Novel plastic biochips for colorimetric detection of biomolecules

Improvement of Seed-Mediated Growth of Gold Nanoparticle Labels for DNA Membrane-Based Assays

Gold nanoparticles (AuNPs) are popular labels for colorimetric detection of various analytes, involving proteins, nucleic acids, viruses, and whole cells because of their outstanding optical properties, inertness, and modification variability. In this work, we present an improved approach for enhancement of color intensity for DNA membrane microarrays based on seed-mediated growth of AuNP labels. Biotin-labeled DNA is hybridized with capture oligonucleotide probes immobilized on the microarrays. Then biotin is revealed by a streptavidin-AuNP conjugate followed by the detection of AuNPs. Optimization of seed-mediated enlargement of AuNPs by the reduction of tetrachloroauric acid with hydroxylamine made it possible to change the coloring of specific spots on the microarrays from pink to a more contrasting black with minor background staining. Mean size of the resulting AuNPs was four times larger than before the enhancement. Adjusting the pH of HAuCl₄ solution to 3.5 and use of a large excess of hydroxylamine increased the signal/background ratio by several times. The method's applicability was demonstrated for quantification of a short oligonucleotide of 19 bases and full-length TEM-type β-lactamase genes of 860 bp responsible for the development of bacterial resistance against β-lactam antibiotics. Improved protocol for AuNP enlargement may be further transferred to any other membrane-based assays of nucleic acids with both instrumental and visual colorimetric detection.

Information Visualisation for Antibiotic Detection Biochip Design and Testing

Biochips are engineered substrates that have different spots that change colour according to biochemical reactions. These spots can be read together to detect different analytes (such as different types of antibiotic, pathogens, or biological agents). While some chips are designed so that each spot on its own can detect a particular analyte, chip designs that use a combination of spots to detect different analytes can be more efficient and detect a larger number of analytes with a smaller number of spots. These types of chip can, however, be more difficult to design, as an efficient and effective combination of biosensors needs to be selected for the chip. These need to be able to differentiate between a range of different analytes so the values can be combined in a way that demonstrates the confidence that a particular analyte is present or not. The study described in this paper examines the potential for information visualisation to support the process of designing and reading biochips by developing and evaluating applications that allow biologists to analyse the results of experiments aimed at detecting candidate bio-sensors (to be used as biochip spots) and examining how biosensors can combine to identify different analytes. Our results demonstrate the potential of information visualisation and machine learning techniques to improve the design of biochips.

A WiFi scanner in conjunction with disposable multiplex paper assay for the quantitation of disease markers in blood plasma

Herein we report a quantitative, multiplex assay for disease markers in plasma based on an integrated setup of a portable scanner and a disposable paper-based analytical device (PAD). The quantitative analysis relies on the digital colorimetric reading of the three-layer PAD with 30 assay sites for performing respective chromogenic reactions for plasma uric acid, glucose, and triglyceride, which are considered as important risk factors for cardiovascular diseases. A portable scanner with WiFi transmission capability was used to produce high-quality color images of the PADs and wirelessly transfer them to a smartphone or other mobile devices for data processing. The concentrations of biomarkers in both standard solutions and plasma samples can be directly obtained using a custom-designed smartphone app that is also capable of constructing calibration curves. The detection limits of uric acid, glucose, and triglyceride were determined to be 0.50 mg/dL, 0.84 mmol/L, and 14 mg/dL, respectively, which are below the normal limits and adequate for clinical validation. Owing to the distinct advantages-simple, portable, and cost-effective-this mobile assay protocol can be used for point-of-care (POC) settings or resource-limited situations, and potentially for the diagnosis and prevention of infectious diseases.

Flow-through microfluidic immunosensors with refractive index-matched silica monoliths as volumetric optical detection elements

A sensitive and rapid absorbance based immunosensor that utilizes ex situ functionalized porous silica monoliths as volumetric optical detection elements is demonstrated in this study. The porous monolith structure facilitates high capture probe density and short diffusion length scales, enabling sensitive and rapid assays. Silica monoliths, synthesized and functionalized with immunocapture probes off-chip before integration into a sealed thermoplastic microfluidic device, serve to capture target antigens during perfusion through the porous structure. Gold nanoparticle immunoconjugates are combined with silver enhancement to create microscale silver clusters, followed by perfusion of an aqueous sucrose solution to limit light scattering and enhance optical signal. Using this approach, detection limits as low as 1 ng/mL are achieved for a sandwich assay, with a dynamic range of at least 4 logs. The results confirm that the combination of on-chip index matching with functionalized porous silica monoliths can enables simple and practical flow-through immunoassays for the sensitive and rapid detection of target antigens.

