Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes

Structurally Diverse Nitric Oxide-Releasing Poly(propylene Imine) Dendrimers

Structurally diverse secondary amine-functionalized poly(propylene imine) (PPI) dendrimers capable of tunable nitric oxide (NO) release were synthesized in a straightforward, one-step manner using ring-opening or conjugate-addition reactions with propylene oxide (PO), styrene oxide (SO), acrylonitrile (ACN), poly(ethylene glycol) methyl ether acrylate (average Mn = 480) (PEG) or 1,2-epoxy-9-decene (ED). N-Diazeniumdiolate nitric oxide donors were formed on the resulting secondary amine-functionalized G2-G5 PPI dendrimers by reaction with NO gas in basic solution. The NO storage and release kinetics for the resulting dendritic scaffolds were diverse (0.9-3.8 μmol NO/mg totals and 0.3 to 4.9 h half lives), illustrating the importance of the exterior chemical modification (e.g., steric environments, hydrophobicity, etc.) on diazeniumdiolate stability/decomposition. Tunable NO release was demonstrated by combining two donor systems on the exterior of one macromolecular scaffold. Additionally, a mathematical model was developed that allows for the simulation of dual NO release kinetics using the NO release data from the two single NO donor systems. The approaches described herein extend the range and scope of NO-releasing macromolecular scaffolds by unlocking a series of materials for use as dopants in biomedical polymers or stand-alone therapeutics depending on the exterior modification.

Advances of multiplex and high throughput biomolecular detection technologies based on encoding microparticles

The rapid developments of genomics and proteomics have driven the demand for multiplex and high throughput analysis of large numbers of biomolecules in the fields of medical diagnostics, drug discovery, and environmental monitoring. Encoding the biomolecular binding events is the key technique to fulfill this demand, in which microparticles play the most important roles. This review outlines the development of multiplex and high throughput biodetections, and highlights the most recent advances in the field of encoding microparticles, together with problems that need to be resolved.

Engineering DNA-based functional materials

While DNA is a genetic material, it is also an inherently polymeric material made from repeating units called nucleotides. Although DNA's biological functions have been studied for decades, the polymeric features of DNA have not been extensively exploited until recently. In this tutorial review, we focus on two aspects of using DNA as a polymeric material: (1) the engineering methods, and (2) the potential real-world applications. More specifically, various strategies for constructing DNA-based building blocks and materials are introduced based on DNA topologies, which include linear, branched/dendritic, and networked. Different applications in nanotechnology, medicine, and biotechnology are further reviewed.

Multiplexed detection of nucleic acids in a combinatorial screening chip

Multiplexed diagnostic testing has the potential to dramatically improve the quality of healthcare. Simultaneous measurement of health indicators and/or disease markers reduces turnaround time and analysis cost and speeds up the decision making process for diagnosis and treatment. At present, however, most diagnostic tests only provide information on a single indicator or marker. Development of efficient diagnostic tests capable of parallel screening of infectious disease markers could significantly advance clinical and diagnostic testing in both developed and developing parts of the world. Here, we report the multiplexed detection of nucleic acids as disease markers within discrete wells of a microfluidic chip using molecular beacons and total internal reflection fluorescence microscopy (TIRFM). Using a 4 × 4 array of 200 pL wells, we screened for the presence of four target single stranded oligonucleotides encoding for conserved regions of the genomes of four common viruses: human immunodeficiency virus-1 (HIV-1), human papillomavirus (HPV), Hepatitis A (Hep A) and Hepatitis B (Hep B). Target oligonucleotides are accurately detected and discriminated against alternative oligonucleotides with different sequences. This combinatorial chip represents a versatile platform for the development of clinical diagnostic tests for simultaneous screening, detection and monitoring of a wide range of biological markers of disease and health using minimal sample size.

One-step synthesized silver micro-dendrites used as novel separation mediums and their applications in multi-DNA analysis

A new kind of silver micro-dendrites have been synthesized for the separation and multiplex detection of DNA merely by earth gravity. Through this approach, the DNA strands of the sickle cell disease, human T-lymphotropic virus type I, the anthrax lethal factor can be detected down to 100 pM with the detection range from 100 pM to 100 nM at the same time.

