interactions between two precisely defined three-dimensional architectures (DNA and dendrimers) are described. Highly synergetic effects occur, as illustrated in two cases: dendrimers can be used as three-dimensional linkers for oligonucleotides, affording highly sensitive microarrays (biochips), and positively charged dendrimers strongly interact with DNA, allowing penetration inside cells (genetic transfection).

Nanostructures as analytical tools in bioassays

We critically evaluate the usefulness of different nanostructures described as labels, nanoscaffolds or separation media in immunoassays and nucleic-acid hybridization assays. Many of the great number of publications describe only theoretical aspects of using these nanostructures or nanoparticles, but do not verify their applicability in the presence of potential interferents that can be present in the sample matrix. We attempt a systematic study of the advantages and the limitations of using these new reagents in bioassays, the different assay formats for individual and multiplexed detection, and the capability of these assays in analyzing real samples.

Enhanced immunostimulatory activity of oligodeoxynucleotides by Y-shape formation

DNA containing unmethylated CpG dinucleotides (CpG DNA) is a potent activator of innate and acquired immune responses. Although the sequence-specific immunostimulatory activity of CpG DNA has been extensively explored, little information is available about the importance of the stereochemical properties of CpG DNA. In this study, Y-shaped oligodeoxynucleotides (Y-ODNs) were prepared using three ODNs with the halves of each ODN being partially complementary to a half of the other two ODNs. Y-ODN induced greater amounts of tumour necrosis factor-alpha and interleukin-6 from RAW264.7 macrophage-like cells than did conventional single-stranded ODN (ssODN) or double-stranded ODN (dsODN). The Y-ODN was less stable in serum than dsODN, but greater amounts of Y-ODN were taken up by macrophage-like cells compared with dsODN. A newly designed Y-ODN containing three potent CpG motifs generated significantly higher levels of cytokines compared with dsODN containing the identical sequences. These results indicate that the Y-shaped form of ODN is a novel, reproducible and reliable approach to enhancing the immunostimulatory activity of ODNs.

Bioconjugated nanoparticle detection of respiratory syncytial virus infection

The integration of nanotechnology with biology has produced major advances in molecular diagnostics, therapeutics, and bioengineering. Recent advances have led to the development of functionalized nanoparticles (NPs) that are covalently linked to biological molecules such as antibodies, peptides, proteins, and nucleic acids. These functionalized NPs allow for development of novel diagnostic tools and methods, particularly for pathogens, as rapid and sensitive diagnostics are essential for defining the emergence of infection, determining the period that preventive measures should be applied, for evaluating drug and vaccine efficacy, and for controlling epidemics. In this study, we show that functionalized NPs conjugated to monoclonal antibodies can be used to rapidly and specifically detect respiratory syncytial virus in vitro and in vivo. These results suggest that functionalized NPs can provide direct, rapid, and sensitive detection of viruses and thereby bridge the gap between current cumbersome virus detection assays and the burgeoning need for more rapid and sensitive detection of viral agents.

Zyvex Corporation

Founded in 1997, Zyvex is the first molecular nanotechnology company. The company's vision is to become the worldwide supplier of tools, products and services that enable adaptable, affordable and molecularly precise manufacturing. Zyvex technology is being used in biomaterials and subcellular characterization, nanomaterial composites for biomedical implants and 3D microsystems for miniature instrumentation. Nanotechnology is pervasive within biological systems, from membranes (tens of nanometers thick) that facilitate molecular trafficking into and within cells, to proteins (just a few nanometers in size) that perform most structural and functional duties of living organisms. It therefore stands to reason that tools to enable exploration and characterization of biological nanosystems and materials to enhance and repair these systems will be required to realize the full potential of nanomedicine.

