Ligand-Based Stability Changes in Duplex DNA Measured with a Microscale Electrochemical Platform.

Development of technologies for rapid screening of DNA secondary structure thermal stability and the effects on stability for binding of small molecule drugs is important to the drug discovery process. In this report, we describe the capabilities of an electrochemical, microdevice-based approach for determining the melting temperatures (Tm) of electrode-bound duplex DNA structures. We also highlight new features of the technology that are compatible with array development and adaptation for high-throughput screening. As a foundational study to exhibit device performance and capabilities, melting-curve analyses were performed on 12-mer DNA duplexes in the presence/absence of two binding ligands: diminazene aceturate (DMZ) and proflavine. By measuring electrochemical current as a function of temperature, our measurement platform has the ability to determine the effect of binding ligands on Tm values with high signal-to-noise ratios and good reproducibility. We also demonstrate that heating our three-electrode cell with either an embedded microheater or a thermoelectric module produces similar results. The ΔTm values we report show the stabilizing ability of DMZ and proflavine when bound to duplex DNA structures. These initial proof-of-concept studies highlight the operating characteristics of the microdevice platform and the potential for future application toward other immobilized samples.

The Optoelectronic Nose: Colorimetric and Fluorometric Sensor Arrays.

A comprehensive review on the development and state of the art of colorimetric and fluorometric sensor arrays is presented. Chemical sensing aims to detect subtle changes in the chemical environment by transforming relevant chemical or physical properties of molecular or ionic species (i.e., analytes) into an analytically useful output. Optical arrays based on chemoresponsive colorants (dyes and nanoporous pigments) probe the chemical reactivity of analytes, rather than their physical properties (e.g., mass). The chemical specificity of the olfactory system does not come from specific receptors for specific analytes (e.g., the traditional lock-and-key model of substrate-enzyme interactions), but rather olfaction makes use of pattern recognition of the combined response of several hundred olfactory receptors. In a similar fashion, arrays of chemoresponsive colorants provide high-dimensional data from the color or fluorescence changes of the dyes in these arrays as they are exposed to analytes. This provides chemical sensing with high sensitivity (often down to parts per billion levels), impressive discrimination among very similar analytes, and exquisite fingerprinting of extremely similar mixtures over a wide range of analyte types, in both the gas and liquid phases. Design of both sensor arrays and instrumentation for their analysis are discussed. In addition, the various chemometric and statistical analyses of high-dimensional data (including hierarchical cluster analysis (HCA), principal component analysis (PCA), linear discriminant analysis (LDA), support vector machines (SVMs), and artificial neural networks (ANNs)) are presented and critiqued in reference to their use in chemical sensing. A variety of applications are also discussed, including personal dosimetry of toxic industrial chemical, detection of explosives or accelerants, quality control of foods and beverages, biosensing intracellularly, identification of bacteria and fungi, and detection of cancer and disease biomarkers.

Colorimetric Recognition of Aldehydes and Ketones.

A colorimetric sensor array has been designed for the identification of and discrimination among aldehydes and ketones in vapor phase. Due to rapid chemical reactions between the solid-state sensor elements and gaseous analytes, distinct color difference patterns were produced and digitally imaged for chemometric analysis. The sensor array was developed from classical spot tests using aniline and phenylhydrazine dyes that enable molecular recognition of a wide variety of aliphatic or aromatic aldehydes and ketones, as demonstrated by hierarchical cluster, principal component, and support vector machine analyses. The aldehyde/ketone-specific sensors were further employed for differentiation among and identification of ten liquor samples (whiskies, brandy, vodka) and ethanol controls, showing its potential applications in the beverage industry.

An optoelectronic nose for identification of explosives.

Compact and portable methods for identification of explosives are increasingly needed for both civilian and military applications. A portable optoelectronic nose for the gas-phase identification of explosive materials is described that uses a highly cross-reactive colorimetric sensor array and a handheld scanner. The array probes a wide range of chemical reactivities using 40 chemically responsive colorimetric indicators, including pH sensors, metal-dye salts, redox-sensitive chromogenic compounds, solvatochromic dyes, and other chromogenic indicators. Sixteen separate analytes including common explosives, homemade explosives, and characteristic explosive components were differentiated into fourteen separate classes with a classification error rate of <1%. Portable colorimetric array sensing could represent an important, complementary part of the toolbox used in practical applications of explosives detection and identification.

