Combinatorial decoding: an approach for universal DNA array fabrication

Sensors that Learn: The Evolution from Taste Fingerprints to Patterns of Early Disease Detection

The McDevitt group has sustained efforts to develop a programmable sensing platform that offers advanced, multiplexed/multiclass chem-/bio-detection capabilities. This scalable chip-based platform has been optimized to service real-world biological specimens and validated for analytical performance. Fashioned as a sensor that learns, the platform can host new content for the application at hand. Identification of biomarker-based fingerprints from complex mixtures has a direct linkage to e-nose and e-tongue research. Recently, we have moved to the point of big data acquisition alongside the linkage to machine learning and artificial intelligence. Here, exciting opportunities are afforded by multiparameter sensing that mimics the sense of taste, overcoming the limitations of salty, sweet, sour, bitter, and glutamate sensing and moving into fingerprints of health and wellness. This article summarizes developments related to the electronic taste chip system evolving into a platform that digitizes biology and affords clinical decision support tools. A dynamic body of literature and key review articles that have contributed to the shaping of these activities are also highlighted. This fully integrated sensor promises more rapid transition of biomarker panels into wide-spread clinical practice yielding valuable new insights into health diagnostics, benefiting early disease detection.

Charge Transport in 2D DNA Tunnel Junction Diodes

Recently, deoxyribonucleic acid (DNA) is studied for electronics due to its intrinsic benefits such as its natural plenitude, biodegradability, biofunctionality, and low-cost. However, its applications are limited to passive components because of inherent insulating properties. In this report, a metal-insulator-metal tunnel diode with Au/DNA/NiO_x junctions is presented. Through the self-aligning process of DNA molecules, a 2D DNA nanosheet is synthesized and used as a tunneling barrier, and semitransparent conducting oxide (NiO_x ) is applied as a top electrode for resolving metal penetration issues. This molecular device successfully operates as a nonresonant tunneling diode, and temperature-variable current-voltage analysis proves that Fowler-Nordheim tunneling is a dominant conduction mechanism at the junctions. DNA-based tunneling devices appear to be promising prototypes for nanoelectronics using biomolecules.

Surface Functionalization for Immobilization of Probes on Microarrays

The microarray technology has been a tremendous advance in molecular-based testing methods for biochemical and biomedical applications. As a result, the immobilization techniques and grafting chemistries of biochemical molecules have experienced great progress. The particularities of the grafting techniques adapted to the microarray development will be presented here.

Particle-Based Microarrays of Oligonucleotides and Oligopeptides

In this review, we describe different methods of microarray fabrication based on the use of micro-particles/-beads and point out future tendencies in the development of particle-based arrays. First, we consider oligonucleotide bead arrays, where each bead is a carrier of one specific sequence of oligonucleotides. This bead-based array approach, appearing in the late 1990s, enabled high-throughput oligonucleotide analysis and had a large impact on genome research. Furthermore, we consider particle-based peptide array fabrication using combinatorial chemistry. In this approach, particles can directly participate in both the synthesis and the transfer of synthesized combinatorial molecules to a substrate. Subsequently, we describe in more detail the synthesis of peptide arrays with amino acid polymer particles, which imbed the amino acids inside their polymer matrix. By heating these particles, the polymer matrix is transformed into a highly viscous gel, and thereby, imbedded monomers are allowed to participate in the coupling reaction. Finally, we focus on combinatorial laser fusing of particles for the synthesis of high-density peptide arrays. This method combines the advantages of particles and combinatorial lithographic approaches.

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.

