DNA detection on ultrahigh-density optical fiber-based nanoarrays

Off-axis microsphere photolithography patterned nanohole array and other structures on an optical fiber tip for glucose sensing

Off-axis microsphere photolithography (MPL) was used as a method to create a plasmonic fiber-based sensor for glucose sensing. Sensitivity of 906 nm per RIU has been achieved. And multiple nanostructures have been successfully created on a fiber tip.

Evaluation of optical detection platforms for multiplexed detection of proteins and the need for point-of-care biosensors for clinical use

This review investigates optical sensor platforms for protein multiplexing, the ability to analyze multiple analytes simultaneously. Multiplexing is becoming increasingly important for clinical needs because disease and therapeutic response often involve the interplay between a variety of complex biological networks encompassing multiple, rather than single, proteins. Multiplexing is generally achieved through one of two routes, either through spatial separation on a surface (different wells or spots) or with the use of unique identifiers/labels (such as spectral separation-different colored dyes, or unique beads-size or color). The strengths and weaknesses of conventional platforms such as immunoassays and new platforms involving protein arrays and lab-on-a-chip technology, including commercially-available devices, are discussed. Three major public health concerns are identified whereby detecting medically-relevant markers using Point-of-Care (POC) multiplex assays could potentially allow for a more efficient diagnosis and treatment of diseases.

Optical sensor arrays for chemical sensing: the optoelectronic nose

A comprehensive review is presented on the development and state of the art of colorimetric and fluorometric sensor arrays. Optical arrays based on chemoresponsive colorants (dyes and nanoporous pigments) probe the chemical reactivity of analytes, rather than their physical properties. This provides a high dimensionality to chemical sensing that permits high sensitivity (often down to ppb levels), impressive discrimination among very similar analytes and exquisite fingerprinting of extremely similar mixtures over a wide range of analyte types, both in the gas and liquid phases.

An enhanced LSPR fiber-optic nanoprobe for ultrasensitive detection of protein biomarkers

A miniaturized, localized surface plasmon resonance (LSPR)-coupled fiber-optic (FO) nanoprobe is reported as a biosensor that is capable of label-free, sensitive detection of a cancer protein biomarker, free prostate specific antigen (f-PSA). The biosensor is based on the LSPR at the reusable dielectric-metallic hybrid interface with a robust, gold nano-disk array at the fiber end facet that is directly fabricated using EBL and metal lift-off process. The f-PSA has been detected with a mouse anti-human PSA monoclonal antibody (mAb) as a specific receptor linked with a self-assembled monolayer at the LSPR-FO facet surfaces. Experimental investigation and data analysis found near field refractive index (RI) sensitivity at ~226 nm/RIU with current LSPR-FO nanoprobe, and demonstrated the lowest limit of detection (LOD) at 100 fg/mL (~3 fM) of f-PSA in PBS solutions. The control experimentation using 5mg/mL bovine serum albumin in PBS and nonspecific surface test shows the excellent specificity and selectivity in the detection of f-PSA in PBS. These results present important progress towards a miniaturized, multifunctional fiber-optic technology that integrates informational communication and sensing function for developing a high performance, label-free, point-of-care (POC) device.

Counting the number of magnesium ions bound to the surface-immobilized thymine oligonucleotides that comprise spherical nucleic acids

Label-free studies carried out under aqueous phase conditions quantify the number of Mg(2+) ions binding to surface-immobilized T40 sequences, the subsequent reordering of DNA on the surface, and the consequences of Mg(2+) binding for DNA-DNA interactions. Second harmonic generation measurements indicate that, within error, 18-20 Mg(2+) ions are bound to the T40 strand at saturation and that the metal-DNA interaction is associated with a near 30% length contraction of the strand. Structural reordering, evaluated using vibrational sum frequency generation, atomic force microscopy, and dynamic light scattering, is attributed to increased charge screening as the Mg(2+) ions bind to the negatively charged DNA, reducing repulsive Coulomb forces between nucleotides and allowing the DNA single strands to collapse or coil upon themselves. The impact of Mg(2+) binding on DNA hybridization and duplex stability is assessed with spherical nucleic acid (SNA) gold nanoparticle conjugates in order to determine an optimal working range of Mg(2+) concentrations for DNA-DNA interactions in the absence of NaCl. The findings are consistent with a charge titration effect in which, in the absence of NaCl, (1) hybridization does not occur at room temperature if an average of 17.5 or less Mg(2+) ions are bound per T40 strand, which is not reached until the bulk Mg(2+) concentration approaches 0.5 mM; (2) hybridization proceeds, albeit with low duplex stability having an average Tm of 31(3)°C, if an average of 17.5-18.0 Mg(2+) ions are bound; and (3) highly stable duplexes having a Tm of 64(2)°C form if 18.5-19.0 Mg(2+) ions are bound, corresponding to saturation of the T40 strand.

Emergent properties of nanosensor arrays: applications for monitoring IgG affinity distributions, weakly affined hypermannosylation, and colony selection for biomanufacturing

It is widely recognized that an array of addressable sensors can be multiplexed for the label-free detection of a library of analytes. However, such arrays have useful properties that emerge from the ensemble, even when monofunctionalized. As examples, we show that an array of nanosensors can estimate the mean and variance of the observed dissociation constant (KD), using three different examples of binding IgG with Protein A as the recognition site, including polyclonal human IgG (KD μ = 19 μM, σ(2) = 1000 mM(2)), murine IgG (KD μ = 4.3 nM, σ(2) = 3 μM(2)), and human IgG from CHO cells (KD μ = 2.5 nM, σ(2) = 0.01 μM(2)). Second, we show that an array of nanosensors can uniquely monitor weakly affined analyte interactions via the increased number of observed interactions. One application involves monitoring the metabolically induced hypermannosylation of human IgG from CHO using PSA-lectin conjugated sensor arrays where temporal glycosylation patterns are measured and compared. Finally, the array of sensors can also spatially map the local production of an analyte from cellular biosynthesis. As an example, we rank productivity of IgG-producing HEK colonies cultured directly on the array of nanosensors itself.