Nanoscience in Veterinary Medicine

Nanotechnology, as an enabling technology, has the potential to revolutionize veterinary medicine. Examples of potential applications in animal agriculture and veterinary medicine include disease diagnosis and treatment delivery systems, new tools for molecular and cellular breeding, identity preservation of animal history from birth to a consumer's table, the security of animal food products, major impact on animal nutrition scenarios ranging from the diet to nutrient uptake and utilization, modification of animal waste as expelled from the animal, pathogen detection, and many more. Existing research has demonstrated the feasibility of introducing nanoshells and nanotubes into animals to seek and destroy targeted cells. Thus, building blocks do exist and are expected to be integrated into systems over the next couple of decades on a commercial basis. While it is reasonable to presume that nanobiotechnology industries and unique developments will revolutionize veterinary medicine in the future, there is a huge concern, among some persons and organizations, about food safety and health as well as social and ethical issues which can delay or derail technological advancements.

Binding of lectins to DNA micro-assemblies: Modification of nucleo-cages with lactose-conjugated psoralen

Spherical DNA micro-assemblies appended with lactose units (Lactose-nucleo-cages, Lac-NC) are newly developed. DNA spherical assemblies self-assembled from suitably designed three oligodeoxyribonucleotides (ODNs) 1-3 were cross-linked by lactose-conjugated psoralen derivative 4. Confocal laser scanning fluorescence microscopy (CLSM) observation of Lac-NC shows that rhodamine labeled peanut lectin (Rho-PNA: a galactose-specific lectin) binds to lactose-modified nucleo-cages with higher affinity compared to that of unmodified nucleo-cages. Binding isotherm experiments indicated that the apparent affinity constant of Rho-PNA to Lac-NC was in the order of 10(5) M(-1).

Polychromatic microarrays: simultaneous multicolor array hybridization of eight samples

High-throughput microscale platforms have transformed modern analytical investigations. Traditional microarray analyses involve a comparative approach, with two samples, a known control and an unknown sample, hybridized side-by-side and then contrasted for genetic differences. The samples are labeled with separate dyes and hybridized together, providing a differential expression pattern based on the reporter intensities. In contrast, the fiber-optic microarray platform described herein is analyzed with a microscope, thereby enabling the use of virtually any reporter, including quantum dots. The instrumentation takes advantage of the narrow emission bands characteristic of quantum dots to perform multiplexed detection of Bacillus anthracis. Advancing beyond the standard red/green microarray experiment, a panel of eight reporters were linked to eight B. anthracis samples and simultaneously analyzed in a microarray format. The ability to employ an assortment of reporters, along with the capacity to simultaneously hybridize eight samples confers an unprecedented flexibility to array-based analyses, providing a 4-fold increase in throughput over standard two-color assays.

Fluorescent DNA nanotags: supramolecular fluorescent labels based on intercalating dye arrays assembled on nanostructured DNA templates

Fluorescence detection and imaging are vital technologies in the life sciences and clinical diagnostics. The key to obtaining high-resolution images and sensitive detection is to use fluorescent molecules or particles that absorb and emit visible light with high efficiency. We have synthesized supramolecular complexes consisting of a branched DNA template and fluorogenic intercalating dyes. Because dyes can intercalate up to every other base pair, high densities of fluorophores are assembled yet the DNA template keeps them far enough away from each other to prevent self-quenching. The efficiency with which these noncovalent assemblies absorb light is more than 10-fold greater than that of the individual dye molecules. Förster resonance energy transfer from the intercalated dyes to covalently attached acceptor dyes is very efficient, allowing for wavelength shifting of the emission spectrum. Simple biotinylation of the DNA template allows for labeling of streptavidin-coated synthetic microspheres and mouse T-cells.