Differentiation among peroxide explosives with an optoelectronic nose.

Forensic identification of batches of homemade explosives (HME) poses a difficult analytical challenge. Differentiation among peroxide explosives is reported herein using a colorimetric sensor array and handheld scanner with a field-appropriate sampling protocol. Clear discrimination was demonstrated among twelve peroxide samples prepared from different reagents, with a classification accuracy >98%.

Hand-Held Reader for Colorimetric Sensor Arrays.

An inexpensive hand-held device for analysis of colorimetric sensor arrays (CSAs) has been developed. The device makes use of a contact image sensor (CIS), technology commonly used in business card scanners, to rapidly collect low-noise colorimetric data for chemical sensing. The lack of moving parts and insensitivity to vibration allow for lower noise and improved scan rates compared to other digital imaging techniques (e.g., digital cameras, flatbed scanners); signal-to-noise ratios are a factor of 3-10 higher than currently used methods, and scan rates are up to 250 times faster without compromising sensitivity. The device is capable of real-time chemical analysis at scan rates up to 48 Hz.

Identification of accelerants, fuels and post-combustion residues using a colorimetric sensor array.

A linear (1 × 36) colorimetric sensor array has been integrated with a pre-oxidation technique for detection and identification of a variety of fuels and post-combustion residues. The pre-oxidation method permits the conversion of fuel vapor into more detectable species and therefore greatly enhances the sensitivity of the sensor array. The pre-oxidation technique used a packed tube of chromic acid on an oxide support and was optimized in terms of the support and concentration. Excellent batch to batch reproducibility was observed for preparation and use of the disposable pre-oxidation tubes. Twenty automotive fuels including gasolines and diesel from five gasoline retailers were individually identifiable with no confusions or misclassifications in quintuplicate trials. Limits of detection were at sub-ppm concentrations for gasoline and diesel fuels. In addition, burning tests were performed on commonly used fire accelerants, and clear differentiation was achieved among both the fuels themselves and their volatile residues after burning.

Solvatochromic sensor array for the identification of common organic solvents.

A cross-reactive colorimetric sensor array composed of solvatochromic dyes in semi-liquid matrices was used to successfully discriminate among eleven common solvents. The multidimensional array response is attributed to both chemical (i.e., analyte-dye interactions) and physical (i.e., spot blooming and refractive index alteration) changes in the sensor spot.

An array sensor consisting of a single indicator with multiple concentrations and its application in ion discrimination.

Optical sensor arrays typically require a large set of chemically responsive colorants to enhance discrimination capability. Conversely, we have proven that by using multiple concentrations of one indicator, the discrimination of various analytes could be realized.

Identification of pathogenic fungi with an optoelectronic nose.

Human fungal infections have gained recent notoriety following contamination of pharmaceuticals in the compounding process. Such invasive infections are a more serious global problem, especially for immunocompromised patients. While superficial fungal infections are common and generally curable, invasive fungal infections are often life-threatening and much harder to diagnose and treat. Despite the increasing awareness of the situation's severity, currently available fungal diagnostic methods cannot always meet diagnostic needs, especially for invasive fungal infections. Volatile organic compounds produced by fungi provide an alternative diagnostic approach for identification of fungal strains. We report here an optoelectronic nose based on a disposable colorimetric sensor array capable of rapid differentiation and identification of pathogenic fungi based on their metabolic profiles of emitted volatiles. The sensor arrays were tested with 12 human pathogenic fungal strains grown on standard agar medium. Array responses were monitored with an ordinary flatbed scanner. All fungal strains gave unique composite responses within 3 hours and were correctly clustered using hierarchical cluster analysis. A standard jackknifed linear discriminant analysis gave a classification accuracy of 94% for 155 trials. Tensor discriminant analysis, which takes better advantage of the high dimensionality of the sensor array data, gave a classification accuracy of 98.1%. The sensor array is also able to observe metabolic changes in growth patterns upon the addition of fungicides, and this provides a facile screening tool for determining fungicide efficacy for various fungal strains in real time.

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.