Analysis methods for DNA genotyping and sequencing are linked into multi-step processing systems that begin with DNA source material and extract genetic information. In conventional methods, the processing system operates on batches of microliter-volume reaction samples, together with matched liquid handling devices and electrophoretic analysis equipment. Project 3 will provide component-level design and testing of improved nanoliter-volume processing components for DNA sequencing and genotyping. To fulfill the goal of high-quality, continuous DNA sequencing significant improvements in fluorescence detection and gel electrophoresis will be required. New or improved fabrication technologies will also be examined for biochemical compatibility, ease of fabrication, cost, or reproducibility. All of the components developed in the Project retain the target of eventual integration into the complex system of Project 1. Project 3 has three Specific Aims: 1) Development of polymer-silicon micromachined components. Both thin film polymer channels and molding/embossing patterns on polymer substrates will be used for integrated device construction. Thin film methods will be extended to thicker channel walls, thereby reducing evaporative liquid loss. Bonding of thermoplastic and silicon surfaces to generate hermetic sealed channels will also be developed using two types of polymer handling methods. 2) Development of enhanced sensitivity fluorescence detectors. The initial diode detector we have constructed will be improved to (a) maximize its response to the DNA fluorescent signal, (b) minimize its dark current noise, and (c) electrically isolate the detector from the electrophoresis stage. We anticipate at 10- to 100-fold improved in the signal to noise ratio for the detector. 3) Development of non-collinear fluorescence excitation. In the current device arrangement, the excitation illumination is collinear with the detector. We will develop non-collinear illumination schemes relying on either micromachined reflecting surfaces on polymer wave-guides.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Program Projects (P01)
Project #
5P01HG001984-03
Application #
6442985
Study Section
Project Start
2001-04-01
Project End
2003-03-31
Budget Start
Budget End
Support Year
3
Fiscal Year
2001
Total Cost
$164,078
Indirect Cost
Name
University of Michigan Ann Arbor
Department
Type
DUNS #
791277940
City
Ann Arbor
State
MI
Country
United States
Zip Code
48109
Kim, Sung-Jin; Wang, Fang; Burns, Mark A et al. (2009) Temperature-programmed natural convection for micromixing and biochemical reaction in a single microfluidic chamber. Anal Chem 81:4510-6
Wang, Fang; Burns, Mark A (2009) Performance of nanoliter-sized droplet-based microfluidic PCR. Biomed Microdevices 11:1071-80
Rhee, Minsoung; Burns, Mark A (2009) Microfluidic pneumatic logic circuits and digital pneumatic microprocessors for integrated microfluidic systems. Lab Chip 9:3131-43
Wang, Fang; Yang, Ming; Burns, Mark A (2008) Microfabricated valveless devices for thermal bioreactions based on diffusion-limited evaporation. Lab Chip 8:88-97
Zeitoun, Ramsey I; Chen, Zheng; Burns, Mark A (2008) Transverse imaging and simulation of dsDNA electrophoresis in microfabricated glass channels. Electrophoresis 29:4768-74
Rhee, Minsoung; Burns, Mark A (2008) Microfluidic assembly blocks. Lab Chip 8:1365-73
Rhee, Minsoung; Burns, Mark A (2008) Drop mixing in a microchannel for lab-on-a-chip platforms. Langmuir 24:590-601
Srivastava, Nimisha; Burns, Mark A (2007) Microfluidic pressure sensing using trapped air compression. Lab Chip 7:633-7
Chang, Dustin S; Langelier, Sean M; Burns, Mark A (2007) An electronic Venturi-based pressure microregulator. Lab Chip 7:1791-9
Chisa, Jennifer L; Burke, David T (2007) Mammalian mRNA splice-isoform selection is tightly controlled. Genetics 175:1079-87

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