Skip to main content
SpringerLink
Log in

Magnetic Beads Based Nucleic Acid Purification for Molecular Biology Applications

  • Protocol
Sample Preparation Techniques for Soil, Plant, and Animal Samples

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

During the last decade there has been a significant increase in usage of magnetic beads for nucleic acid purification. Using magnetic particles in nucleic acid isolation over the other existing methods offers several advantages: a possibility to automate process; scalability and the capability to move particles form well to well; and avoiding the cross-contamination caused by splashing of droplets when pipetting liquid materials. There are numerous commercial kits developed for specific sample types and downstream applications. This chapter discusses advantages of using magnetic beads over the membrane or resin based separation. It describes the most common materials that magnetic beads are made off, their characteristics and efficiency of separation. It also presents current automated systems used for low-, medium-, and high-throughput sample processing.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Tan SC, Yiap BC (2009) DNA, RNA, and protein extraction: the past and the present. J Biomed Biotechnol 2009, 574398. doi:10.1155/2009/574398

    Article  PubMed Central  PubMed  Google Scholar 

  2. Bowtell DD (1987) Rapid isolation of eukaryotic DNA. Anal Biochem 162:463–465

    Article  CAS  PubMed  Google Scholar 

  3. Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, van der Noorda J (1990) Rapid and simple method for purification of nucleic acids. J Clin Microbiol 28:495–503

    PubMed Central  CAS  PubMed  Google Scholar 

  4. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidium thiocyanate-phenol-chloroform extraction. Anal Biochem 162:156–159

    Article  CAS  PubMed  Google Scholar 

  5. Guesdon JL, Avrameas S (1977) Magnetic solid phase enzyme-immunoassay. Immunochemistry 14:443–447

    Article  CAS  PubMed  Google Scholar 

  6. Ugelstad J, Soderberg L, Berge A, Uhlen M (1983) Nature 303:95–96

    Article  Google Scholar 

  7. Uhlen M (1989) Magnetic separation of DNA. Nature 340:733–734

    Article  CAS  PubMed  Google Scholar 

  8. Grüttner C, Rudershausen S, Teller J (2001) Improved properties of magnetic particles by combination of different polymer materials as particle matrix. J Magn Magn Mater 225:1–7

    Article  Google Scholar 

  9. Gericke M, Trygg J, Fardim P (2013) Functional cellulose beads: preparation, characterization, and applications. Chem Rev 113:4812–4836. doi:10.1021/cr300242j

    Article  CAS  PubMed  Google Scholar 

  10. Rosenholm JM, Mamaeva V, Sahlgren C, Lindén M (2012) Nanoparticles in targeted cancer therapy: mesoporous silica nanoparticles entering preclinical development stage. Nanomedicine 7:111–120

    Article  CAS  PubMed  Google Scholar 

  11. Akbarzadeh A, Zarghami N, Mikaeili H, Asgari D, Goganian AM, Khiabani HK, Samiei M, Davaran S (2012) Synthesis, characterization, and in vitro evaluation of novel polymer-coated magnetic nanoparticles for controlled delivery of doxorubicin. Nanotechnol Sci Appl 5:13–25. doi:10.2147/NSA.S24328. eCollection 2012

    PubMed Central  CAS  PubMed  Google Scholar 

  12. Satoh S, Fugetsu B, Nomizu M, Nisji N (2005) Functional DNA–silica composite prepared by sol–gel method. Polym J 37:94–101

    Article  CAS  Google Scholar 

  13. Du P, Li H, Cai W (2009) Construction of DNA sandwich electrochemical biosensor with nanoPbS and nanoAu tags on magnetic microbeads. Biosens Bioelectron 24:3223–3228

    Article  CAS  PubMed  Google Scholar 

  14. Ding C, Zhang Q, Lin J-M, Zhang S-h (2009) Electrochemical detection of DNA hybridization based on bio-bar code method. Biosens Bioelectron 24:3140–3143

    Article  CAS  PubMed  Google Scholar 

  15. Berensmeir S (2006) Magnetic particles for the separation and purification of nucleic acids. Appl Microbiol Biotechnol 73:495–504. doi:10.1007/s00253-006-0675-0

