Abstract
Microfluidic platforms have been developed to demonstrate DNA purification via liquid extraction techniques at the microscale using an aqueous phase containing either protein, DNA, or a complex cell lysate and an immiscible receiving organic (phenol) phase. Initially, a serpentine device was used to investigate protein partitioning between the aqueous and organic phase, and DNA purification when both protein and DNA were mixed in the aqueous phase and infused conjunctly with the phenol phase. This two-phase system was studied using both stratified and droplet-based flow conditions. The droplet-based flow resulted in a significant improvement of protein partitioning from the aqueous phase into the organic phase due to the convective flow recirculation inside each droplet improving material transport to the organic–aqueous interface. A second device was designed and fabricated to specifically extract plasmid DNA from bacterial lysates using only droplet-based flows. The plasmid recovery using the microdevice was high (>92%) and comparable to the recovery achieved using commercial DNA purification kits and standard macroscale phenol extraction. This study presents the initial steps toward the miniaturization of an efficient on-chip DNA sample preparation using phenol extraction which could be integrated with post-extraction DNA manipulations for integrated genomic analysis modules.
Similar content being viewed by others
References
Atencia J, Beebe DJ (2005) Controlled microfluidic interfaces. Nature 437:648–655
Bhattacharyya A, Klapperich CM (2008) Microfluidics-based extraction of viral RNA from infected mammalian cells for disposable molecular diagnostics. Sens Actuators B 129:693–698
Breadmore MC, Wolfe KA, Arcibal IG, Leung WK, Dickson D, Giordano BC, Power ME, Ferrance JP, Feldman SH, Norris PM, Landers JP (2003) Microchip-based purification of DNA from biological samples. Anal Chem 75:1880–1886
Chen X, Cui da F, Liu CC (2008) On-line cell lysis and DNA extraction on a microfluidic biochip fabricated by microelectromechanical system technology. Electrophoresis 29:1844–1851
Christel LA, Petersen K, McMillan W, Northrup MA (1999) Rapid, automated nucleic acid probe assays using silicon microstructures for nucleic acid concentration. J Biomech Eng 121:22–27
Christopher GF, Anna SL (2007) Microfluidic methods for generating continuous droplet streams. J Phys D 40:R319–R336
Dreyfus R, Tabeling P, Willaime H (2003) Ordered and disordered patterns in two-phase flows in microchannels. Phys Rev Lett 90:144505
Easley CJ, Karlinsey JM, Bienvenue JM, Legendre LA, Roper MG, Feldman SH, Hughes MA, Hewlett EL, Merkel TJ, Ferrance JP, Landers JP (2006) A fully integrated microfluidic genetic analysis system with sample-in-answer-out capability. Proc Natl Acad Sci USA 103:19272–19277
Guillot P, Colin A (2005) Stability of parallel flows in a microchannel after a T junction. Phys Rev E 72:066301–066304
Gunther A, Jensen KF (2007) Multiphase microfluidics: from flow characteristics to chemical and materials synthesis. Lab Chip 7:935–938
Hagan KA, Meier WL, Ferrance JP, Landers JP (2009) Chitosan-coated silica as a solid phase for RNA purification in a microfluidic device. Anal Chem 81:5249–5256
Haubert K, Drier T, Beebe D (2006) PDMS bonding by means of a portable, low-cost corona system. Lab Chip 6:1548–1549
Hibara A, Kasai K, Miyaguchi H, Kitamori T (2008) Novel two-phase flow control concept and multistep extraction microchip. In: Proceedings of the 12th international conference on miniaturized systems for chemistry and life sciences (mTAS 2008), San Diego, CA, pp 1326–1328
Kulinski MD, Mahalanabis M, Gillers S, Zhang JY, Singh S, Klapperich CM (2009) Sample preparation module for bacterial lysis and isolation of DNA from human urine. Biomed Microdevices 11:671–678
Lagally ET, Emrich CA, Mathies RA (2001) Fully integrated PCR-capillary electrophoresis microsystem for DNA analysis. Lab Chip 1:102–107
Legendre LA, Bienvenue JM, Roper MG, Ferrance JP, Landers JP (2006) A simple, valveless microfluidic sample preparation device for extraction and amplification of DNA from nanoliter-volume samples. Anal Chem 78:1444–1451
Mao X, Yang S, Zahn J (2006) Experimental demonstration and numerical simulation of organic-aqueous liquid extraction enhanced by droplet formation in a microfluidic channel. In: Proceedings of the ASME-IMECE, IMECE 2006-16084, Chicago, IL
Morales M, Zahn J (2008) Development of a diffusion limited microfluidic module for dna purification via phenol extraction. In: Proceedings of the ASME-IMECE, IMECE 2008-68086, Boston, MA
Qiagen (2003) QIAprep miniprep handbook. Qiagen Distributors
Reddy V, Zahn JD (2005) Interfacial stabilization of organic-aqueous two-phase microflows for a miniaturized DNA extraction module. J Colloid Interface Sci 286:158–165
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, NY
Shui L, Eijkel JCT, van den Berg A (2007a) Multiphase flow in micro- and nanochannels. Sens Actuators B 121:263–276
Shui L, Eijkel JCT, van den Berg A (2007b) Multiphase flow in microfluidic systems—control and applications of droplets and interfaces. Adv Colloid Interface Sci 133:35–49
Sober H, Harte R (1968) Handbook of biochemistry selected data for molecular biology. The Chemical Rubber Company, Cleveland, OH
Song H, Chen D, Ismagilov R (2006) Reactions in droplets in microfluidic channels. Angew Chem Int Ed 45:7336–7356
Tian H, Hühmer AFR, Landers JP (2000) Evaluation of silica resins for direct and efficient extraction of DNA from complex biological matrices in a miniaturized format. Anal Biochem 283:175–191
Tice JD, Song H, Lyon AD, Ismagilov RF (2003) Formation of droplets and mixing in multiphase microfluidics at low values of the Reynolds and the capillary numbers. Langmuir 19:9127–9133
Tice J, Lyon A, Ismagilov R (2004) Effects of viscosity on droplet formation and mixing in microfluidic channels. Anal Chim Acta 507:73–77
Wen J, Guillo C, Ferrance JP, Landers JP (2007) Microfluidic-based DNA purification in a two-stage, dual-phase microchip containing a reversed-phase and a photopolymerized monolith. Anal Chem 79:6135–6142
Wu QR, Bienvenue JM, Hassan BJ, Kwok YC, Giordano BC, Norris PM, Landers JP, Ferrance JP (2006) Microchip-based macroporous silica sol–gel monolith for efficient isolation of DNA from clinical samples. Anal Chem 78:5704–5710
Xia Y, Whitesides GM (1998) Soft lithography. Angew Chem Int Ed 37:550–575
Xu J, Li S, Tan J, Luo G (2008) Correlations of droplet formation in T-junction microfluidic devices: from squeezing to dripping. Microfluid Nanofluid 5:711–717
Zahn J, Reddy V (2006) Two phase micromixing and analysis using electrohydrodynamic instabilities. Microfluid Nanofluid 2:399–415
Acknowledgments
The authors thank Dr. Li Cai for the use of GELDOC and spectrophotometry instruments. This work is supported by the National Science Foundation (NSF), award number CBET 0721341.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Morales, M.C., Zahn, J.D. Droplet enhanced microfluidic-based DNA purification from bacterial lysates via phenol extraction. Microfluid Nanofluid 9, 1041–1049 (2010). https://doi.org/10.1007/s10404-010-0623-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10404-010-0623-2