Skip to main content
SpringerLink
Log in

A two-stage electrophoretic microfluidic device for nucleic acid collection and enrichment

  • Research Paper
  • Published:
Microfluidics and Nanofluidics Aims and scope Submit manuscript

Abstract

Sample purification and enrichment is an important and usually time-consuming step for on-chip nucleic acid detection and analysis. This paper presents an electrophoretic DNA focusing method in microfluidic devices to enrich nucleic acid concentration by around 2700-fold. The electrical waveforms applied to five individual electrodes are such designed that DNAs move successively to the collection electrodes at high speed, while the interferences from bubbles due to electrohydrolysis are minimized. In a spiral channel with a total length of 48 cm, 1 ml DNA sample is purified and enriched by 57 times at a flow rate of 30 μl/min at first. The captured DNAs are then released and transported to the second microfluidic chamber where DNAs are collected and concentrated by 49 times. Thus, in about 40 min, the two-stage device can extract DNAs from 1 ml sample volume and enrich its concentration by 2790-fold. A trade-off exists between the process throughput and the DNA collection efficiency. A DNA capture efficiency of 99.7 % is reached when the flow rate is 1 μl/min, and the maximum DNA capture throughput is achieved at a flow rate of 30 μl/min. As a platform technology, the device can be integrated into bio-sensing and genetic analysis assays for DNA extraction and pre-concentration.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Allison SA, Mazur S (1998) Modeling the free solution electrophoretic mobility of short DNA fragments. Biopolymers 46(6):359–373

    Article  Google Scholar 

  • Bahga SS, Han CM, Santiago JG (2013) Integration of rapid DNA hybridization and capillary zone electrophoresis using bidirectional isotachophoresis. Analyst 138(1):87–90

    Article  Google Scholar 

  • Barrat JL, Joanny JF (1996) Theory of polyelectrolyte solutions. Adv Chem Physics 94:1–66

    Google Scholar 

  • Bown MR, Meinhart CD (2006) AC electroosmotic flow in a DNA concentrator. Microfluid Nanofluid 2(6):513–523

    Article  Google Scholar 

  • Braun D, Libchaber A (2002) Trapping of DNA by thermophoretic depletion and convection. Phys Rev Lett 89(18):188103

    Article  Google Scholar 

  • Chiu RWK et al (2004) Quantitative analysis of circulating mitochondrial DNA in plasma (vol 49, pg 719, 2003). Clin Chem 50(2):461

    Article  Google Scholar 

  • Di Carlo D (2009) Inertial microfluidics. Lab Chip 9(21):3038–3046

    Article  Google Scholar 

  • Du JR, Wei HH (2010) Focusing and trapping of DNA molecules by head-on ac electrokinetic streaming through join asymmetric polarization. Biomicrofluidics 4(3):034108

    Article  Google Scholar 

  • Escobedo C et al (2012) Optofluidic concentration: plasmonic nanostructure as concentrator and sensor. Nano Lett 12(3):1592–1596

    Article  Google Scholar 

  • Fang WF et al (2012) Locally enhanced concentration and detection of oligonucleotides in a plug-based microfluidic device. Lab Chip 12(5):923–931

    Article  Google Scholar 

  • Fixe F et al (2005) Electric-field assisted immobilization and hybridization of DNA oligomers on thin-film microchips. Nanotechnology 16(10):2061–2071

    Article  Google Scholar 

  • Holdenrieder S et al (2005) Cell-free DNA in serum and plasma: comparison of ELISA and quantitative PCR. Clin Chem 51(8):1544–1546

    Article  Google Scholar 

  • Hou HW et al (2015) Direct detection and drug-resistance profiling of bacteremias using inertial microfluidics. Lab Chip 15(10):2297–2307

    Article  Google Scholar 

  • Iloeje UH et al (2006) Predicting cirrhosis risk based on the level of circulating hepatitis B viral load. Gastroenterology 130(3):678–686

    Article  Google Scholar 

  • Jiang H et al (2010) Concentrating molecules in a simple microchannel. J Colloid Interface Sci 347(2):324–331

    Article  Google Scholar 

  • Jiang L et al (2012) Direct microRNA detection with universal tagged probe and time-resolved fluorescence technology. Biosens Bioelectron 34(1):291–295

    Article  Google Scholar 

  • Kalyanasundaram D et al (2012) Electric field-induced concentration and capture of DNA onto microtips. Microfluid Nanofluid 13(2):217–225

    Article  Google Scholar 

  • Krishnan R et al (2008) Alternating current electrokinetic separation and detection of DNA nanoparticles in high-conductance solutions. Electrophoresis 29(9):1765–1774

    Article  Google Scholar 

  • Kuntaegowdanahalli SS et al (2009) Inertial microfluidics for continuous particle separation in spiral microchannels. Lab Chip 9(20):2973–2980

    Article  Google Scholar 

  • Kuo CH, Wang JH, Lee GB (2009) A microfabricated CE chip for DNA pre-concentration and separation utilizing a normally closed valve. Electrophoresis 30(18):3228–3235

    Article  Google Scholar 

  • Li YG, Cu YTH, Luo D (2005) Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes. Nat Biotechnol 23(7):885–889

    Article  Google Scholar 

  • Lin CC, Hsu JL, Lee GB (2011) Sample preconcentration in microfluidic devices. Microfluid Nanofluid 10(3):481–511

    Article  MathSciNet  Google Scholar 

  • Marshall LA, Han CM, Santiago JG (2011) Extraction of DNA from malaria-infected erythrocytes using isotachophoresis. Anal Chem 83(24):9715–9718