    Article  Google Scholar 

  16. Rittich B, Spanova A (2013) SPE and purification of DNA using magnetic particles. J Sep Sci 36:2472–2485

    Article  CAS  PubMed  Google Scholar 

  17. Vogelstein B, Gillespie D (1979) Preparative and analytical purification of DNA from agarose. Proc Natl Acad Sci U S A 76:615–619

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Chen CW, Thomas CA Jr (1980) Recovery of DNA segments from agarose gels. Anal Biochem 101:339–341

    Article  CAS  PubMed  Google Scholar 

  19. Marko MA, Chipperfield R, Birnboi HC (1982) A procedure for the large-scale isolation of highly purified plasmid DNA using alkaline extraction and binding to glass powder. Anal Biochem 121:382–387

    Article  CAS  PubMed  Google Scholar 

  20. del Campo A, Sen T, Lellouche JP, Bruce IJ (2005) Multifunctional magnetite and silica–magnetite nanoparticles: synthesis, surface activation and applications in life sciences. J Magn Magn Mater 293:33–40

    Article  Google Scholar 

  21. Nakagawa T, Hashimoto R, Maruyama K, Tanaka T, Takeyama H, Matsunaga Y (2006) Capture and release of DNA using aminosilane-modified bacterial magnetic particles for automated detection system of single nucleotide polymorphisms. Biotechnol Bioeng 94:862–868

    Article  CAS  PubMed  Google Scholar 

  22. Tanaka T, Sakai R, Kobayashi R, Hatakeyama K, Matsunaga T (2009) Contributions of phosphate to DNA adsorption/desorption behaviors on aminosilane-modified magnetic nanoparticles. Langmuir 25:2956–2961

    Article  CAS  PubMed  Google Scholar 

  23. Horak D, Babic M, Macková H, Benes MJ (2007) Preparation and properties of magnetic nano- and microsized particles for biological and environmental separations. J Sep Sci 30:1751–1772

    Article  CAS  PubMed  Google Scholar 

  24. Klien K, Godnić-Cvar J (2012) Genotoxicity of metal nanoparticles: focus on in vivo studies. Arh Hig Rada Toksikol 63:133–145

    Article  CAS  PubMed  Google Scholar 

  25. Hwang DW, Lee DS, Kim S (2012) Gene expression profiles for genotoxic effects of silica-free and silica-coated cobalt ferrite nanoparticles. J Nucl Med 53:106–112

    Article  CAS  Google Scholar 

  26. Anas A, Akita H, Harashima H, Itoh T, Ishikawa M, Biju V (2008) Photosensitized breakage and damage of DNA by CdSe-ZnS quantum dots. J Phys Chem B 112:10005–10011

    Article  CAS  PubMed  Google Scholar 

  27. Rosenholm JM, Sahlgren C, Lindén M (2011) Multifunctional mesoporous silica nanoparticles for combined therapeutic, diagnostic and targeted action in cancer treatment. Curr Drug Targets 12:1166–1186

    Article  CAS  PubMed  Google Scholar 

  28. Sun N, Deng C, Lio L, Zhao X, Tang Y, Liu R, Xia Q, Yan W, Ge G (2014) Optimization of influencing factors of nucleic acid adsorption onto silica-coated magnetic particles: application to viral nucleic acid extraction from serum. J Chromatogr A 1325:31–39

    Article  CAS  PubMed  Google Scholar 

  29. ThermoFisher (2005) Surface Activated Dynabeads®. http://helix.mcmaster.ca/Surface_Activated_Dynabeads.pdf. Accessed on 2 Jun 2014

  30. Baker MJ (2008) Isolation of nucleic acids. Invitrogen Corporation US Patent 20080305528 A. Accessed on 2 June 2014

    Google Scholar 

  31. Zhang J, Li X, Rosenholm JM, Gu H-C (2011) Synthesis and characterization of pore size-tunable magnetic mesoporous silica nanoparticles. J Colloid Interface Sci 361:16–24

