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.

Detection of an amphiphilic biosample in a paper microchannel based on length

“…The figures improved on strengthening the contrast of the photograph to assist the visualization of the length of the faint yellow flow amphiphilic property. In hence applying our method to accomplish a simple and quick DNA quantification, to perform the experiments we chose DNA of two kinds: DNA labeled with FAM (DNA-FAM) or TAMRA (DNA-TAMRA) respectively; FAM possesses a hydrophilic functional group whereas TAMRA possesses a lipophilic one(Fang et al 2012). The aqueous solution containing DNA wicked along the paper channel, and the molecules of DNA interacted with the wax barrier and filter paper, finally producing a specific flow length.…”

Microfluidic Devices for Forensic DNA Analysis: A Review

“…Many microfluidic devices for droplet generation or microfluidic DNA amplification are made of PDMS [ 166 , 167 , 168 , 169 , 170 ]. The benefit of using PDMS is the fact that the surface of the channel is hydrophobic.…”

Studies of Intensified Small-scale Processes for Liquid-Liquid Separations in Spent Nuclear Fuel Reprocessing

“…Kinoshita et al (Kinoshita et al, 2007) obtained three-dimensional velocity information and circulation patterns inside a moving aqueous droplet by confocal microscopy, while other investigators (Kashid et al, 2005, Sarrazin et al, 2006) qualitatively compared velocity fields acquired from PIV with CFD simulations, proving the suitability of the experimental technique for these flows. More recently, Fang et al (Fang et al, 2012) proposed a technique to locally enhance DNA concentration by using a plug flow microdevice. PIV velocity data within water plugs were used to locally quantify the shear strain rate, while mixing was investigated by using a continuous dye.…”