Use of Magnetic probe in wet lab biology
Magnetic beads are widely used in wet lab biology to purify molecules such as DNA, RNA and proteins from solutions. Magnetic beads are used to selectively attract the molecules of interest from a mixture of enzymes. This is very common in various life science research settings.The ability to artificially create DNA (Synthetic) has significantly transformed the field of biomedical sciences. Various applications in medicine, food and materials technology have opened up and resulted in establishment of industries and research facilities that use synthetic DNA on a day-to-day basis.
During DNA synthesis, the strand separation post-dsDNA synthesis and the extraction of single stranded DNA from a pool of enzymes are key steps. Usage of paramagnetic beads that selectively bind to modified DNA base pairs of a single strand, is an attractive option for this purpose (see Fig. 1). This is done by heating the reaction-well (≥ 65°C) to denature the DNA strands, leading one strand available to attach to the paramagnetic beads and the other strand freely floating in the solution. At this point, a magnetic probe is used to isolate the magnetic beads (which have the attached ssDNA). As a result ssDNA is successfully isolated and the next steps are carried out.
Figure 1: Magnetic bead separation using a magnetic probe. a) Single strand DNA molecules are attached to magnetic beads b) A magnetic probe is lowered into the solution and magnetic beads (along with the DNA molecules) are magnetically attached at the bottom of a magnetic probe c) Magnetic probe brings the beads (along with the DNA) into a new solution d) A permanent magnet near the tube will release the magnetic beads back into the new solution e) Finally magnetic probe is removed from the solution.
Why using a permanent magnetic probe is not a viable solution for high-throughput applications.
This isolation process can be scaled up for high throughput DNA synthesis by equipping a robotic handler (ex: OpenTrons) with a magnetic probe device. Permanent magnetic probes exist in the market to extract the magnetic beads after the denaturation process. However, the harsh environment of the DNA synthesis process (which involves multiple heating and cooling cycles) introduces hysteresis and permanent magnet slowly loses its magnetic property. Moreover, it is also very difficult to find permanent magnets that can fit the standard disposable pipette tips. Therefore, we were contacted by a start-up company to design a special magnetic probe for isolation of DNA
Design and fabrication of magnetic probe
To overcome the hysteresis problems of a permanent magnetic, we would like to make a magnetic probe that exploits electromagnetism (EM). The advantage of the EM probe is that it can be with a customised shape to fit to standard disposable pipette tip. The basic design of the Magnetic Probe is given by the start-up company.
The design of the EM probe started with a copper coil harvested from a relay switch. For the initial testing, we kept a nail as the core of the electromagnet (Fig. 2a). We simply applied 5 volts and the probe started to attract the iron dust (see the video here https://www.youtube.com/watch?v=HlXHz4GMDSs). When the prototype was working, we designed a holder using OpenScad (Fig. 2b). Surprisingly, it took us more time to design the holder that can hold the copper coil in place. In the initial prototype we used a nail as the core for the EM probe (Fig. 2c). We used a knitting needle as the core of the EM probe. Dimensions of this needle perfectly matched to use with disposable pipette tips (Fig. 2d).
Figure 2: a) Prototype of an EM probe made with a Copper-coil harvested from a relay switch b) CAD diagram of the EM probe holder c) First Assembled EM probe d) Final assembled EM probe.
Future scope
In the future, we would like to mount this magnetic probe on an Opentron liquid handling robot and validate the whole device with a few DNA samples. The same process could be extended towards RNA and protein isolation as well.
Acknowledgements
Nimesh, Vamsi, Uday and SMART – Servier Medical ART