A fully automated, open source robot for DNA purification
It purifies DNA with magnetic beads (SPRI beads). It can run 2 procedures:
It removes short DNA strands (primers). Used for PCR cleanup.
It removes both short and long DNA strands. Used for library prep.
Robot adds the beads to the sample. The desired DNA binds to the beads, while undesired impurities stay in the solution. Then, magnet approaches the tube and pulls the beads with DNA to the wall of the tube. The pipette removes liquid with impurities, while DNA stays on beads. After washing, robot adds an eluent to the tube. The eluent is detaching DNA from magnetic beads. Robot then pulls the beads to the wall of the tube again and transfers eluted DNA to a new tube.
In case when a user needs to remove a large DNA as well, purification is done in two steps. At first step, robot adds little volume of the beads to the sample, so only large DNA is bound. Then, robot moves the liquid with the desired DNA and small impurities to a new tube. There, robot performs the second stage of purification, which is identical to the previous paragraph.
Make sure the robot has tip box with enough tips and the trash box is empty
Place the reagents: beads, 80% ethanol, water or another eluent
Place the samples and empty tubes
Specify parameters of purification (sample volume, desired DNA size or amount of beads to add, etc.)
Press “start”
Robot will do the rest. It will test the provided parameters for errors. Then, if necessary, it will calibrate the pipette tip rack, to make sure it properly picks up the tips. After that, it will perform the purification.
Depending on the number of samples and the protocol, the purification will take 20-45 minutes.
Robot will remember the amounts of reagents in the tubes, as well as which tips were used. You can perform next purification without the need to specify amounts of reagents (assuming you do not use them for some other purposes).
See also the detailed documentation.
It works as well as a human does.
It will not make an accidental mistake, such as pipetting into the wrong tube, or forgetting a step in the protocol.
Footprint: 54 x 57 cm (1 ft. 9 in X 1 ft. 10 in)
Height: 53 cm (1 ft. 8 1/2 in)
Number of purified samples: 12 samples when removing small DNA, 6 samples when removing both small and large DNA.
Pipette volume: 250 uL (0.25 mL)
Pipette standard: 250 uL LTE ("green" Rainin pipettes)
Sample tubes: 1.5 mL "Eppendorf" tubes
Reagent tubes: 50 mL or 5 mL tubes
Electronics: Arduino-based
Firmware: Marlin-based, modified
Software: Python 3.x
No. Robot will automatically probe all the racks and tubes and find all necessary coordinates.
Zero dead volume.
Bernie has load sensors. When it touches something with the tip, sensors register how hard does it presses.
Before performing a protocol, Bernie will touch the bottom of every tube, finding its exact Z coordinate. With that, it will know at which exact height to pipette to remove all liquid.
Good question, since any beads cleanup protocol includes vortexing steps.
Bernie pipettes up and down until solutions are mixed.
The software will pick the right procedure depending on the sample type and the amount of liquid.
Several. After all, I was the only developer on that project so far.
Electronics is still a mess. With your support, I will be able to develop a decent breadboard.
Motors are noisy. Will be fixed before shipping.
Still too bulky. I will be able to reduce the size for at least 20% before shipment.
Not super fast. While it performs the protocol with the same speed a human does, we can still do better. We can use very fast DC servo motors, for one. However, it will happen in the next versions.
Controlled software needs improvement. GUI is not yet ready (but will be ready before shipment).
There might be some minor bugs. There may be even some major bugs, although I will do my best to make sure there are none.