Synthesis and application of highly reactive amino linkers for functional oligonucleotides

Oligonucleotides are functionalized by conjugation with a variety of molecules, and aliphatic amino linkers have been frequently used as a tether for their modifications. This unit describes the syntheses and applications of novel amino linkers having a carbamate structure. Two major chemical properties of the primary amine are induced by the neighboring effect of the carbamate group, which are found to be optimum in an aminoethyl carbamate structure. First, the hydrophobic monomethoxytrityl group can be rapidly removed from the aminoethyl carbamate under very mild acidic conditions, while the deprotection is not completed in standard aliphatic amines even under high acid concentration. This significant feature enables the convenient purification of amino-modified oligonucleotides by using the hydrophobic interaction of the monomethoxytrityl group with a reverse-phase resin. Second, the introduction of the carbamate linkage reduces the pK(a) value of the neighboring primary amine, resulting in an increase in the conjugation yields with various functional molecules, such as those having active esters. The novel amino linkers that have an aminoethyl carbamate linkage indicate potent activity and are applicable for the preparation of various functional oligonucleotides.

Optical tweezers directed one-bead one-sequence synthesis of oligonucleotides

An optical tweezers directed parallel DNA oligonucleotide synthesis methodology is described in which controlled pore glass (CPG) beads act as solid substrates in a two-stream microfluidic reactor. The reactor contains two parallel sets of physical confinement features that retain beads in the reagent stream for synthetic reaction but allow the beads to be optically trapped and transferred between the reagent and the inert streams for sequence programming. As a demonstration, we synthesized oligonucleotides of target sequence 25-nt, one deletion and one substitution using dimethoxytrityl (DMT) nucleoside phosphoramidite chemistry. In detecting single-nucleotide mismatches, fluorescence in situ hybridization of the bead-conjugated probes showed high specificity and signal-to-noise ratios. These preliminary results suggest further possibilities of creating a novel type of versatile, sensitive and multifunctional reconfigurable one-bead one-compound (OBOC) bead array.

Lanthanide-containing polymer microspheres by multiple-stage dispersion polymerization for highly multiplexed bioassays

We describe the synthesis and characterization of metal-encoded polystyrene microspheres by multiple-stage dispersion polymerization with diameters on the order of 2 mum and a very narrow size distribution. Different lanthanides were loaded into these microspheres through the addition of a mixture of lanthanide salts (LnCl(3)) and excess acrylic acid (AA) or acetoacetylethyl methacrylate (AAEM) dissolved in ethanol to the reaction after about 10% conversion of styrene, that is, well after the particle nucleation stage was complete. Individual microspheres contain ca. 10(6)-10(8) chelated lanthanide ions, of either a single element or a mixture of elements. These microspheres were characterized one-by-one utilizing a novel mass cytometer with an inductively coupled plasma (ICP) ionization source and time-of-flight (TOF) mass spectrometry detection. Microspheres containing a range of different metals at different levels of concentration were synthesized to meet the requirements of binary encoding and enumeration encoding protocols. With four different metals at five levels of concentration, we could achieve a variability of 624, and the strategy we report should allow one to obtain much larger variability. To demonstrate the usefulness of element-encoded beads for highly multiplexed immunoassays, we carried out a proof-of-principle model bioassay involving conjugation of mouse IgG to the surface of La and Tm containing particles and its detection by an antimouse IgG bearing a metal-chelating polymer with Pr.

Bio-Functional, Lanthanide-Labeled Polymer Particles by Seeded Emulsion Polymerization and their Characterization by Novel ICP-MS Detection

We present the synthesis and characterization of monodisperse, sub-micron poly(styrene) (PS) particles loaded with up to and including 10(7) lanthanide (Ln) ions per particle. These particles have been synthesized by seeded emulsion polymerization with a mixture of monomer and a pre-formed Ln complex, and analyzed on a particle-by-particle basis by a unique inductively coupled plasma mass cytometer. Seed particles were prepared by surfactant-free emulsion polymerization (SFEP) to obtain large particle sizes in aqueous media. Extensive surface acid functionality was introduced using the acid-functional initiator ACVA, either during seed latex synthesis or in the second stage of polymerization. The loading of particles with three different Ln ions (Eu, Tb, and Ho) has proven to be close to 100 % efficient on an individual and combined basis. Covalent attachment of metal-tagged peptides and proteins such as Neutravidin to the particle surface was shown to be successful and the number of bound species can be readily determined. We believe these particles can serve as precursors for multiplexed, bead-based bio-assays utilizing mass cytometric detection.