Novel functionalities of hybrid paper-polymer centrifugal devices for assay performance enhancement

The presented work demonstrates novel functionalities of hybrid paper-polymer centrifugal devices for assay performance enhancement that leverage the advantages of both paper-based and centrifugal microfluidic platforms. The fluid flow is manipulated by balancing the capillary force of paper inserts with the centrifugal force generated by disc rotation to enhance the signal of a colorimetric lateral flow immunoassay for pathogenic E. coli. Low-cost centrifugation for pre-concentration of bacteria was demonstrated by sample sedimentation at high rotational speeds before supernatant removal by a paper insert via capillary force after deceleration. The live bacteria capture efficiency of the device was similar to a commercial centrifuge. This pre-concentrated sample when combined with gold nanoparticle immunoconjugate probes resulted in a detection limit that is 10× lower than a non-concentrated sample for a lateral flow immunoassay. Signal enhancement was also demonstrated through rotational speed variation to prevent the flow for on-device incubation and to reduce the flow rate, thus increasing the sample residence time for the improved capture of gold nanoparticle-bacteria complexes in an integrated paper microfluidic assay. Finally, multiple sequential steps including sample pre-concentration, filtration, incubation, target capture by an integrated paper microfluidic assay, silver enhancement and quenching, and index matching were completed within a single device. The detection limit was 105 colony forming units per ml, a 100× improvement over a similar paper-based lateral flow assay. The techniques utilize the advantages of paper-based microfluidic devices, while facilitating additional functionalities with a centrifugal microfluidic platform for detection performance enhancement in a low-cost, automated platform amenable to point-of-care environments.

Analytical Protein Microarrays: Advancements Towards Clinical Applications

Protein microarrays represent a powerful technology with the potential to serve as tools for the detection of a broad range of analytes in numerous applications such as diagnostics, drug development, food safety, and environmental monitoring. Key features of analytical protein microarrays include high throughput and relatively low costs due to minimal reagent consumption, multiplexing, fast kinetics and hence measurements, and the possibility of functional integration. So far, especially fundamental studies in molecular and cell biology have been conducted using protein microarrays, while the potential for clinical, notably point-of-care applications is not yet fully utilized. The question arises what features have to be implemented and what improvements have to be made in order to fully exploit the technology. In the past we have identified various obstacles that have to be overcome in order to promote protein microarray technology in the diagnostic field. Issues that need significant improvement to make the technology more attractive for the diagnostic market are for instance: too low sensitivity and deficiency in reproducibility, inadequate analysis time, lack of high-quality antibodies and validated reagents, lack of automation and portable instruments, and cost of instruments necessary for chip production and read-out. The scope of the paper at hand is to review approaches to solve these problems.

Optical detection enhancement in porous volumetric microfluidic capture elements using refractive index matching fluids

Porous volumetric capture elements in microfluidic sensors are advantageous compared to planar capture surfaces due to higher reaction site density and decreased diffusion lengths that can reduce detection limits and total assay time. However a mismatch in refractive indices between the capture matrix and fluid within the porous interstices results in scattering of incident, reflected, or emitted light, significantly reducing the signal for optical detection. Here we demonstrate that perfusion of an index-matching fluid within a porous matrix minimizes scattering, thus enhancing optical signal by enabling the entire capture element volume to be probed. Signal enhancement is demonstrated for both fluorescence and absorbance detection, using porous polymer monoliths in a silica capillary and packed beds of glass beads within thermoplastic microchannels, respectively. Fluorescence signal was improved by a factor of 3.5× when measuring emission from a fluorescent compound attached directly to the polymer monolith, and up to 2.6× for a rapid 10 min direct immunoassay. When combining index matching with a silver enhancement step, a detection limit of 0.1 ng mL(-1) human IgG and a 5 log dynamic range was achieved. The demonstrated technique provides a simple method for enhancing optical sensitivity for a wide range of assays, enabling the full benefits of porous detection elements in miniaturized analytical systems to be realized.