    Article  CAS  PubMed  Google Scholar 

  32. Schagat T, Wieczorek D, Helt C, Smith D, White D, Vincent E (2013) Comparing manual and automated genomic DNA purification methods for genotyping arrays. Promega Corporation. http://www.promega.com/resources/pubhub/comparing-manual-and-automated-genomic-dna-purification-methods-for-genotyping-arrays/. Accessed on 2 Jun 2014

  33. Schwartz DC, Cantor CR (1984) Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37:67–75

    Article  CAS  PubMed  Google Scholar 

  34. ThermoFisher (2008) T009‐Technical Bulletin NanoDrop 1000 & 8000 http://www.nanodrop.com/Library/T009-NanoDrop%201000-&-NanoDrop%208000-Nucleic-Acid-Purity-Ratios.pdf. Accessed on 2 Jun 2014

  35. Gehrig HH, Winter K, Cushman J, Bornald A, Taybi J (2000) An improved RNA isolation method for succulent plant species rich in polyphenols and polysaccharides. Plant Mol Biol Rep 18:369–376

    Article  CAS  Google Scholar 

  36. Haymes KM, Ibrahim IA, Mischke S, Scott DL, Saunders JA (2004) Rapid isolation of DNA from chocolate and date palm tree crops. J Agric Food Chem 52:5456–5462

    Article  CAS  PubMed  Google Scholar 

  37. Shan Z, Zhou Z, Chen H, Zhang Z, Zhou Y, Wen A, Oakes KD, Servos MR (2012) PCR-ready human DNA extraction from urine samples using magnetic nanoparticles. J Chromatogr B Analyt Technol Biomed Life Sci 881–882:63–68

    Article  PubMed  Google Scholar 

  38. Chockalingam AM, Babu HK, Chittor R, Tiwari JP (2010) Gum arabic modified Fe3O4 nanoparticles cross linked with collagen for isolation of bacteria. J Nanobiotechnol 8:30. doi:10.1186/1477-3155-8-30

    Article  CAS  Google Scholar 

  39. Safarik I, Safarikova M (1999) Use of magnetic techniques for the isolation of cells. J Chromatogr B Analyt Technol Biomed Life Sci 722:33–53

    Article  CAS  Google Scholar 

  40. Nagrath S, Sequist LV, Maheswaran S, Bell DW, Irimia D, Ulkus L, Smith MR, Kwak EL, Digumarthy S, Muzikansky A, Ryan P, Balis UJ, Tompkins RG, Haber DA, Toner M (2007) Isolation of rare circulating tumour cells in cancer patients by microchip technology. Nature 450:1235–1239

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  41. Yu M, Stott S, Toner M, Maheswaran S, Haber DA (2011) Circulating tumor cells: approaches to isolation and characterization. J Cell Biol 192:373–382. doi:10.1083/jcb.201010021

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  42. Stemmer C, Beau-Faller M, Pencreac’h E, Guerin E, Schneider A, Jaqmin D, Quoix E, Gaub MP, Oudet P (2003) Use of magnetic beads for plasma cell-free DNA extraction: toward automation of plasma DNA analysis for molecular diagnostics. Clin Chem 49:1953–1955

    Article  CAS  PubMed  Google Scholar 

  43. Donner H (2011) Use of TDE for isolation of nucleic acids. (Roche) US Patent 20110266172 A1. Accessed on 2 Jun 2014

    Google Scholar 

  44. Bordelon H, Russ PK, Wright DW, Haselton FR (2013) A magnetic bead-based method for concentrating DNA from human urine for downstream detection. PLoS One 8(7):e68369. doi:10.1371/journal.pone.0068369

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  45. Alderton RP, Eccleston LM, Howe RP, Read CA, Reeve MA, Beck S (1992) Magnetic bead purification of M13 DNA sequencing templates. Anal Biochem 201:166–169

    Article  CAS  PubMed  Google Scholar 

  46. Wahlberg J, Holmberg A, Bergh S, Hultman T, Uhlen M (1992) Automated magnetic preparation of DNA templates for solid phase sequencing. Electrophoresis 13:547–551

