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Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation

Phil Oberacker, Peter Stepper, Donna M Bond, Sven Höhn, Jule Focken, Vivien Meyer, Luca Schelle, Victoria J Sugrue, Gert-Jan Jeunen, Tim Moser, View ORCID ProfileSteven R Hore, Ferdinand von Meyenn, Katharina Hipp, Timothy A Hore, View ORCID ProfileTomasz P Jurkowski
doi: https://doi.org/10.1101/414516
Phil Oberacker
1Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Allmandring 31, University of Stuttgart, Stuttgart D-70569, Germany;
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Peter Stepper
1Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Allmandring 31, University of Stuttgart, Stuttgart D-70569, Germany;
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Donna M Bond
2Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand;
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Sven Höhn
1Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Allmandring 31, University of Stuttgart, Stuttgart D-70569, Germany;
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Jule Focken
1Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Allmandring 31, University of Stuttgart, Stuttgart D-70569, Germany;
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Vivien Meyer
1Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Allmandring 31, University of Stuttgart, Stuttgart D-70569, Germany;
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Luca Schelle
1Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Allmandring 31, University of Stuttgart, Stuttgart D-70569, Germany;
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Victoria J Sugrue
2Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand;
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Gert-Jan Jeunen
2Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand;
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Tim Moser
2Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand;
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Steven R Hore
3CENENG Ltd, 66 Leask Street, Omakau, 9376, New Zealand;
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  • ORCID record for Steven R Hore
Ferdinand von Meyenn
4Department of Medical and Molecular Medicine, Kings College London, Guys Hospital, London SE1 9RT, United Kingdom;
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Katharina Hipp
5Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
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Timothy A Hore
2Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand;
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  • For correspondence: tomasz.jurkowski@ibtb.uni-stuttgart.de tim.hore@otago.ac.nz
Tomasz P Jurkowski
1Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Allmandring 31, University of Stuttgart, Stuttgart D-70569, Germany;
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  • ORCID record for Tomasz P Jurkowski
  • For correspondence: tomasz.jurkowski@ibtb.uni-stuttgart.de tim.hore@otago.ac.nz
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Abstract

Current molecular biology laboratories rely heavily on the purification and manipulation of nucleic acids. Yet, commonly used centrifuge-and column-based protocols require specialised equipment, often use toxic reagents and are not economically scalable or practical to use in a high-throughput manner. Although it has been known for some time that magnetic beads can provide an elegant answer to these issues, the development of open-source protocols based on beads has been limited. In this article, we provide step-by-step instructions for an easy synthesis of functionalised magnetic beads, and detailed protocols for their use in the high-throughput purification of plasmids, genomic DNA and total RNA from different sources, as well as environmental TNA and PCR amplicons. We also provide a bead-based protocol for bisulfite conversion, and size selection of DNA and RNA fragments. Comparison to other methods highlights the capability, versatility and extreme cost-effectiveness of using magnetic beads. These open source protocols and the associated webpage (https://bomb.bio) can serve as a platform for further protocol customisation and community engagement.

Abbreviations
BOMB
Bio-On-Magnetic-Beads
SPRI
Solid-Phase Reversible Immobilisation
MNP
magnetic nanoparticle
Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 12, 2018.
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Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation
Phil Oberacker, Peter Stepper, Donna M Bond, Sven Höhn, Jule Focken, Vivien Meyer, Luca Schelle, Victoria J Sugrue, Gert-Jan Jeunen, Tim Moser, Steven R Hore, Ferdinand von Meyenn, Katharina Hipp, Timothy A Hore, Tomasz P Jurkowski
bioRxiv 414516; doi: https://doi.org/10.1101/414516
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Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation
Phil Oberacker, Peter Stepper, Donna M Bond, Sven Höhn, Jule Focken, Vivien Meyer, Luca Schelle, Victoria J Sugrue, Gert-Jan Jeunen, Tim Moser, Steven R Hore, Ferdinand von Meyenn, Katharina Hipp, Timothy A Hore, Tomasz P Jurkowski
bioRxiv 414516; doi: https://doi.org/10.1101/414516

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