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.

Microbeads on microposts: an inverted architecture for bead microarrays

The rapid development of genomics and proteomics requires accelerated improvement of the microarrays density, multiplexing, readout capabilities and cost-effectiveness. The bead arrays are increasingly attractive because of their self-assembly-based fabrication, which alleviates many problems of top-down microfabrication. Here we present a simple, reliable, robust and modular technique for the fabrication of bead microarrays, which combines the directed assembling of beads in microstructures and PDMS-based replica molding. The beads are first self-assembled in pyramidal microwells fabricated by anisotropic etching of silicon substrates, then transferred on the apex of PDMS pyramids that replicate the silicon microstructures. The arrays are chemically and biochemically robust; they are spatially addressable and have the potential for being informationally addressable; and they appear to offer better readout capabilities than the classical microarrays.

Automated analytical microarrays: a critical review

Microarrays provide a powerful analytical tool for the simultaneous detection of multiple analytes in a single experiment. The specific affinity reaction of nucleic acids (hybridization) and antibodies towards antigens is the most common bioanalytical method for generating multiplexed quantitative results. Nucleic acid-based analysis is restricted to the detection of cells and viruses. Antibodies are more universal biomolecular receptors that selectively bind small molecules such as pesticides, small toxins, and pharmaceuticals and to biopolymers (e.g. toxins, allergens) and complex biological structures like bacterial cells and viruses. By producing an appropriate antibody, the corresponding antigenic analyte can be detected on a multiplexed immunoanalytical microarray. Food and water analysis along with clinical diagnostics constitute potential application fields for multiplexed analysis. Diverse fluorescence, chemiluminescence, electrochemical, and label-free microarray readout systems have been developed in the last decade. Some of them are constructed as flow-through microarrays by combination with a fluidic system. Microarrays have the potential to become widely accepted as a system for analytical applications, provided that robust and validated results on fully automated platforms are successfully generated. This review gives an overview of the current research on microarrays with the focus on automated systems and quantitative multiplexed applications.

Multiplexed spectroscopic detections

This review describes various platforms used for multiplexed spectroscopic analysis. We highlight the use of different types of spectroscopy for multiplexed detections, including Raman spectroscopy, surface-enhanced Raman spectroscopy, surface plasmon resonance, and fluorescence. This review also explores the use of cross-reactive sensors in combination with pattern-recognition algorithms to monitor multiple analytes in aqueous and vapor matrices. It also discusses applications of these techniques, paying special attention to their use in the detection of biologically relevant analytes.

Novel amino linkers enabling efficient labeling and convenient purification of amino-modified oligonucleotides

We developed new amino linker reagents for an oligonucleotide (ONT) terminus. These reagents consist of an aminoethyl carbamate main linkage and a side-chain residue, which was a naphthylmethoxymethyl, methoxymethyl, or methyl group or a hydrogen atom. The primary amine was protected with a monomethoxytrityl (MMT) group. The chemical properties of ONTs containing these amino-modifications were investigated. The MMT group of these amino-modifications could be quite rapidly removed from the amine under very mild acidic conditions, which are not strong enough for the deprotection of a conventional aliphatic amine. This significant feature enabled the amino-modified ONTs to be conveniently purified with a reverse phase column. Furthermore, the amino-modifications efficiently reacted to active esters, as compared with other amino-modifications. We also found that the pK(a) values of the amino-modifications were lower than that of the aliphatic amine. All of the experimental results showed that these chemical properties are closely related to their structures. We report here the chemical properties and the availability of the new amino linker reagents.