RGB colour coding of Y-shaped DNA for simultaneous tri-analyte solid phase hybridization detection

We present a new concept for tri-analyte DNA detection based on the idea of a Y-shaped capture probe which, after tri-target and fluorescently labeled reporter probe binding, becomes colour-coded to generate images in an RGB colour scheme. Hence, the RGB value of the resulting secondary pseudo-colour presented by the hybridized Y-DNA can be related to the ratio of the primary pseudo-colours present in its make-up, and thus to the ratio of the three target concentrations. As a proof of concept we detect sequences from the genes of the pathogenic bacterial strains Escherichia coli O157:H7, Vibrio cholera and Salmonella enteric in a semi-quantitative manner across the range 20-167 nM. The assay was relatively quick, with a time from hybridization to completed data interpretation of approximately 4 h.

Detection of bacteria using glyco-dendronized polylysine prepared by continuous flow photofunctionalization

Biocompatible glyco-dendronized poly-l-lysine (PLL) polymers carry either three or nine mannose- or galactose-bearing dendrons that selectively bind, and thus can be used to detect, bacteria. Central to the synthesis of glyco-dendronized polymers was the development of a continuous flow [2 + 2] photocycloaddition reaction to connect the dendrons and PLL. Glycodendronized polymers cluster bacteria by binding to cell-surface carbohydrate receptors and thereby result in an easy read-out using microscopic analyses.

Photoresponsive DNA-cross-linked hydrogels for controllable release and cancer therapy

We have developed a photoresponsive DNA-cross-linked hydrogel that can be photoregulated by two wavelengths with a reversible sol-gel conversion. This photoinduced conversion can be further utilized for precisely controllable encapsulation and release of multiple loads. Specifically, photosensitive azobenzene moieties are incorporated into DNA strands as cross-linkers, such that their hybridization to complementary DNAs (cDNAs) responds differently to different wavelengths of light. On the basis of the rheology variation of hydrogels, it is possible to utilize this material for storing and releasing molecules and nanoparticles. To prove the concept, three different materials--fluorescein, horseradish peroxidase, and gold nanoparticles--were encapsulated inside the gel at 450 nm and then released by photons at 350 nm. Further experiments were carried out to deliver the chemotherapy drug doxorubicin in a similar manner in vitro. Our results show a net release rate of 65% within 10 min, and the released drug maintained its therapeutic effect. This hydrogel system provides a promising platform for drug delivery in targeted therapy and in biotechnological applications.

Magnetic nanoparticle enhanced surface plasmon resonance sensing and its application for the ultrasensitive detection of magnetic nanoparticle-enriched small molecules

Magnetic nanoparticles (MNPs) have been frequently used in bioseparation, but their applicability in bioassays is limited due to their extremely small size so that sensitive detection is difficult to achieve using a general technique. Here, we present an amplification technique using MNPs for an enhanced surface plasmon resonance (SPR) bioassay. The amplification effect of carboxyl group modified Fe(3)O(4) MNPs of two sizes on SPR spectroscopy is first demonstrated by assembling MNPs on amino group modified SPR gold substrate. To further evaluate the feasibility of the use of Fe(3)O(4) MNPs in enhancing a SPR bioassay, a novel SPR sensor based on an indirect competitive inhibition assay (ICIA) is developed for detecting adenosine by employing Fe(3)O(4) MNP-antiadenosine aptamer conjugates as the amplification reagent. The results confirm that Fe(3)O(4) MNPs can be used as a powerful amplification agent to provide a sensitive approach to detect adenosine by SPR within the range of 10-10,000 nM, which is much superior to the detection result obtained by a general SPR sensor. Importantly, the present detection methodology could be easily extended to detect other biomolecules of interest by changing the corresponding aptamer in Fe(3)O(4) MNP-aptamer conjugates. This novel technique not only explores the possibility of the use of SPR spectroscopy in a highly sensitive detection of an MNP-based separation product but also offers a new direction in the use of Fe(3)O(4) MNPs as an amplification agent to design high performance SPR biosensors.

A reagentless, disposable and multiplexed electronic biosensing platform: application to molecular logic gates

The construction of a reagentless, sensitive, disposable and multiplexed electronic sensing platform for one-spot simultaneous determination of biomolecules with significant difference in size (proteins and small molecules) is described. The sensing surface is fabricated by the hybridization of two types of redox-tags conjugated aptamers with the corresponding complementary DNAs, which are self-assembled on a gold nanoparticle-modified screen printed carbon electrode. The presence of the target analytes leads to the release of the tagged signaling aptamers from the sensing surface, and the surface-remained tags exhibit well-resolved peaks, whose positions and sizes reflect the identities and concentrations of the target analytes, respectively. The application of the proposed sensing platform for molecular logic gate operations is also demonstrated.

