KEYWORDS: Microfluidics, Silicon, Waveguides, Temperature metrology, Resistance, Computer aided design, Fluorescence resonance energy transfer, Semiconducting wafers, Etching, Control systems
A microheater array device is designed and fabricated using the SwIFT-LiteTM process at Sandia National Laboratories. The device contains 18 individually controllable microheaters in a 3×6 array on a silicon substrate. The microheater array device was designed for use as a biosensor platform with a waveguide for real-time detection of DNA hybridization and melting as well as microfluidics for sample delivery. The design process including modeling, fabrication, and characterization of the heaters and waveguide is detailed. A FRET (florescence resonance energy transfer) system for DNA melting experiments is described, and the associated surface chemistry and microfluidic systems are discussed.
DNA analysis, specifically single nucleotide polymorphism (SNP) detection, is becoming increasingly important in rapid
diagnostics and disease detection. Temperature is often controlled to help speed reaction rates and perform melting of
hybridized oligonucleotides. The difference in melting temperatures, Tm, between wild-type and SNP sequences,
respectively, to a given probe oligonucleotide, is indicative of the specificity of the reaction. We have characterized
Tm's in solution and on a solid substrate of three sequences from known mutations associated with Cystic Fibrosis.
Taking advantage of Tm differences, a microheater array device was designed to enable individual temperature control
of up to 18 specific hybridization events. The device was fabricated at Sandia National Laboratories using surface
micromachining techniques. The microheaters have been characterized using an IR camera at Sandia and show
individual temperature control with minimal thermal cross talk. Development of the device as a real-time DNA
detection platform, including surface chemistry and associated microfluidics, is described.
DNA analysis, specifically single nucleotide polymorphism (SNP) detection, is becoming increasingly important in rapid
diagnostics and disease detection. Temperature is often controlled to help speed reaction rates and perform melting of
hybridized oligonucleotides. The difference in melting temperatures, Tm, between wild-type and SNP sequences,
respectively, to a given probe oligonucleotide, is indicative of the specificity of the reaction. We have characterized
Tm's in solution and on a solid substrate of three sequences from known mutations associated with Cystic Fibrosis.
Taking advantage of Tm differences, a microheater array device was designed to enable individual temperature control
of up to 18 specific hybridization events. The device was fabricated at Sandia National Laboratories using surface
micromachining techniques. The microheaters have been characterized using an IR camera at Sandia and show
individual temperature control with minimal thermal cross talk. Development of the device as a real-time DNA
detection platform, including surface chemistry and associated microfluidics, is described.
With the goal of a portable diagnostic system in mind, we have designed a disposable platform for DNA detection. Surface micromachining using the SwIFT process at Sandia National Laboratories was used to make the new device, combining a waveguide, grating optics, heating structures, on-chip pumping, and microfluidics in a disposable package. PDMS microfluidic channels are integrated with the surface micromachined device to enable higher flow rates and added fluid complexity. Work on DNA hybridization under flow is presented, as applies to the function of the sensor. A description of the platform covering heating of the waveguide surface, laser coupling into the waveguide using grating optics, attachment chemistry for the sensor surface, and sealing of the PDMS microfluidic system to the device is given.
An evanescent field waveguide DNA biosensor coupled with a microfluidic sample delivery system is the platform for our studies. By employing microfluidics our aim is to reduce sample size and scale to large arrays, thereby increasing the efficiency of the sensor. We are studying the hybridization rate in small sensing zones under flow conditions, with a capture oligonucleotide immobilized on the surface of the waveguide. We are also investigating what effect passive mixing structures placed in the sensing zone have on the hybridization kinetics of the system.
A major challenge in many biosensing applications is the real-time detection of a multitude of analytes from a small sample volume. Achieving these goals would perhaps eliminate the need for an intermediate molecular amplification step. Our approach to this challenge involves the investigation of high sensitivity and scalable integrated optical transduction and scalable microfluidic sample delivery. The microfluidic architecture has small cross-section and allows the sample to visit each sensing zone, where a biospecific monolayer performs molecular recognition. Signal transduction occurs via a resonant optical microcavity, which has the dramatically increased signal to noise ratio in fluorescence detection necessary to detect small molecular numbers. Important performance issues in this architecture are sample flow rates, sensing zone size, and the use of passive mixing structures. In addition, microfabrication issues such as optical and microfluidic design, materials, and monolayer patterning are discussed.
Optical microcavities can be used to enhance the detection sensitivity of evanescent-wave fluorescence biosensors to the binding of a labeled analyte to a biospecific monolayer. The enhancement results form the buildup of intensity within the microcavity on resonance, which thereby increases fluorescence output from species specifically bound on the surface of the microcavity. Target studies are directed at nucleic acid hybridization, and initial results using high-Q dielectric microspheres have been obtained.
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