Self-assembled combinatorial encoding nanoarrays for multiplexed biosensing

Multiplexed and sensitive detection of nucleic acids, proteins, or other molecules from a single solution and a small amount of sample is of great demand in biomarker profiling and disease diagnostics. Here we describe a new concept using combinatorial self-assembly of DNA nanotiles into micrometer-sized two-dimensional arrays that carry nucleic acid probes and barcoded fluorescent dyes to achieve multiplexed detection. We demonstrated the specificity and sensitivity of the arrays by detecting multiple DNA sequences and aptamer binding molecules. This DNA tile-array-based sensor platform can be constructed through DNA self-assembly. The attachment of different molecular probes can be achieved by simple DNA hybridization so bioconjugation is not necessary for the labeling. Accurate control of the interprobe distances and solution-based binding reactions ensures fast target binding kinetics.

Enzyme-catalysed assembly of DNA hydrogel

DNA is a remarkable polymer that can be manipulated by a large number of molecular tools including enzymes. A variety of geometric objects, periodic arrays and nanoscale devices have been constructed. Previously we synthesized dendrimer-like DNA and DNA nanobarcodes from branched DNA via ligases. Here we report the construction of a hydrogel entirely from branched DNA that are three-dimensional and can be crosslinked in nature. These DNA hydrogels were biocompatible, biodegradable, inexpensive to fabricate and easily moulded into desired shapes and sizes. The distinct difference of the DNA hydrogel to other bio-inspired hydrogels (including peptide-based, alginate-based and DNA (linear)-polyacrylamide hydrogels) is that the crosslinking is realized via efficient, ligase-mediated reactions. The advantage is that the gelling processes are achieved under physiological conditions and the encapsulations are accomplished in situ-drugs including proteins and even live mammalian cells can be encapsulated in the liquid phase eliminating the drug-loading step and also avoiding denaturing conditions. Fine tuning of these hydrogels is easily accomplished by adjusting the initial concentrations and types of branched DNA monomers, thus allowing the hydrogels to be tailored for specific applications such as controlled drug delivery, tissue engineering, 3D cell culture, cell transplant therapy and other biomedical applications.

Gold Nanoparticle Based FRET Asssay for the Detection of DNA Cleavage

We report gold nanoparticle based FRET assay to monitor the cleavage of DNA by nucleases. Fluorescence signal enhancement is observed by a factor of 120 after the cleavage reaction in the presence of S1 nuclease. The mechanism of distant dependent fluorescence quenching has been discussed. Our experimental results on distance dependent fluorescence quenching match quite well with theoretical findings obtained from the fluorescence quenching model by Gersten and Nitzan (Surf. Sci. 1985, 158, 165). Our experimental observation paradigm for the design of optical based molecular ruler strategies at distances more than double the distances achievable using traditional dipole-dipole Columbic energy transfer based methods.

Dendrimer-like DNA-based fluorescence nanobarcodes

A major challenge in clinical diagnostics and environmental analysis is the difficulty in rapid and sensitive detection of multiple target molecules simultaneously (i.e., multiplexed detections). Our group has designed and synthesized a dendrimer-like DNA (DL-DNA) that is multivalent and anisotropic; using this unique DNA structure, we have developed a fluorescence-tagged nanobarcode system for multiplex detection. This nanobarcode system allows the rapid and sensitive detection of multiple pathogens simultaneously using the ratios of two different fluorescent dyes, green and red, with which different DL-DNAs are labeled. The key step of our nanobarcode model lies in the monodisperse preparation of DL-DNA. Two methods, solution phase and solid phase, are presented here. With slight modifications, this platform technology can also be extended to the multiplexed detection of RNA and proteins. This protocol can be completed in 2-5 d.

Analysis of hybridization on the molecular barcode GeneChip microarray

Microarrays have been developed for analysis of transcriptional profiles in many organisms. For experimental simplicity and systems for which microarrays do not exist, it would be desirable to use a standard microarray platform for the analysis of multiple systems. The molecular barcode (MB) Affymetrix GeneChip could serve as such a platform. The reproducibility and quantitative capacity of the MB GeneChip were examined. Using mixed PCR templates of defined template quantity, the individual concentration responses of 384 array features were measured and shown to be highly reproducible. Moreover, the binding behaviors of the mismatched array features mirror those of the matched features, at reduced intensity. Additional analysis defined the importance of particular sequence motifs in the prediction of high-affinity and low-affinity target hybridization. The data support the future application of MB GeneChips for quantitative applications. It is proposed that at least seven orders-of-magnitude in accurate concentration sensitivity could be achieved.