Emerging technologies for biomedical analysis

Options for biomedical analysis continue to evolve from many fields of study, employing diverse detection and quantification methods. New technologies in this arena focus on improving the sensitivity of analysis and the speed of testing, as well as producing systems at low cost which can be used on site as a point-of-care device for telemedicine applications. In this article, the most important original experimental platforms as well as current commercial approaches to biomedical analysis are critically chosen and reviewed, covering January 2010 to January 2014. While literature is quite broad and numerous, there is clear emphasis on biological recognition and imaging for the most impactful works. The analytical approaches are discussed in terms of their utility in diagnostics and biomedical testing.

Binary DNA hairpin-based colorimetric biochip for simultaneous detection of Pb2+ and Hg2+ in real-world samples

A novel microarray-format colorimetric biochip was constructed for simultaneously detecting the trace amounts of Pb²⁺ and Hg²⁺ in various real-world samples.

DNA molecular beacon-based plastic biochip: a versatile and sensitive scanometric detection platform

In this paper, we report a novel DNA molecular beacon (MB)-based plastic biochip platform for scanometric detection of a range of analytical targets. Hairpin DNA strands, which are dually modified with amino and biotin groups at their two ends are immobilized on a disposable plastic (polycarbonate) substrate as recognition element and gold nanoparticle-assisted silver-staining as signal reading protocol. Initially, the immobilized DNA probes are in their folded forms; upon target binding the hairpin secondary structure of the probe strand is "forced" open (i.e., converted to the unfolded state). Nanogold-streptavidin conjugates can then bind the terminal biotin groups and promote the deposition of rather large silver particles which can be either directly visualized or quantified with a standard flatbed scanner. We demonstrate that with properly designed probe sequences and optimized preparation conditions, a range of molecular targets, such as DNA strands, proteins (thrombin) and heavy metal ions (Hg(2+)), can be detected with high sensitivity and excellent selectivity. The detection can be done in both standard physiological buffers and real world samples. This constitutes a platform technology for performing rapid, sensitive, cost-effective, and point-of-care (POC) chemical analysis and medical diagnosis.

Transmissive Nanohole Arrays for Massively-Parallel Optical Biosensing

A high-throughput optical biosensing technique is proposed and demonstrated. This hybrid technique combines optical transmission of nanoholes with colorimetric silver staining. The size and spacing of the nanoholes are chosen so that individual nanoholes can be independently resolved in massive parallel using an ordinary transmission optical microscope, and, in place of determining a spectral shift, the brightness of each nanohole is recorded to greatly simplify the readout. Each nanohole then acts as an independent sensor, and the blocking of nanohole optical transmission by enzymatic silver staining defines the specific detection of a biological agent. Nearly 10000 nanoholes can be simultaneously monitored under the field of view of a typical microscope. As an initial proof of concept, biotinylated lysozyme (biotin-HEL) was used as a model analyte, giving a detection limit as low as 0.1 ng/mL.

Aptamer-functionalized silver nanoparticles for scanometric detection of platelet-derived growth factor-BB

In this work, we reported a scanometric assay system based on the aptamer-functionalized silver nanoparticles (apt-AgNPs) for detection of platelet-derived growth factor-BB (PDGF-BB) protein. The aptamer and ssDNA were bound with silver nanoparticles by self-assembly of sulfhydryl group at 5' end to form the apt-AgNPs probe. The apt-AgNPs probe can catalyze the reduction of metallic ions in color agent to generate metal deposition that can be captured both by human eyes and a flatbed scanner. Two different color agents, silver enhancer solution and color agent 1 (10 mM HAuCl4+2 mM hydroquinone) were used to develop silver and gold shell on the surface of AgNPs separately. The results demonstrated that the formation of Ag core-Au shell structure had some advantages especially in the low concentrations. The apt-AgNPs probe coupled with color agent 1 showed remarkable superiority in both sensitivity and detection limit compared to the apt-AuNPs system. The apt-AgNPs system also produced a wider linear range from 1.56 ng mL(-1) to 100 ng mL(-1) for PDGF-BB with the detection limit lower than 1.56 ng mL(-1). The present strategy was applied to the determination of PDGF-BB in 10% serum, and the results showed that it had good specificity in complex biological media.