Integrated bio-inorganic hybrid systems for nano-forensics

This tutorial review describes a new class of data processing system that applies information theory at the molecular level. We also summarize the recent multidisciplinary advances in biotechnology and nanotechnology that have facilitated the development of reliable nano-level code systems. After a brief introduction of information theory, we present possible ways to adapt this concept to the molecular world. This review explains the requirements and solutions for each step necessary to apply a nano code system to real products. Finally, we introduce a designed nano code system for agricultural products as one example of the many possible applications for nano codes.

Novel DNA materials and their applications

The last two decades have witnessed the exponential development of DNA as a generic material instead of just a genetic material. The biological function, nanoscale geometry, biocompatibility, biodegradability, and molecular recognition capacity of DNA make it a promising candidate for the construction of novel functional nanomaterials. As a result, DNA has been recognized as one of the most appealing and versatile nanomaterial building blocks. Scientists have used DNA in this way to construct various amazing nanostructures, such as ordered lattices, origami, supramolecular assemblies, and even three-dimensional objects. In addition, DNA has been utilized as a guide and template to direct the assembly of other nanomaterials including nanowires, free-standing membranes, and crystals. Furthermore, DNA can also be used as structural components to construct bulk materials such as DNA hydrogels, demonstrating its ability to behave as a unique polymer. Overall, these novel DNA materials have found applications in various areas in the biomedical field in general, and nanomedicine in particular. In this review, we summarize the development of DNA assemblies, describe the innovative progress of multifunctional and bulk DNA materials, and highlight some real-world nanomedical applications of these DNA materials. We also show our insights throughout this article for the future direction of DNA materials.

Self-assembly of three-dimensional DNA nanostructures and potential biological applications

A current challenge in nanoscience is to achieve controlled organization in three-dimensions, to provide tools for biophysics, molecular sensors, enzymatic cascades, drug delivery, tissue engineering, and device fabrication. DNA displays some of the most predictable and programmable interactions of any molecule, natural or synthetic. As a result, 3D-DNA nanostructures have emerged as promising tools for biology and materials science. In this review, strategies for 3D-DNA assembly are discussed. DNA cages, nanotubes, dendritic networks, and crystals are formed, with deliberate variation of their size, shape, persistence length, and porosities. They can exhibit dynamic character, allowing their selective switching with external stimuli. They can encapsulate and position materials into arbitrarily designed patterns, and show promise for numerous biological and materials applications.

Single quantum dot-based nanosensor for multiple DNA detection

Owing to their unique optical properties, quantum dots (QDs) with different colors have been applied for simultaneous detection of multiple analytes. However, the use of single QD for multiplex detection of analytes with single-molecule detection has not been explored. Here we report a single QD-based nanosensor for multiplex detection of HIV-1 and HIV-2 at single-molecule level in a homogeneous format. In this single QD-based nanosensor, the QD functions not only as a fluorescence pair for coincidence detection and as a fluorescence-resonance-energy-transfer (FRET) donor for FRET detection but also as a local nanoconcentrator which significantly amplifies the coincidence-related fluorescence signals and the FRET signals. This single-QD-based nanosensor takes advantage of a simple 'mix and detection' assay with extremely low sample consumption, high sensitivity, and short analysis time and has the potential to be applied for rapid point-of-care testing, gene expression studies, high-throughput screening, and clinical diagnostics.

Highly efficient nonradiative energy transfer mediated light harvesting in water using aqueous CdTe quantum dot antennas

We present light harvesting of aqueous colloidal quantum dots to nonradiatively transfer their excitonic excitation energy efficiently to dye molecules in water, without requiring ligand exchange. These as-synthesized CdTe quantum dots that are used as donors to serve as light-harvesting antennas are carefully optimized to match the electronic structure of Rhodamine B molecules used as acceptors for light harvesting in aqueous medium. By varying the acceptor to donor concentration ratio, we measure the light harvesting factor, along with substantial lifetime modifications of these water-soluble quantum dots, from 25.3 ns to 7.2 ns as a result of their energy transfer with efficiency levels up to 86%. Such nonradiative energy transfer mediated light harvesting in aqueous medium holds great promise for future quantum dot multiplexed dye biodetection systems.

DNA self-assembly for nanomedicine

Self-assembling DNA nanostructures based on rationally designed DNA branch junction molecules has recently led to the construction of patterned supramolecular structures with increased complexities. An intrinsic value of DNA tiles and patterns lies in their utility as molecular pegboard for deterministic positioning of molecules or particles with accurate distance and architectural control. This review will discuss the state-of-art developments in self-assembled DNA nanostructural system. Biomedical aspects of information guided DNA nanostructures will also be summarized. We illustrate both the use of simple DNA artworks for sensing, computation, drug delivery and the application of more complex DNA architectures as scaffolds for the construction of protein and nanoparticle arrays.

DNA nanomedicine: Engineering DNA as a polymer for therapeutic and diagnostic applications

Nanomedicine, the application of nanotechnology to medicine, encompasses a broad spectrum of fields including molecular detection, diagnostics, drug delivery, gene regulation and protein production. In recent decades, DNA has received considerable attention for its functionality and versatility, allowing it to help bridge the gap between materials science and biological systems. The use of DNA as a structural nanoscale material has opened a new avenue towards the rational design of DNA nanostructures with different polymeric topologies. These topologies, in turn, possess unique characteristics that translate to specific therapeutic and diagnostic strategies within nanomedicine.

Patterned multiplex pathogen DNA detection by Au particle-on-wire SERS sensor

A Au particle-on-wire system that can be used as a specific, sensitive, and multiplex DNA sensor is developed. A pattern formed by multiple Au nanowire sensors provides positional address and identification for each sensor. By using this system, multiplex sensing of target DNAs was possible in a quantitative manner with a detection limit of 10 pM. Target DNAs from reference bacteria and clinical isolates were successfully identified by this sensor system, enabling diagnostics for infectious diseases.

Nanotechnology for the Food and Bioprocessing Industries

Several complex set of engineering and scientific challenges in the food and bioprocessing industries for manufacturing high quality and safe food through efficient and sustainable means can be solved through nanotechnology. Bacteria identification and food quality monitoring using biosensors; intelligent, active, and smart food packaging systems; and nanoencapsulation of bioactive food compounds are few examples of emerging applications of nanotechnology for the food industry. We review the background about the potential of nanotechnology, provide an overview of the current and future applications of nanotechnology relevant to food and bioprocessing industry, and identify the societal implications for successful implementation of nanotechnology.

DNA-based nanostructures for molecular sensing

Nanotechnology has opened up new avenues towards ultra-sensitive, highly selective detection of biological molecules and toxic agents, as well as for therapeutic targeting and screening. Though the goals may seem singular, there is no universal method to identify or detect a molecular target. Each system is application-specific and must not only identify the target, but also transduce this interaction into a meaningful signal rapidly, reliably, and inexpensively. This review focuses on the current capabilities and future directions of DNA-based nanostructures in sensing and detection.

Fluorescence logic-signal-based multiplex detection of nucleases with the assembly of a cationic conjugated polymer and branched DNA

An energy-transfer cascade is generated from a cationic conjugated polymer (PFP) and negatively charged, Y-shaped DNA labeled with three dyes at its termini (fluorescein (Fl), Tex Red, and Cy5). Multistep fluorescence resonance energy transfer regulates the fluorescence intensities of PFP and the dyes. Different types of logic gates can be operated by observing the emission wavelengths of different dyes with multiplex nucleases as inputs.

Multifunctional nanoarchitectures from DNA-based ABC monomers

The ability to attach different functional moieties to a molecular building block could lead to applications in nanoelectronics, nanophotonics, intelligent sensing and drug delivery. The building unit needs to be both multivalent and anisotropic, and although many anisotropic building blocks have been created, these have not been universally applicable. Recently, DNA has been used to generate various nanostructures or hybrid systems, and as a generic building block for various applications. Here, we report the creation of anisotropic, branched and crosslinkable building blocks (ABC monomers) from which multifunctional nanoarchitectures have been assembled. In particular, we demonstrate a target-driven polymerization process in which polymers are generated only in the presence of a specific DNA molecule, leading to highly sensitive pathogen detection. Using this monomer system, we have also designed a biocompatible nanovector that delivers both drugs and tracers simultaneously. Our approach provides a general yet versatile route towards the creation of a range of multifunctional nanoarchitectures.

