ATmega32 in your home-built DNA sequencer

The May 2013 issue of Circuit Cellar magazine has a great article by Fergus Dixon, who uses an Atmel ATmega32 microcontroller to operate a DNA sequencer.

One of the dozen ways to sequence DNA is to apply a reagent to the DNA sample. If the reagent reacts with the base pair on the end of the DNA strand it splits the pair and emits a tiny burst of light. If it is a double pair the burst of light is twice as strong. Then you just work your way up the DNA strand “zipper,” breaking the pairs and recording which of the 4 pairs you just broke. Now you understand why it took years to sequence even a short DNA strand.

Here is a control board from a DNA sequencer designed by Fergus Dixon

Fergus had the usual engineering fun you might expect when doing something this cool. The flat-black box he housed the light sensor in had a tiny hole. Light variance in the room showed up as noise. He had to figure out a method to drive stepper motors so they were smooth and got to 3000 RPM. He designed reagent solenoid injector drivers that worked off of 100V pulses, while also fiddling with the SPI ports. My consultant buddy John Haggis swears that any serial interface will take up 6-person months of labor.

I used to laugh at that – but I now think he is right. You have to get the hardware working, develop protocols, test for exception conditions – yeah, I can see six months just getting two devices to talk to each other.

You can see that Circuit Cellar has some great articles. The same May 2013 issue has an article on a wi-fi connected energy monitor, a serial port to SPI programmer, a G-code CNC router, a MIDI communication device, and a reprint of a radiation monitor – like a Geiger counter.

Now I can’t show you these articles on-line, since Circuit Cellar is a print magazine. And you have to give them 50 bucks a year to get it. You can get it as a digital pdf if you want to save trees. Its $85 a year for the both print and digital versions. There are large discounts for two- or three-year subscriptions. Best of all, you can give them something like $225 and get every single issue in history on a thumb drive. Then with your combo subscription you can add your monthly pdf to the archive thumb drive, and still have the print edition to impress your friends and boss.