Designed DNA molecules: principles and applications of molecular nanotechnology

Long admired for its informational role in the cell, DNA is now emerging as an ideal molecule for molecular nanotechnology. Biologists and biochemists have discovered DNA sequences and structures with new functional properties, which are able to prevent the expression of harmful genes or detect macromolecules at low concentrations. Physical and computational scientists can design rigid DNA structures that serve as scaffolds for the organization of matter at the molecular scale, and can build simple DNA-computing devices, diagnostic machines and DNA motors. The integration of biological and engineering advances offers great potential for therapeutic and diagnostic applications, and for nanoscale electronic engineering.

Quantum-dots-FRET nanosensors for detecting unamplified nucleic acids by single molecule detection

Evaluation of: Zhang CY, Yeh HC, Kuroki MT, Wang TH: Single-quantum-dot-based DNA nanosensor. Nat. Mater. 4(11), 826–831 (2005) [1] .

Quantitative and sensitive detection of minute copies of nucleic acid sequences is critical in diagnosing disease and in understanding biomolecular processes. An inorganic–organic hybrid fluorescence resonance energy transfer (FRET) nanosensor based on quantum dots (QDs) was developed to overcome the limitations of conventional FRET-based probes. Functionalized QDs served as FRET donors and as nanoassemblies that can couple to multiple targets hybridized as a sandwich between a capture probe and a reporter probe. Target sequences are detected directly in solution by single molecule detection (SMD) without prior separation or amplification. This system is sensitive enough to detect approximately 50 or fewer copies and to discriminate point mutations. QD-FRET and SMD are platform technologies that will find many applications for detecting biomarkers or studying various biomolecules in a highly sensitive and quantitative manner.

Highly sensitive biomolecular fluorescence detection using nanoscale ZnO platforms

Fluorescence detection is currently one of the most widely used methods in the areas of basic biological research, biotechnology, cellular imaging, medical testing, and drug discovery. Using model protein and nucleic acid systems, we demonstrate that engineered nanoscale zinc oxide structures can significantly enhance the detection capability of biomolecular fluorescence. Without any chemical or biological amplification processes, nanoscale zinc oxide platforms enabled increased fluorescence detection of these biomolecules when compared to other commonly used substrates such as glass, quartz, polymer, and silicon. The use of zinc oxide nanorods as fluorescence enhancing substrates in our biomolecular detection permitted sub-picomolar and attomolar detection sensitivity of proteins and DNA, respectively, when using a conventional fluorescence microscope. This ultrasensitive detection was due to the presence of ZnO nanomaterials which contributed greatly to the increased signal-to-noise ratio of biomolecular fluorescence. We also demonstrate the easy integration potential of zinc oxide nanorods into periodically patterned nanoplatforms which, in turn, will promote the assembly and fabrication of these materials into multiplexed, high-throughput, optical sensor arrays. These zinc oxide nanoplatforms will be extremely beneficial in accomplishing highly sensitive and specific detection of biological samples involving nucleic acids, proteins and cells, particularly under detection environments involving extremely small sample volumes of ultratrace-level concentrations.

Analysis of human sera that are polyreactive in an addressable laser bead immunoassay

BACKGROUND

Following the introduction of addressable laser bead immunoassays (ALBIA) into our clinical laboratory, it was noted that certain sera would exhibit reactivity to numerous antigens in the array. To further understand the nature of this reactivity, we analyzed the reactivity of sequential sera that were identified over a 1 year period.