Particles and microfluidics merged: perspectives of highly sensitive diagnostic detection

There is a growing need for diagnostic technologies that provide laboratories with solutions that improve quality, enhance laboratory system productivity, and provide accurate detection of a broad range of infectious diseases and cancers. Recent advances in micro- and nanoscience and engineering, in particular in the areas of particles and microfluidic technologies, have advanced the "lab-on-a-chip" concept towards the development of a new generation of point-of-care diagnostic devices that could significantly enhance test sensitivity and speed. In this review, we will discuss many of the recent advances in microfluidics and particle technologies with an eye towards merging these two technologies for application in medical diagnostics. Although the potential diagnostic applications are virtually unlimited, the most important applications are foreseen in the areas of biomarker research, cancer diagnosis, and detection of infectious microorganisms.

Biosensors as rapid diagnostic tests for tropical diseases

Effective diagnosis of infectious pathogens is essential for disease identification and subsequent adequate treatment, to prevent drug resistance and to adopt suitable public health interventions for the prevention and control of epidemic outbreaks. Particular situations under which medical diagnostics operate in tropical environments make the use of new easy-to-use diagnostic tools the preferred (or even unique) option. These diagnostic tests and devices, usually based on biosensing methods, are being increasingly exploited as promising alternatives to classical, "heavy" lab instrumentation for clinical diagnosis, allowing simple, inexpensive and point-of-care testing. However, in many developing countries the lack of accessibility and affordability for many commercial diagnostic tests remains a major cause of high disease burden in such regions. We present a comprehensive overview about the problems of conventional medical diagnosis of infectious pathologies in tropical regions, while pointing out new methods and analytical tools for in-the-field and decentralized diagnosis of current major infectious tropical diseases. The review includes not only biosensor-based rapid diagnostic tests approved by regulatory entities and already commercialized, but also those at the early stages of research.

Miniaturization and parallelization of biological and chemical assays in microfluidic devices

Microfluidic systems are an attractive solution for the miniaturization of biological and chemical assays. The typical sample volume can be reduced up to 1 million-fold, and a superb level of spatiotemporal control is possible, facilitating highly parallelized assays with drastically increased throughput and reduced cost. In this review, we focus on systems in which multiple reactions are spatially separated by immobilization of reagents on two-dimensional arrays, or by compartmentalization in microfabricated reaction chambers or droplets. These systems have manifold applications, and some, such as next-generation sequencing are already starting to transform biology. This is likely the first step in a biotechnological transformation comparable to that already brought about by the microprocessor in electronics. We discuss both current applications and likely future impacts in areas such as the study of single cells/single organisms and high-throughput screening.

Electric field directed assembly of high-density microbead arrays

We report a method for rapid, electric field directed assembly of high-density protein-conjugated microbead arrays. Photolithography is used to fabricate an array of micron to sub-micron-scale wells in an epoxy-based photoresist on a silicon wafer coated with a thin gold film, which serves as the primary electrode. A thin gasket is used to form a microfluidic chamber between the wafer and a glass coverslip coated with indium-tin oxide, which serves as the counter electrode. Streptavidin-conjugated microbeads suspended in a low conductance buffer are introduced into the chamber and directed into the wells via electrophoresis by applying a series of low voltage electrical pulses across the electrodes. Hundreds of millions of microbeads can be permanently assembled on these arrays in as little as 30 seconds and the process can be monitored in real time using epifluorescence microscopy. The binding of the microbeads to the gold film is robust and occurs through electrochemically induced gold-protein interactions, which allows excess beads to be washed away or recycled. The well and bead sizes are chosen such that only one bead can be captured in each well. Filling efficiencies greater than 99.9% have been demonstrated across wafer-scale arrays with densities as high as 69 million beads per cm(2). Potential applications for this technology include the assembly of DNA arrays for high-throughput genome sequencing and antibody arrays for proteomic studies. Following array assembly, this device may also be used to enhance the concentration-dependent processes of various assays through the accelerated transport of molecules using electric fields.

Single bead-based electrochemical biosensor

A simple, robust, single bead-based electrochemical biosensor was fabricated and characterized. The sensor's working electrode consists of an electrochemically etched platinum wire, with a nominal diameter of 25 microm, hermetically heat-fusion sealed in a pulled glass capillary (micropipette). The sealing process does not require any epoxy or glue. A commercially available, densely functionalized agarose bead was mounted on the tip of the etched platinum wire. The use of a pre-functionalized bead eliminates the tedious and complicated surface functionalization process that is often the bottleneck in the development of electrochemical biosensors. We report on the use of a biotin agarose bead-based, micropipette, electrochemical (Bio-BMP) biosensor to monitor H(2)O(2) concentration and the use of a streptavidin bead-based, micropipette, electrochemical (SA-BMP) biosensor to detect DNA amplicons. The Bio-BMP biosensor's response increased linearly as the H(2)O(2) concentration increased in the range from 1 x 10(-6) to 1.2 x10(-4)M with a detection limit of 5 x 10(-7)M. The SA-BMP was able to detect the amplicons of 1pg DNA template of B. Cereus bacteria, thus providing better detection sensitivity than conventional gel-based electropherograms.