Microchip capillary gel electrophoresis with electrochemical detection for the analysis of known SNPs.

A novel microchip-based single nucleotide polymorphism (SNP) screening system has been developed. The system utilizes capillary gel electrophoresis (CGE) with electrochemical detection in a chip-based format to accomplish rapid scoring of a mock SNP site. The accuracy of the thermostable polymerase and the advantages of coupling this technique to microfluidics are demonstrated. An electrochemically labeled chain terminator is used in the single base extension (SBE) reaction, in which the terminator is incorporated only when its Watson-Crick complementary base is present at the mock SNP site. The resulting electrochemically active extension product is subsequently separated from any excess terminator by CGE and detected by sinusoidal voltammetry. Although no attempts at optimization have been made, the analysis is performed in less than 4 min. The technique presented could lead to a fast, simple, and cost effective SNP scoring system.

Rapid fabrication of a poly(dimethylsiloxane) microfluidic capillary gel electrophoresis system utilizing high precision machining.

In this work, we demonstrate a rapid protocol to address one of the major barriers that exists in the fabrication of chip devices, creating the micron-sized structures in the substrate material. This approach makes it possible to design, produce, and fabricate a microfluidic system with channel features >10 microm in poly(dimethylsiloxane)(PDMS) in under 8 hours utilizing instrumentation common to most machine shops. The procedure involves the creation of a master template with negative features, using high precision machining. This master is then employed to create an acrylic mold that is used in the final fabrication step to cast channel structures into the PDMS substrate. The performance of the microfluidic system prepared using this fabrication procedure is evaluated by constructing a miniaturized capillary gel electrophoresis (micro-CGE) system for the analysis of DNA fragments. Agarose is utilized as the sieving medium in the micro-CGE device and is shown to give reproducible (RSD (n= 34) approximately 5.0%) results for about 34 individual separations without replenishing the gel. To demonstrate the functionality of the micro-CGE device, a DNA restriction ladder (spanning 26-700 base pairs) and DNA fragments generated by PCR are separated and detected with laser-induced fluorescence (LIF). The microchip is shown to achieve a separation efficiency of 2.53 x 10(5) plates m(-1).

Independently-addressable micron-sized biosensor elements.

With the continuing development of micro-total analysis systems and sensitive biosensing technologies, it is often desirable to immobilize biomolecules onto a surface in a small well-defined area. A novel method was developed to electrochemically attach DNA probes to micron-sized regions of a gold surface using biotin-LC-hydrazide (BH). Previously, we have found that the radical produced during the oxidation of BH will attach to a wide variety of electroactive surfaces. An array of micron-sized gold band electrodes (75 microm wide) was fabricated onto glass microscope slides and BH was deposited onto each electrode through the application of an oxidizing potential. Subsequent attachment of avidin to the biotinylated surface created the 'molecular sandwich' architecture necessary for further immobilization of biotinylated biomolecules to the surface. In this work, we utilized biotinylated DNA probes of varying sequence to illustrate the specificity of the attachment scheme. The immobilization of avidin, DNA probe, and hybridization of DNA target is visualized with fluorescence tags and the spatially selective attachment and hybridization of unique DNA sequences is demonstrated.

A single base extension technique for the analysis of known mutations utilizing capillary gel electrophoreisis with electrochemical detection.

A novel single nucleotide polymorphism (SNP) detection system is described in which the accuracy of DNA polymerase and advantages of electrochemical detection are demonstrated. A model SNP system is presented to illustrate the potential advantages in coupling the single base extension (SBE) technique to capillary gel electrophoresis (CGE) with electrochemical detection. An electrochemically labeled primer, with a ferrocene acetate covalently attached to its 5' end, is used in the extension reaction. When the Watson-Crick complementary ddNTP is added to the SBE reaction, the primer is extended by a single nucleotide. The reaction mixture is subsequently separated by CGE, and the ferrocene-tagged fragments are detected at the separation anode with sinusoidal voltammetry. This work demonstrates the first single base resolution separation of DNA coupled with electrochemical detection. The unextended primer (20-mer) and the 21-mer extension product are separated with a resolution of 0.8.

Microchip capillary electrophoresis coupled to sinusoidal voltammetry for the detection of native carbohydrates.

The development of a microchip electrophoresis system involving integrated frequency based electrochemical detection is described. The use of poly(dimethylsiloxane) (PDMS) as the channel substrate greatly simplifies the fabrication process while decreasing cost and time consumption. Characterization of this system is accomplished through the detection of native carbohydrates at planar copper electrodes. Various photolithographic techniques are explored in the optimization of electrode area. Separation efficiency of 1 x 10(5) theoretical plates per meter is demonstrated. Sinusoidal voltammetry utilizes information in the frequency domain to achieve sensitive detection through either of two approaches, maximization of signal or minimization of noise. Mass detection limits (S/N = 3) of less than 200 amol have been accomplished for glucose and sucrose. Sinusoidal voltammetry also facilitated the selective isolation of an analyte signal from a pair of chromatographically unresolved species through the use of phase discrimination.

A microchip electrophoresis device with integrated electrochemical detection: a direct comparison of constant potential amperometry and sinusoidal voltammetry.

A microchip electrophoresis system with integrated electrochemical detection is described in this work. The hybrid device utilizes poly(dimethylsiloxane) as the electrophoresis channel substrate and a planar gold electrode lithographically fabricated onto a glass slide for electrochemical detection. The system is characterized by the separation and detection of various neurotransmitters. The gold working electrode is placed just inside the separation channel without adverse effects on the detection sensitivity, due to the electrical decoupling of the detection and electrophoresis systems. The close proximity of the working electrode to the exit of the separation channel results in symmetric peak shapes and efficient separations (50,000-100,000 plates/m). A direct comparison between the frequency-based electrochemical technique, sinusoidal voltammetry, and the more commonly used constant potential (DC) amperometry is made. Sinusoidal voltammetry is found to be roughly an order of magnitude more sensitive than DC amperometry, with calculated mass detection limits (S/N = 3) of 12 amol and 15 amol for dopamine and isoproterenol, respectively.

Performance of pyrolyzed photoresist carbon films in a microchip capillary electrophoresis device with sinusoidal voltammetric detection.

Pyrolyzed photoresist films (PPF) are introduced as planar carbon electrodes in a PDMS-quartz hybrid microchip device. The utility of PPF in electroanalytical applications is demonstrated by the separation and detection of various neurotransmitters. PPF is found to form a stable, low-capacitance, durable layer on quartz, which can then be used in conjunction with a microchip capillary electrophoretic device. Sinusoidal voltammetric detection at PPF electrodes is shown to be very sensitive, with a detection limit (S/N = 3) of 100 nM for dopamine, corresponding to a mass detection limit (S/N = 3) of 2 amol. The selectivity of analysis in the frequency domain is demonstrated by isolating each individual signal in a pair of analytes that are chromatographically unresolved. Effectively decoupling the electrophoresis and electrochemical systems allows the electrodes to be placed just inside the separation channel, which results in efficient separations (80 000-100 000 plates/m).