Abstract
The conceptual simulation study of DNA extraction and separation from salivary fluid sample are mainly divided into two parts. The initial study covered microfluidic channel design and effective DNA extraction by using mobilizing superparamagnetic (SPM) beads in COMSOL Multiphysics® software. The subsequent part presented simulation work for DNA separation from SPM beads in electromagnetization field. The main objective of this study in microfluidic platform in presence of electromagnetic field was to achieve higher and uncontaminated yield of DNA as sample preparation step which can be applied for clinical analysis. COMSOL Multiphysics® simulation software was used to study the entire work and presented in this paper with complete study steps. The attached DNA onto SPM beads was separated by specifying computational fluid dynamics in laminar flow, particle tracing module and electromagnetic field by using external electromagnetic coil as magnet array. Most of the SPM beads were captured and held by magnetic field when 100 mT/min was generated by electromagnetic coil. 82.01% of uncontaminated DNA yield from salivary fluid was able to separate from SPM beads after DNA extraction in microfluidic channel. In the absence of external magnetic field, the produced superparamagnetism enable SPM beads to flip in an isotropy provide efficient separation. The mechanical and chemical stability of silica surface of SPM beads provide an excellent chromatography separation medium for DNA sample preparation for further downstream analysis.
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References
Akbarzadeh A, Samiei M, Davaran S (2012a) Magnetic nanoparticles: preparation, physical properties, and applications in biomedicine. Nanoscale Res Lett 7:144. https://doi.org/10.1186/1556-276X-7-144
Akbarzadeh A, Haleh M, Nosratollah Z, Rahmati M, Amin B, Soodabeh D (2012b) Preparation and in vitro evaluation of doxorubicin-loaded Fe3O4 magnetic nanoparticles modified with biocompatible copolymers. Int J Nanomed 7:1–16. https://doi.org/10.2147/IJN.S24326
Arthur CL, Pawliszyn J (1990) Solid phase microextraction with thermal desorption using fused silica optical fibers. Anal Chem 62(1990):2145–2148. https://doi.org/10.1021/ac00218a019
Bailey VJ, Zhang Y, Keeley BP, Yin C, Pelosky KL, Brock M, Baylin SB, Herman JG, Wang T-H (2010) Single-tube analysis of DNA methylation with silica superparamagnetic bead. Clin Chem 56(6):1022–1025. https://doi.org/10.1373/clinchem.2009.140244
Clerk MP (1865) A dynamical theory of the electromagnetic field. J Trans R Soc Lond 155:459–512
Dawes C (2003) Estimates from salivary analyses of the turnover time of the oral mucosal epithelium in humans and the number of bacteria in an edentulous mouth. Arch Oral Biol 48:329–336
Gu H, Li X, Zhang J (2012) Study on the adsorption mechanism of DNA with mesoporous silica nanoparticles in aqueous solution. Langmuir 28:2827–2834. https://doi.org/10.1021/la204443j
Hansen TV, Simonsen MK, Nielsen FC, Hundrup YA (2007) Collection of blood, saliva, and buccal cell samples in a pilot study on the Danish nurse cohort: comparison of the response rate and quality of genomic DNA. Cancer Epidemiol Biomark Prev 16(10):2072–2076. https://doi.org/10.1158/1055-9965.epi-07-0611
Hawkins A (1998) DNA purification and isolation using magnetic particles. Google Patents. http://www.google.com/patents/US5705628. Accessed 24 July 2017
Landers JP, Jackson KR, Borba JC, Meija M, Mills DL, Haverstick DM, Olson KE, Aranda R, Garner GT, Carrilho E (2016) DNA purification using dynamic solid-phase extraction on a rotationally-driven polyethylene-terephthalate microdevice. Anal Chim Acta 937:1–10. https://doi.org/10.1016/j.aca.2016.06.036
Larsona RG, Poeckha T, Lopezb S, Fullerb AO, Solomona MJ (2008) Adsorption and elution characteristics of nucleic acids on silica surfaces and their use in designing a miniaturized purification unit. Anal Biochem 373(2):253–262. https://doi.org/10.1016/j.ab.2007.10.026
Lee CS, Lee H, Westervelt RM (2001) Microelectromagnets for the control of magnetic nanoparticles. Appl Phys Lett 79:3308–3310. https://doi.org/10.1063/1.1419049
Lee H, Purdon AM, Westervelt RM (2004) Manipulation of biological cells using a microelectromagnet matrix. Appl Phys Lett 85:1063. https://doi.org/10.1063/1.1776339
Lee H, Liu Y, Ham D, Westervelt RM (2007) Integrated cell manipulation system—CMOS/microfluidic hybrid. Lab Chip 7:331–337. https://doi.org/10.1039/b700373k
Leiss E (2007) Interdisciplinary electromagnetic, mechanic and biomedical problems. IOS Press, Technology and Engineering, Amsterdam, p 25
Marjoram RJ, Guiluy C, Burridge K (2016) Using magnets and magnetic beads to dissect signaling pathways activated by mechanical tension applied to cells. Methods 94:19–26. https://doi.org/10.1016/j.ymeth.2015.09.025
Mathieu J-B, Martel S (2007) Magnetic microparticle steering within the constraints of an mri system: proof of concept of a novel targeting approach. Biomed Microdevices 9:801–808. https://doi.org/10.1007/s10544-007-9092-0
Min JH, Woob M-K, Yoon HY, Jang JW, Wub JW, Lim C-S, Kim YK (2014) Isolation of DNA using magnetic nanoparticles coated with dimercaptosuccinic acid. Anal Biochem 447:114–118. https://doi.org/10.1016/j.ab.2013.11.018
Norbury G, Norbury CJ (2006) DNA analysis: what and when to request? Arch Dis Child 91:357–360. https://doi.org/10.1136/adc.2005.089219
Pamme N (2006) Magnetism and microfluidics. Lab Chip 6(1):24–38. https://doi.org/10.1039/b513005k
Quinque D, Kittler R, Kayser M, Stoneking M, Nasidze I (2006) Evaluation of saliva as a source of human DNA for population and association studies. Anal Biochem 353(2):272–277. https://doi.org/10.1016/j.ab.2006.03.021
Ramadan Q, Daniel P, Yu C (2009) Customized trapping of magnetic particles. Microfluid Nanofluid 6:53–62. https://doi.org/10.1007/s10404-008-0296-2
Reichenberger EJ, Sun F (2014) Saliva as source of genomic DNA for genetic studies: review of current methods and applications. OHDM 13:2
Samla G, Gan KB, Then SM (2016) Modeling microfluidic DNA extraction using superparamagnetic bead particles in COMSOL multiphysics simulation. Microsyst Technol. https://doi.org/10.1007/s00542-016-3170-2
Samla G, Gan KB, Then SM (2017) Solid phase microextraction based micro-device for extraction of PCR amplifiable DNA. Int J Nanoelectron Mater 10(1):75–92
Savini A, Turowski J (2012) Electromagnetic fields in electrical engineering. Springer Science and Business Media, Technology and Engineering, Berlin
Schork NJ (2015) Personalized medicine: time for one-person trials. Nature 520:609–611. https://doi.org/10.1038/520609a
Shevkoplyas SS, Siegel AC, Westervelt RM, Prentiss MG, Whitesides GM (2007) The force acting on a superparamagnetic bead due to an applied magnetic field. Lab Chip 7(10):1294–1302. https://doi.org/10.1039/b705045
Smistrup K, Tang PT, Hansen O, Hansen MF (2006) Microelectromagnet for magnetic manipulation in lab-on-a-chip systems. J Magn Magn Mater 300:418–426. https://doi.org/10.1016/j.jmmm.2005.05.031
Tan MD, Pamme N (2014) Microfluidics. Reference Module in Chemistry. Mol Sci Chem Eng. https://doi.org/10.1016/B978-0-12-409547-2.05351-8
Wierucka M, Biziuk M (2014) Application of magnetic nanoparticles for magnetic solid-phase extraction in preparing biological, environmental and food samples. Trends Anal Chem 59:50–58. https://doi.org/10.1016/j.trac.2014.04.007
Wu J, Kodzius R, Cao W, Wen W (2014) Extraction, amplification and detection of DNA in microfluidic Chip-based assays. Microchim Acta 181(13–14):1611–1631. https://doi.org/10.1007/s00604-013-1140-2
Xia N, Hunt TP, Mayers BT, Alsberg E, Whitesides GM, Westervelt RM, Ingber DE (2006) Combined microfluidic–micromagnetic separation of living cells in continuous flow. Biomed Microdevices 8:299–308. https://doi.org/10.1007/s10544-006-0033-0
Zhang Y, Park S, Yang S, Wang T-H (2010) An all-in-one microfluidic device for parallel DNA extraction and gene analysis. Biomed Microdevices 12:1043–1104. https://doi.org/10.1007/s10544-010-9458-6
Acknowledgements
This research was supported by the Ministry of Higher Education Malaysia (MoHE) under the Fundamental Research Grant Scheme (FRGS/1/2016/TK04/UKM/02/5).
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Gauri, S., Gan, K.B. & Then, SM. Simulation of DNA extraction and separation from salivary fluid by superparamagnetic beads and electromagnetic field in microfluidic platform. Microsyst Technol 25, 1379–1385 (2019). https://doi.org/10.1007/s00542-018-4102-0
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DOI: https://doi.org/10.1007/s00542-018-4102-0