Analytical and Bioanalytical Chemistry

, Volume 405, Issue 6, pp 1977–1983 | Cite as

Rapid extraction and preservation of genomic DNA from human samples

  • D. Kalyanasundaram
  • J.-H. Kim
  • W.-H. Yeo
  • K. Oh
  • K.-H. LeeEmail author
  • M.-H. Kim
  • S.-M. Ryew
  • S.-G. Ahn
  • D. Gao
  • G. A. Cangelosi
  • J.-H. ChungEmail author
Original Paper


Simple and rapid extraction of human genomic DNA remains a bottleneck for genome analysis and disease diagnosis. Current methods using microfilters require cumbersome, multiple handling steps in part because salt conditions must be controlled for attraction and elution of DNA in porous silica. We report a novel extraction method of human genomic DNA from buccal swab and saliva samples. DNA is attracted onto a gold-coated microchip by an electric field and capillary action while the captured DNA is eluted by thermal heating at 70 °C. A prototype device was designed to handle four microchips, and a compatible protocol was developed. The extracted DNA using microchips was characterized by qPCR for different sample volumes, using different lengths of PCR amplicon, and nuclear and mitochondrial genes. In comparison with a commercial kit, an equivalent yield of DNA extraction was achieved with fewer steps. Room-temperature preservation for 1 month was demonstrated for captured DNA, facilitating straightforward collection, delivery, and handling of genomic DNA in an environment-friendly protocol.


Portable microtip device for human genomic DNA extraction


DNA extraction Microtip Electric field Human genomic DNA Human samples 



We would like to acknowledge Ms. Sijie Sun, Department of Bioengineering at the University of Washington, for help with gel electrophoresis. We would like to acknowledge Dr. Xia You and Dr. John Stamatoyannopoulos at the Department of Genome Sciences at University of Washington for providing K562 cells. We acknowledge the support of NSF STTR II award (0956876), NSF Career Award (ECCS-0846454), and NIH SBIR (NIH/NIGMS 1R43GM099347).

Supplementary material


(WMV 2,579 kb)

216_2012_6637_MOESM2_ESM.doc (918 kb)
ESM 2 (DOC 918 kb)


