title: Microfluidic linear hydrogel array for multiplexed single nucleotide polymorphism (SNP) detection.
abstract: A PDMS-based microfluidic linear hydrogel array is developed for multiplexed single nucleotide polymorphism (SNP) detection. A sequence of three-dimensional (3D) hydrogel plugs containing the desired DNA probes is prepared by UV polymerization within a PDMS microchannel system. The fluorescently labeled target DNA is then electrophoresed through the sequence of hydrogel plugs for hybridization. Continued electrophoresis provides an electrophoretic wash that removes nonspecific binders. The capture gel array is imaged after washing at various temperatures (temperature gradient electrophoresis) to further distinguish perfect matches from mismatches. The ability of this microdevice to perform multiplex SNP genotyping is demonstrated by analyzing a mixture of model E. coli bacterial targets. This microfluidic hydrogel array is ∼1000 times more sensitive than planar microarrays due to the 3D gel capture, the hybridization time is much shorter due to electrophoretic control of the transport properties, and the stringent wash with temperature gradient electrophoresis enables analysis of single nucleotide mismatches with high specificity.
authors: †Department of Chemistry, University of California, Berkeley, California 94720, United States.|‡School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea.
authors: Yun Kyung
authors: YK
authors: Jung
authors: †Department of Chemistry, University of California, Berkeley, California 94720, United States.|§Department of Mechanical Engineering, Texas Tech University, Lubbock, Texas 79409, United States.
authors: Jungkyu
authors: J
authors: Kim
authors: †Department of Chemistry, University of California, Berkeley, California 94720, United States.
authors: Richard A
authors: RA
authors: Mathies
mesh_terms: D000483:Alleles; D001483:Base Sequence; D015342:DNA Probes / Q000737:chemistry / Q000235:genetics; D004129:Dimethylpolysiloxanes / Q000737:chemistry; D020136:Hydrogel, Polyethylene Glycol Dimethacrylate / Q000737:chemistry*; D057230:Limit of Detection; D046210:Microfluidic Analytical Techniques / Q000379:methods*; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D055668:Photochemical Processes; D058105:Polymerization; D020641:Polymorphism, Single Nucleotide; D044366:Transition Temperature
chemical_list: D015342:DNA Probes; D004129:Dimethylpolysiloxanes; D020136:Hydrogel, Polyethylene Glycol Dimethacrylate; C013830:baysilon