title: Pinched flow fractionation devices for detection of single nucleotide polymorphisms.
abstract: We demonstrate a new and flexible microfluidic based method for genotyping single nucleotide polymorphisms (SNPs). The method relies on size separation of selectively hybridized polystyrene microspheres in a microfluidic pinched flow fractionation (PFF) device. The microfluidic PFF devices with 13 mum deep channels were fabricated by thermal nanoimprint lithography (NIL) in a thin film of cyclic-olefin copolymer (mr-I T85) on a silicon wafer substrate, and the channels were sealed by thermal polymer bonding. Streptavidin coated polystyrene microspheres with a mean diameter of 3.09 microm and 5.6 microm were functionalized with biotin-labeled oligonucleotides for the detection of a mutant (Mt) or wild-type (Wt) DNA sequence in the HBB gene, respectively. Hybridization to functionalized beads was performed with fluorescent targets comprising synthetic DNA oligonucleotides or amplified RNA, synthesized using human DNA samples from individuals with point mutations in the HBB gene. Following a stringent wash, the beads were separated in a PFF device and the fluorescent signal from the beads was analyzed. Patients being wildtypes, heterozygotes or mutated respectively for the investigated mutation could reliably be diagnosed in the PFF device. This indicates that the PFF technique can be used for accurate and fast genotyping of SNPs.
authors.affiliation: DTU Nanotech-Department of Micro and Nanotechnology, Technical University of Denmark (DTU), Building 345east, Oersted Plads, DK-2800, Lyngby, Denmark.
authors.forename: Asger Vig
authors.initials: AV
authors.lastname: Larsen
authors.forename: Lena
authors.initials: L
authors.lastname: Poulsen
authors.forename: Henrik
authors.initials: H
authors.lastname: Birgens
authors.forename: Martin
authors.initials: M
authors.lastname: Dufva
authors.forename: Anders
authors.initials: A
authors.lastname: Kristensen
mesh_terms: D005591:Chemical Fractionation / Q000295:instrumentation / Q000379:methods*; D004247:DNA / Q000032:analysis* / Q000235:genetics; D005838:Genotype; D006801:Humans; D046210:Microfluidic Analytical Techniques / Q000295:instrumentation / Q000379:methods*; D008863:Microspheres; D009154:Mutation; D009841:Oligonucleotides / Q000737:chemistry; D010316:Particle Size; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011137:Polystyrenes / Q000737:chemistry; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods; D019809:Streptavidin / Q000737:chemistry
chemical_list: D009841:Oligonucleotides; D011137:Polystyrenes; D004247:DNA; D019809:Streptavidin