Microparticle encoding technologies for high-throughput multiplexed suspension assays

The requirement for analysis of large numbers of biomolecules for drug discovery and clinical diagnostics has driven the development of low-cost, flexible and high-throughput methods for simultaneous detection of multiple molecular targets in a single sample (multiplexed analysis). The technique that seems most likely to satisfy all of these requirements is the multiplexed suspension (bead-based) assay, which offers a number of advantages over alternative approaches such as ELISAs and microarrays. In a bead based assay, different probe molecules are attached to different beads (of a few tens of microns in size), which are then reacted in suspension with the target sample. After reaction, the beads must be identifiable in order to determine the attached probe molecule, and thus each bead must be labelled (encoded) with a unique identifier. A large number of techniques have been proposed for encoding beads. This critical review analyses each technology on the basis of its ability to fulfil the practical requirements of assays, whilst being compatible with low-cost, high-throughput manufacturing processes and high-throughput detection methods. As a result, we identify the most likely candidates to be used for future integrated device development for practical applications.

A cell-free protein-producing gel

Proteins are important biomaterials and are generally produced in living cells. Here, we show a novel DNA hydrogel that is capable of producing functional proteins without any living cells. This protein-producing gel (termed 'the P-gel system' or 'P-gel') consists of genes as part of the gel scaffolding. This is the first time that a hydrogel has been used to produce proteins. The efficiency was about 300 times higher than current, solution-based systems. In terms of volumetric yield, the P-gel produced up to 5 mg ml(-1) of functional proteins. The mechanisms behind the high efficiency and yield include improved gene stability, higher local concentration and a faster enzyme turnover rate due to a closer proximity of genes. We have tested a total of 16 different P-gels and have successfully produced all 16 proteins including membrane and toxic proteins, demonstrating that the P-gel system can serve as a general protein production technology.

Fluorescent DNA nanotags based on a self-assembled DNA tetrahedron

Progress in fluorescence detection and imaging technologies depends on the availability of fluorescent labels with strong light absorption/emission characteristics. We have synthesized intercalator dye arrays on a compact 3-dimensional DNA-tetrahedron nanostructure. The template tolerates the structural distortions introduced by intercalation and allows concentration of multiple fluorophores within a small volume, resulting in brightly fluorescent nanotags with effective extinction coefficients in the order of 10(6) M(-1) cm(-1). Efficient energy transfer from intercalated donor dyes to covalently attached acceptor dyes in the nanotags allows the emission wavelength to be shifted to the red relative to the excitation light, providing wavelength tunability. The compact nature of the supramolecular DNA tetrahedron also provides a protective medium for the fluorophores, leading to improved photostability and enhanced resistance to nuclease digestion, relative to one- or two-dimensional nanotags described previously.

Enzyme enhanced quantitative determination of multiple DNA targets based on capillary electrophoresis

In the current paper, enzyme enhanced simultaneous quantitative determination of multiple DNA targets based on capillary electrophoresis (CE) was described. We used three biotin-modified DNA probes, which reacted with avidin-conjugated horseradish peroxidase (avidin-HRP) conjugate to obtain the HRP labeled probes, to hybridize with three corresponding targets. The resulting mixture containing double-strand DNA (dsDNA)-HRP, excess single-strand DNA (ssDNA)-HRP and remaining avidin-HRP was separated by capillary electrophoresis, and then the system of HRP catalyzing H(2)O(2)/o-aminophenol (OAP) reaction was adopted. The catalytic product was detected with electrochemical detection. With this protocol, the limits of quantification for the hybridization assay of 21-, 39- and 80-mer DNA fragments were of 1.2 x 10(-11), 2.4 x 10(-11) and 3.0 x 10(-11)M, respectively. The multiplex assay also provided good specificity without any cross-reaction.

Sequencing by Cyclic Ligation and Cleavage (CycLiC) directly on a microarray captured template

Next generation sequencing methods that can be applied to both the resequencing of whole genomes and to the selective resequencing of specific parts of genomes are needed. We describe (i) a massively scalable biochemistry, Cyclical Ligation and Cleavage (CycLiC) for contiguous base sequencing and (ii) apply it directly to a template captured on a microarray. CycLiC uses four color-coded DNA/RNA chimeric oligonucleotide libraries (OL) to extend a primer, a base at a time, along a template. The cycles comprise the steps: (i) ligation of OLs, (ii) identification of extended base by label detection, and (iii) cleavage to remove label/terminator and undetermined bases. For proof-of-principle, we show that the method conforms to design and that we can read contiguous bases of sequence correctly from a template captured by hybridization from solution to a microarray probe. The method is amenable to massive scale-up, miniaturization and automation. Implementation on a microarray format offers the potential for both selection and sequencing of a large number of genomic regions on a single platform. Because the method uses commonly available reagents it can be developed further by a community of users.