Preparation of carbodiimide-terminated dithiolane self-assembly monolayers as a new DNA-immobilization method

A carbodiimide derivative having a dithiolane part at its terminus was designed and synthesized for use to construct carbodiimide-coated self-assembly monolayers (SAMs) on a gold surface with 6-mercaptohexanol (6MH). When treated with poly(dT), poly(dA), or poly(dA)poly(dT), only poly(dT) was immobilized on the surface of the SAMs through a specific reaction of the free imino moiety of thymine (T) with the carbodiimide moiety. The carbodiimide-covered SAM treated with probe DNA was tested in hybridization with sample DNA. Its hybridization efficiency was estimated by ferrocenylnaphthalene diimide (FND), described previously and the result revealed that the carbodiimide-covered SAM electrode can immobilize a DNA probe through the thymine moiety not involved in base pairing. The resulting electrode was capable of hybridizing with the target DNA, as proven by an increased current response of FND.

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.

RhI-Catalyzed Bimolecular Cyclization between Two Different 1,5-Bisallenes: A Combinatorial One-Step Approach to Heterosteroids and Mechanistic Implications

In this paper, a bimolecular-cyclization reaction between two different bis(allene)s with at least one heteroatom as the tether under the catalysis of trans-[RhCl(CO)(PPh3)2] is described. This protocol provides an efficient entry to different heterocyclic 18,19-norsteroid-like scaffolds. The tricyclic product was formed highly selectively from the cyclization reaction of bis(2,3-butadienyl)sulfide with dimethyl 2-bis(2',3'-butadienyl)malonate, which sheds light on the mechanism involving the metalla-[4.3.0]-bicyclic intermediate formed by the cyclometallation of the terminal and the internal C=C bonds of each of the two allene moieties in 2-bis(2',3'-butadienyl)malonate.

Design of fluorescent materials for chemical sensing

There is an enormous demand for chemical sensors for many areas and disciplines. High sensitivity and ease of operation are two main issues for sensor development. Fluorescence techniques can easily fulfill these requirements and therefore fluorescent-based sensors appear as one of the most promising candidates for chemical sensing. However, the development of sensors is not trivial; material science, molecular recognition and device implementation are some of the aspects that play a role in the design of sensors. The development of fluorescent sensing materials is increasingly captivating the attention of the scientists because its implementation as a truly sensory system is straightforward. This critical review shows the use of polymers, sol-gels, mesoporous materials, surfactant aggregates, quantum dots, and glass or gold surfaces, combined with different chemical approaches for the development of fluorescent sensing materials. Representative examples have been selected and they are commented here.

Fiber-optic microarray for simultaneous detection of multiple harmful algal bloom species

Harmful algal blooms (HABs) are a serious threat to coastal resources, causing a variety of impacts on public health, regional economies, and ecosystems. Plankton analysis is a valuable component of many HAB monitoring and research programs, but the diversity of plankton poses a problem in discriminating toxic from nontoxic species using conventional detection methods. Here we describe a sensitive and specific sandwich hybridization assay that combines fiber-optic microarrays with oligonucleotide probes to detect and enumerate the HAB species Alexandrium fundyense, Alexandrium ostenfeldii, and Pseudo-nitzschia australis. Microarrays were prepared by loading oligonucleotide probe-coupled microspheres (diameter, 3 mum) onto the distal ends of chemically etched imaging fiber bundles. Hybridization of target rRNA from HAB cells to immobilized probes on the microspheres was visualized using Cy3-labeled secondary probes in a sandwich-type assay format. We applied these microarrays to the detection and enumeration of HAB cells in both cultured and field samples. Our study demonstrated a detection limit of approximately 5 cells for all three target organisms within 45 min, without a separate amplification step, in both sample types. We also developed a multiplexed microarray to detect the three HAB species simultaneously, which successfully detected the target organisms, alone and in combination, without cross-reactivity. Our study suggests that fiber-optic microarrays can be used for rapid and sensitive detection and potential enumeration of HAB species in the environment.

