Abstract
DNA electrophoresis is a fundamental technique in molecular biology that allows the separation of DNA molecules up to ~50 Kbp. Pulsed-field gel electrophoresis [PFGE] is a variation of the conventional DNA electrophoresis technique that allows the separation of very large DNA molecules up to ~10 Mbp. PFGE equipment is very expensive and it becomes an access barrier to many laboratories. Also, just a few privative designs of the equipment are available and it becomes difficult for the community to improve or customize their functioning. Here, we provide an open source PFGE equipment capable of the separation of DNA molecules up to, at least, ~2 Mbp and at low cost: USD$850, about 3% of the price of typical commercial equipment.
Highlights
DNA electrophoresis is a frequently used technique in molecular biology that allows the separation of DNA molecules up to ~50 Kbp by applying a single-direction electric field across a slab of agarose gel where small DNA molecules are sieved in a size-dependent manner
Pulsed-field gel electrophoresis [PFGE], developed by Schwartz and Cantor (1), is a variation of the conventional DNA electrophoresis technique that allows the separation of very large DNA molecules up to ~10 Mbp
The equipment implements a rotating gel electrophoresis [RGE] over an uniform electric field [Figure 1 & 2], using the basis of the system described by Southern in 1987 (8).The design considers the use of a standard commercially available electrophoresis chamber and the construction of an agarose gel rotation system using 3D printed parts, a servo motor and simple electronics
Summary
In order to contribute to the democratization and acceleration of hardware development in biochemistry, we present in this work a certified open source hardware that implements rotating gel electrophoresis to perform PFGE. The equipment is capable of the separation of DNA molecules up to, at least, ~2 Mbp, costs about USD$850, about 3% of the price of typical commercial equipment considering the chamber and the power source. OpenPFGE has similar requirements, capabilities and results than commercial equipment in terms of applications, maximum fragment size resolution and experiment run time/setup. As it is the first version of the equipment, further improves in design of components, electronics and software can lead to a more robust implementation. Is expected to develop versions of these components to fit openPFGE in order to bring a whole open source PFGE equipment, with both lower costs and flexible design. Allows for run standard PFGE at low equipment cost Allows for easy and inexpensive maintenance and repair of the PFGE equipment Establishes the first open source PFGE development that enables future equipment improvement by the community
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