    Article  CAS  PubMed  Google Scholar 

  47. Rolfs A, Weber I (1994) Fully-automated, nonradioactive solid-phase sequencing of genomic DNA obtained from PCR. Biotechniques 17:782–787

    CAS  PubMed  Google Scholar 

  48. Fiebelkorn KR, Lee BG, Hill CE, Caliendo AM, Nolte FS (2002) Clinical evaluation of an automated nucleic acid isolation system. Clin Chem 48:1613–1615

    CAS  PubMed  Google Scholar 

  49. Loeffler J, Schmidt KD, Hebart H and Einsele H (2004) Automated nucleic acid extraction. In: Fuchs J, Podda M (eds.), Encyclopedia of genomics and proteomics, 93–96. doi: 10.3109/9780203997352.019

    Google Scholar 

  50. Thomsin A (2007) Insights into lab automation’s future. IVD Technology. http://www.ivdtechnology.com/article/insights-lab-automations-future. Accessed on 2 Jun 2014

  51. Ginocchio CC, Manji R, Lotlikar M, Zhang F (2008) Clinical evaluation of NucliSENS magnetic extraction and NucliSENS analyte-specific reagents for real-time detection of human metapneumovirus in pediatric respiratory specimens. J Clin Microbiol 46:1274–1280

    Article  PubMed Central  PubMed  Google Scholar 

  52. Stray JE, Liu JY, Brevnov MG, Shewale JG (2010) Extraction from Forensic Biological Samples for Genotyping. In: Shewale JG, Liu RH (eds.), Forensic DNA analysis current practices and emerging technologies, Boca Raton, FL: Taylor & Francis, 39–52

    Google Scholar 

  53. Di Pinto A, Forte V, Guastadisegni MC, Martino C, Schena FP, Tantillo G (2007) A comparison of DNA extraction methods for food analysis. Food Control 18:76–80

    Article  Google Scholar 

  54. Loens K, Bergs K, Ursi D, Goossens H, Ieven M (2007) Evaluation of NucliSens easyMAG for automated nucleic acid extraction from various clinical specimens. J Clin Microbiol 45:421–425

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  55. Kwan K, Cooper M, La Duc MT, Vaishampayan P, Stam C, Benardini JN, Scalzi G, Moissl-Eichinger C, Venkateswaran K (2011) Evaluation of procedures for the collection, processing, and analysis of biomolecules from low-biomass surfaces. Appl Environ Microbiol 77:2943–2953

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  56. Schuurman T, van Breda A, de Boer R, Kooistra-Smid M, Beld M, Savelkoul P, Boom R (2005) Reduced PCR sensitivity due to impaired DNA recovery with the MagNA pure LC total nucleic acid isolation kit. J Clin Microbiol 43:4616–4622. doi:10.1128/JCM.43.9.4616-4622.2005

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  57. Kalina WV, Douglas CE, Coyne SR, Minogue TD (2014) Comparative assessment of automated nucleic acid sample extraction equipment for biothreat agents. J Clin Microbiol 52:1232. doi:10.1128/JCM.03453-13

    Article  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgements

Figure 5.2 was generously provided by Dr. Jessica Rosenholm (Adjunct Professor) and Tina Gulin-Sarfraz (Ph.D. student) from Åbo Akademi University, Finland.

Author information

Authors and Affiliations

  1. NorthStar Medical Radioisotopes LLC, Engineering Complex, 5249 Femrite Drive, Madison, WI, 53718, USA

    Nives Kovačević Ph.D.

Authors
  1. Nives Kovačević Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nives Kovačević Ph.D. .

Editor information

Editors and Affiliations

  1. Department of Engineering Design Technology, Cerritos College, Norwalk, California, USA

    Miodrag Micic

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media New York

About this protocol

Cite this protocol

Kovačević, N. (2016). Magnetic Beads Based Nucleic Acid Purification for Molecular Biology Applications. In: Micic, M. (eds) Sample Preparation Techniques for Soil, Plant, and Animal Samples. Springer Protocols Handbooks. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3185-9_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-3185-9_5

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3184-2

  • Online ISBN: 978-1-4939-3185-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation