title: Locally enhanced concentration and detection of oligonucleotides in a plug-based microfluidic device.
abstract: We propose a novel technique that allows oligonucleotides with specific end-modification within a plug in a plug-based microfluidic device to undergo a locally enhanced concentration at the rear of the plug as the plug moves downstream. DNA was enriched and detected in situ upon exploiting a combined effect underlain by an entropic force induced through fluid shear (i.e. a hydrodynamic-repellent effect) and the interfacial adsorption (aqueous/oil interface) attributed to affinity. Flow fields within a plug were visualized quantitatively using micro-particle image velocimetry (micro-PIV); the distribution of the fluid shear strain rate explains how the hydrodynamic-repellent effect engenders a dumbbell-like region with an increased concentration of DNA. The concentration of FAM (6-carboxy-fluorescein)-labeled DNA (FC-DNA) and of TAMRA (tetramethyl-6-carboxyrhodamine)-labeled DNA (TC-DNA), respectively, and the hybridization of probe DNA (modified with FAM) with target DNA (modified with TAMRA) were investigated in devices; a confocal fluorescence microscope (CFM) was utilized to monitor the processes and to resolve the corresponding 2D patterns and 3D reconstruction of the DNA distribution in a plug. TC-DNA, but not FC-DNA, concentrating within a plug was affected by the combined effect so as to achieve a concentration factor (C(r)) twice that of FC-DNA because of the lipophilicity of TAMRA. Using fluorescence resonance-energy transfer (FRET), we characterized the hybridization of the DNA in a plug; the detection limit of a system, improved by virtue of the proposed technique (the locally enhanced concentration), for DNA detection was estimated to be 20-50 nM. This technique enables DNA to concentrate locally in a nL-pL free-solution plug, the locally enhanced concentration to profit the hybridization efficiency and the detection of DNA, prospectively serving as a versatile means to accomplish a rapid DNA detection in a small volume for a Lab-on-a-Chip (LOC) system.
authors.affiliation: Department of Mechanical Engineering, National Taiwan University, Taipei, Taiwan.
authors.forename: Wei-Feng
authors.initials: WF
authors.lastname: Fang
authors.forename: Shang-Chieh
authors.initials: SC
authors.lastname: Ting
authors.forename: Ching-Wen
authors.initials: CW
authors.lastname: Hsu
authors.forename: Yu-Tzu
authors.initials: YT
authors.lastname: Chen
authors.forename: Jing-Tang
authors.initials: JT
authors.lastname: Yang
mesh_terms: D000818:Animals; D006801:Humans; D046210:Microfluidic Analytical Techniques / Q000295:instrumentation / Q000379:methods; D009841:Oligonucleotides / Q000737:chemistry*
chemical_list: D009841:Oligonucleotides