METHODS

Sera that demonstrated reactivity to 6 or more of the 8 antigens in an ALBIA kit (QuantaPlex 8: chromatin, Sm, RNP, Scl-70, ribosomal P protein, SS-A/Ro, SS-B/La, Jo-1) were tested for autoantibodies by indirect immunofluorescence (IIF) on HEp-2 cell substrates, for IgG, IgM and IgA rheumatoid factor, chromatin and ribosomal P protein by ELISA and by LINE immunoassay (LIA) and immunoblotting (IB).

RESULTS

In one calendar year, 40/4096 (0.8%) sera analyzed in a routine clinical laboratory setting demonstrated reactivity to 6 or more antigens in the QuantaPlex 8 kits. There was no common IIF pattern that could be attributed to the polyreactive sera. There was no apparent correlation of polyreactivity with IIF titers, indeed, 4/40 (10%) sera had a negative ANA at the screening dilution of 1/160. When subjected to IB, LIA and ELISA, polyreactivity to three or more antigens was confirmed for 12/40 (30%) of sera while 8/40 (20%) had reactivity to 1-2 antigens and 20 (50%) did not react with any antigens in these assays. Overall agreement of positive or negative tests between the ALBIA and IB, LIA and ELISA was 75% for chromatin, 50% for SS-A, 27.5% for Sm, 25% for Rib-P, 22.5% for RNP, 20% for Scl-70, 15% for Jo-1 and 7.5% for SS-B. 17/40 (42.5%) had a positive IgM, IgG or IgA rheumatoid factor, and 12/40 (30%) had all three isotype rheumatoid factors.

CONCLUSIONS

On average, the agreement between ALBIA and other assays in this study of polyreactive sera was 30%. Approximately, one-half of sera that demonstrate reactivity to multiple autoantigens in a commercial ALBIA were confirmed to have reactivity to at least one autoantigen in another diagnostic assay and 30% could be regarded as polyreactive. Other sera, some of which had rheumatoid factor, appeared to have high background binding without demonstrating specific binding to any of the cognate antigens.

Rational Design of DNA Nanoarchitectures

DNA has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequence-directed hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.

Designing dendrimers for biological applications

Dendrimers are branched, synthetic polymers with layered architectures that show promise in several biomedical applications. By regulating dendrimer synthesis, it is possible to precisely manipulate both their molecular weight and chemical composition, thereby allowing predictable tuning of their biocompatibility and pharmacokinetics. Advances in our understanding of the role of molecular weight and architecture on the in vivo behavior of dendrimers, together with recent progress in the design of biodegradable chemistries, has enabled the application of these branched polymers as anti-viral drugs, tissue repair scaffolds, targeted carriers of chemotherapeutics and optical oxygen sensors. Before such products can reach the market, however, the field must not only address the cost of manufacture and quality control of pharmaceutical-grade materials, but also assess the long-term human and environmental health consequences of dendrimer exposure in vivo.

Homogenous rapid detection of nucleic acids using two-color quantum dots

We report a homogenous method for rapid and sensitive detection of nucleic acids using two-color quantum dots (QDs) based on single-molecule coincidence detection. The streptavidin-coated quantum dots functioned as both a nano-scaffold and as a fluorescence pair for coincidence detection. Two biotinylated oligonucleotide probes were used to recognize and detect specific complementary target DNA through a sandwich hybridization reaction. The DNA hybrids were first caught and assembled on the surface of 605 nm-emitting QDs (605QDs) through specific streptavidin-biotin binding. The 525 nm-emitting QDs (525QDs) were then added to bind the other end of DNA hybrids. The coincidence signals were observed only when the presence of target DNA led to the formation of 605QD/DNA hybrid/525QD complexes. In comparison with a conventional QD-based assay, this assay provided high detection efficiency and short analysis time due to its high hybridization efficiency resulting from the high diffusion coefficient and no limitation of temperature treatment. This QD-based single-molecule coincidence detection offers a simple, rapid and ultra sensitive method for genomic DNA analysis in a homogenous format.