Fiber Optic Array Biosensors

Optical fiber arrays provide a powerful substrate for creating high-density sensing systems that can address a variety of biological problems. The fiber substrate can be used to create femtoliter wells that can be loaded with individual beads to create high-density arrays for multiplexed screening and analysis. In addition, living cells can be loaded into the arrays, and their individual responses monitored over long time periods, enabling functional screening of biologically active compounds. Adherent cells can be attached to the fiber substrate to provide a rapid method for observing cell migration and for screening anti-migratory compounds. Finally, individual enzyme molecules can be loaded into the array wells enabling single molecule detection via enzyme-catalyzed signal amplification.

High-Throughput Physical Organic Chemistry Hammett Parameter Evaluation

High-throughput analysis techniques were developed to allow the rapid assessment of a range of Hammett parameters utilizing positive electrospray mass spectrometry (ESI+ -MS) as the sole quantitative tool, with the core of the approach being a so-called "analytical construct". Hammett substituent parameters were determined for a range of meta- and para-substituted anilines by high-throughput (HT) assessment of relative reaction rates for competitive amide bond formation reaction with up to five parameters determined in a single pot reaction. Sensitivity of the reaction to substituents' effects (materialized by Hammett's rho parameter) was determined in the first instance, with HT Hammett's sigma substituent parameter assessment then carried out successfully for over 30 anilines, with excellent correlation observed between the HT ESI+ -MS method of determination and literature values.

Optical fiber-based sensors: application to chemical biology

Optical fibers have been used to develop sensors based on nucleic acids and cells. Sensors employing DNA probes have been developed for various genomics applications and microbial pathogen detection. Live cell-based sensors have enabled the monitoring of environmental toxins, and have been used for fundamental studies on populations of individual cells. Both single-core optical fiber sensors and optical fiber sensor arrays have been used for sensing based on nucleic acids and live cells.

Development of a Microfluidic Platform with an Optical Imaging Microarray Capable of Attomolar Target DNA Detection

In this paper, DNA hybridization in a microfluidic manifold is performed using fluorescence detection on a fiber-optic microarray. The microfluidic device integrates optics, sample transport, and fluidic interconnects on a single platform. A high-density optical imaging fiber array containing oligonucleotide-labeled microspheres was developed. DNA hybridization was observed at concentrations as low as 10 aM with response times of less than 15 min at a flow rate of 1 microL/min using 50 microL of target DNA samples. The fast response times coupled with the low sample volumes and the use of a high-density, fiber-optic microarray format make this method highly advantageous. This paper describes the initial development, optimization, and integration of the microfluidic platform with imaging fiber arrays.

Detection ofSalmonellaspp. Using Microsphere-Based, Fiber-Optic DNA Microarrays

Salmonella spp. are one of the most problematic food pathogens in public health, as they are responsible for food poisoning associated with contamination of meat, poultry, and eggs. Thus, rapid and sensitive detection of Salmonella spp. is required to ensure food safety. In this study, a fiber-optic DNA microarray using microsphere-immobilized oligonucleotide probes specific for the Salmonella invA and spvB genes was developed for detection of Salmonella spp. Microarrays were prepared by randomly distributing DNA probe-functionalized microspheres (3.1-microm diameter) into microwells created by etching optical fiber bundles. Hybridization of the probe-functionalized microspheres to target DNA from Salmonella was performed and visualized using Cy3-labeled secondary probes in a sandwich-type assay format. In this study, 10(3)-10(4) cfu/mL of the target organism could be detected after 1-h hybridization without any additional amplification. The DNA microarray showed no cross-reactivity with other common food pathogens, including E. coli and Y. enterocolitica, and could even detect Salmonella spp. from cocktails of bacterial strains with only moderate loss of sensitivity due to nonspecific binding. This work suggests that fiber-optic DNA microarrays can be used for rapid and sensitive detection of Salmonella spp. Since fiber-optic microarrays can be prepared with different probes, this approach could also enable the simultaneous detection of multiple food pathogens.