  1. 1.
    Gyorgy C (2006) Present and future of rapid and/or high-throughput methods for nucleic acid testing. Clin Chim Acta 363:6–31CrossRefGoogle Scholar
  2. 2.
    Keijzer H, Endenburg SC, Smits MG, Koopmann M (2010) Automated genomic DNA extraction from saliva using the QIAxtractor. Clin Chem Lab Med 48:641–643CrossRefGoogle Scholar
  3. 3.
    Koni AC, Scott RA, Wang G, Bailey MES, Peplies J, Bammann K, Pitsiladis YP (2011) DNA yield and quality of saliva samples and suitability for large-scale epidemiological studies in children. Int J Obes 35:S113–S118CrossRefGoogle Scholar
  4. 4.
    Garcia-Closas M, Egan KM, Abruzzo J, Newcomb PA, Titus-Ernstoff L, Franklin T, Bender PK, Beck JC, Le Marchand L, Lum A, Alavanja M, Hayes RB, Rutter J, Buetow K, Brinton LA, Rothman N (2001) Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash. Cancer Epidemiol Biomarkers Prev 10(6):687–696Google Scholar
  5. 5.
    Hanselle T, Otte M, Schnibbe T, Smythe E, Krieg-Schneider F (2003) Isolation of genomic DNA from buccal swabs for forensic analysis, using fully automated silica-membrane purification technology. Legal Med 5:S145–S149CrossRefGoogle Scholar
  6. 6.
    Carter MJ, Milton ID (1993) An inexpensive and simple method for DNA purifications on silica particles. Nucleic Acids Res 21(4):1044CrossRefGoogle Scholar
  7. 7.
    Wagner JG, Petry TW, Roth RA (1993) Characterization of monocrotaline pyrrole-induced DNA cross-linking in pulmonary-artery endothelium. Am J Physiology 264:L517–L522Google Scholar
  8. 8.
    Fornace AJ, Dobson PP, Kinsella TJ (1986) Analysis of the effect of DNA alkylation on alkaline elution. Carcinogenesis 7(6):927–932CrossRefGoogle Scholar
  9. 9.
    Ageno M, Dore E, Frontali C (1969) The alkaline denaturation of DNA. Biophys J 9(11):1281–1311CrossRefGoogle Scholar
  10. 10.
    Price CW, Leslie DC, Landers JP (2009) Nucleic acid extraction techniques and application to the microchip. Lab Chip 9:2484–2494CrossRefGoogle Scholar
  11. 11.
    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-T ASME 121:22–27CrossRefGoogle Scholar
  12. 12.
    Wolfe KA, Breadmore MC, Ferrance JP, Power ME, Conroy JF, Norris PM, Landers JP (2002) Toward a microchip-based solid-phase extraction method for isolation of nucleic acids. Electrophoresis 23:727–733CrossRefGoogle Scholar
  13. 13.
    Witek MA, Llopis SD, Wheatley A, McCarley RL, Soper SA (2006) Purification and preconcentration of genomic DNA from whole cell lysates using photoactivated polycarbonate (PPC) microfluidic chips. Nucleic Acids Res 34(10):e74CrossRefGoogle Scholar
  14. 14.
    Pethig R (2010) Review article—dielectrophoresis: status of the theory, technology, and applications. Biomicrofluidics 4(2):022811CrossRefGoogle Scholar
  15. 15.
    Lapizco-Encinas BH, Rito-Palomares M (2007) Dielectrophoresis for the manipulation of nanobioparticles. Electrophoresis 28:4521–4538CrossRefGoogle Scholar
  16. 16.
    Bakewell DJ, Morgan H (2006) Dielectrophoresis of DNA: time- and frequency-dependent collections on microelectrodes. IEEE T Nanobiosci 5(1):1–8CrossRefGoogle Scholar
  17. 17.
    Bonnet J, Colotte M, Coudy D, Couallier V, Portier J, Morin B, Tuffet S (2010) Chain and conformation stability of solid-state DNA: implications for room temperature storage. Nucleic Acids Res 38(5):1531–1546CrossRefGoogle Scholar
  18. 18.
    Frippiat C, Zorbo S, Leonard D, Marcotte A, Chaput M, Aelbrecht C, Noel F (2011) Evaluation of novel forensic DNA storage methodologies. Forensic Sci Int: Gen 5(5):386–392CrossRefGoogle Scholar
  19. 19.
    Lindahl T, Nyberg B (1972) Rate of depurination of native deoxyribonucleic acid. Biochemistry 11:3610–3618CrossRefGoogle Scholar
  20. 20.
    Lindahl T, Karlstrom O (1973) Heat-induced depyrimidination of deoxyribonucleic acid in neutral solution. Biochemistry 12(25):5151–5154CrossRefGoogle Scholar
  21. 21.
    Shapiro R, Klein RS (1966) The deamination of cytidine and cytosine by acidic buffer solutions. Mutagenic implications. Biochemistry 5:2358–2362CrossRefGoogle Scholar
  22. 22.
    Anchordoquy TJ, Molina MC (2007) Preservation of DNA. Cell Preserv Technol 5:180–188CrossRefGoogle Scholar
  23. 23.
    Lee SB, Clabaugh KC, Silva B, Odigie KO, Coble MD, Loreille O, Scheible M, Fourney RM, Stevens J, Carmody GR, Parsons TJ, Pozder A, Eisenberg AJ, Budowle B, Ahmad T, Miller RW, Crouse CA (2012) Assessing a novel room temperature DNA storage medium for forensic biological samples. Forensic Sci Int: Gen 6:31–40CrossRefGoogle Scholar
  24. 24.
    Kim J-H, Yeo W-H, Shu Z, Soelberg SD, Inoue S, Kalyanasundaram D, Ludwig J, Furlong CE, Riley JJ, Weigel K, Cangelosi GA, Oh K, Lee K-H, Gao D, Chung J-H (2012) Immunosensor towards low-cost, rapid diagnosis of tuberculosis. Lab Chip 12(8):1437–1440CrossRefGoogle Scholar
  25. 25.
    Kalyanasundaram D, Inoue S, Kim J-H, Lee H-B, Kawabata Z, Yeo W-H, Cangelosi G, Oh K, Gao D, Lee K-H, Chung J-H (2012) Electric field-induced concentration and capture of DNA onto microtips. Microfluid Nanofluid 13(2):217–225CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • D. Kalyanasundaram
    • 1
  • J.-H. Kim
    • 1
  • W.-H. Yeo
    • 1
  • K. Oh
    • 2
  • K.-H. Lee
    • 2
    Email author
  • M.-H. Kim
    • 3
  • S.-M. Ryew
    • 3
  • S.-G. Ahn
    • 4
  • D. Gao
    • 1
  • G. A. Cangelosi
    • 5
  • J.-H. Chung
    • 1
    Email author
  1. 1.Department of Mechanical EngineeringUniversity of WashingtonSeattleUSA
  2. 2.NanoFacture, Inc.BellevueUSA
  3. 3.KNR Systems, Inc.Yongin-siRepublic of Korea
  4. 4.Department of Industrial DesignUniversity of WashingtonSeattleUSA
  5. 5.Department of Environmental and Occupational Health SciencesUniversity of WashingtonSeattleUSA

Personalised recommendations