    Article  Google Scholar 

  • Meagher RJ, Thaitrong N (2012) Microchip electrophoresis of DNA following preconcentration at photopatterned gel membranes. Electrophoresis 33(8):1236–1246

    Article  Google Scholar 

  • Mei Z et al (2011) Applying an optical space-time coding method to enhance light scattering signals in microfluidic devices. Biomicrofluidics 5(3):034116

    Article  Google Scholar 

  • Mitchell PS et al (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 105(30):10513–10518

    Article  Google Scholar 

  • Morales MC, Lin H, Zahn JD (2012) Continuous microfluidic DNA and protein trapping and concentration by balancing transverse electrokinetic forces. Lab Chip 12(1):99–108

    Article  Google Scholar 

  • Motosuke M et al (2013) Improved particle concentration by cascade AC electroosmotic flow. Microfluid Nanofluid 14(6):1021–1030

    Article  Google Scholar 

  • Netz RR, Andelman D (2003) Neutral and charged polymers at interfaces. Phys Rep Rev Sect Phys Lett 380(1–2):1–95

    MATH  Google Scholar 

  • Nunes JK et al (2014) Fabricating shaped microfibers with inertial microfluidics. Adv Mater 26(22):3712–3717

    Article  MathSciNet  Google Scholar 

  • Puttaswamy SV et al (2013) Electrodeless dielectrophoretic concentrator for analyte pre-concentration on poly-silicon nanowire field effect transistor. Sens Actuators B Chem 178:547–554

    Article  Google Scholar 

  • Qiao W, Cho G, Lo YH (2011) Wirelessly powered microfluidic dielectrophoresis devices using printable RF circuits. Lab Chip 11(6):1074–1080

    Article  Google Scholar 

  • Qiao W et al (2014) Oil-encapsulated nanodroplet array for bio-molecular detection. Ann Biomed Eng 42(9):1932–1941

    Article  Google Scholar 

  • Shaikh FA, Ugaz VM (2006) Collection, focusing, and metering of DNA in microchannels using addressable electrode arrays for portable low-power bioanalysis. Proc Natl Acad Sci USA 103(13):4825–4830

    Article  Google Scholar 

  • Stein D et al (2010) Electrokinetic concentration of DNA polymers in nanofluidic channels. Nano Lett 10(3):765–772

    Article  Google Scholar 

  • Stroun M et al (2001) About the possible origin and mechanism of circulating DNA—apoptosis and active DNA release. Clin Chim Acta 313(1–2):139–142

    Article  Google Scholar 

  • Sunami E et al (2008) Quantification of LINE1 in circulating DNA as a molecular biomarker of breast cancer. Circ Nucleic Acids Plasma Serum V 1137:171–174

    Google Scholar 

  • Tymoczko J, Schuhmann W, Gebala M (2014) Electrical potential-assisted DNA hybridization. How to mitigate electrostatics for surface DNA hybridization. ACS Appl Mater Interfaces 6(24):21851–21858

    Article  Google Scholar 

  • Warkiani ME et al (2015) Membrane-less microfiltration using inertial microfluidics. Sci Rep 5:11018

    Article  Google Scholar 

  • Wong IY, Melosh NA (2009) Directed hybridization and melting of DNA linkers using counterion-screened electric fields. Nano Lett 9(10):3521–3526

    Article  Google Scholar 

  • Wu TF et al (2011) An optical-coding method to measure particle distribution in microfluidic devices. AIP Adv 1(2):022155

    Article  Google Scholar 

  • Wu ZY et al (2012) Flexible and efficient eletrokinetic stacking of DNA and proteins at an HF etched porous junction on a fused silica capillary. Anal Chem 84(16):7085–7091

    Article  Google Scholar 

  • Zheng DL et al (2011) Plasma microRNAs as novel biomarkers for early detection of lung cancer. Int J Clin Exp Pathol 4(6):575–586

    Google Scholar 

Download references

Acknowledgments

The authors acknowledge the technical support from the staff of the Nano3 (Nanoscience, Nanoengineering, and Nanomedicine) facility in Calit2 in University of California at San Diego (UCSD). We thank Dr. Longchuan Chen from the VA Long Beach Health System for providing fluorescently labeled DNA oligos. We also thank Dr. Clark Chen from the UC San Diego Moores Cancer Center for useful discussion and suggestions. The project has been supported by Compliance Decisions, Inc., National Natural Science Funds of China (Grant Nos. 91323303, 61401292), Jiangsu Provincial Natural Science Foundation of China (Grant No. BK20140350), and the Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions.

Author information

Authors and Affiliations

  1. College of Physics, Optoelectronics and Energy and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, 215006, China

    Wen Qiao, Chinhua Wang, Zengqian Ding & XiaoXiao Wei

  2. Key Lab of Advanced Optical Manufacturing Technologies of Jiangsu Province and Key Lab of Modern Optical Technologies of Education Ministry of China, Soochow University, Suzhou, 215006, China

    Wen Qiao, Chinhua Wang, Zengqian Ding & XiaoXiao Wei

  3. Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, 92093-0407, USA

    Junlan Song & Yu-Hwa Lo

Authors
  1. Wen Qiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chinhua Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zengqian Ding
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Junlan Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. XiaoXiao Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yu-Hwa Lo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to XiaoXiao Wei.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 28 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Qiao, W., Wang, C., Ding, Z. et al. A two-stage electrophoretic microfluidic device for nucleic acid collection and enrichment. Microfluid Nanofluid 20, 77 (2016). https://doi.org/10.1007/s10404-016-1743-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10404-016-1743-0

Keywords

Search

Navigation