THP Entry: Polymerase Chain Reaction, Cheaper Than A Hamburger

PCR Invented 30 years ago, polymerase chain reaction , or PCR, is one of the greatest inventions of the 20th century. It’s the technique that allows researchers to map genomes, find genetic causes of diseases, create Jurassic Park, and match crime scene DNA to suspects. When PCR was first invented it was extraordinarily expensive, and even today commercial PCR machines cost about the same as a new car. There is an open source project for a PCR machine that costs about $600, but for his Hackaday Prize entry, [David] is knocking a few more zeros off that cost and building a machine for less than the cost of a fast food meal.

Despite being the work behind a Nobel Prize, PCR is conceptually fairly simple: A strand of DNA is unwound into two strands, an enzyme, or primer, is annealed onto these single strands, and then biochemistry happens, turning those single helix strands of DNA into a complete double helix, ready for the next replication cycle. The key of the PCR technique is getting the enzymes and primers to react. This is only done at a fairly fine range of temperatures, cycling between 90°C, then 60°, then 72°C.

The oldest models of PCR machines used multiple water baths, with newer commercial machines using something that probably justifies their cost. The OpenPCR project uses an aluminum heater block, but [David] is going for a modern twist on the old-school method. He’s trying to figure out how to exploit convection to get local temperature variations in a single vessel. How he’s going to do this is anyone’s guess, but building a PCR machine for $5 is pretty cool.


SpaceWrencherThe project featured in this post is an entry in The Hackaday Prize. Build something awesome and win a trip to space or hundreds of other prizes.

Genetic Research on the Cheap

When you think of DIY hardware, genetic research tools are not something that typically comes to mind. But [Stacey] and [Matt]‘s OpenPCR project aims to enable anyone to do polymerase chain reaction (PCR) research on the cheap.

PCR is a process that multiplies a specific piece of DNA a few million times. It can be used for many purposes, including DNA cloning and DNA fingerprinting for forensics. PCR is also used for paternity testing.

The process involves baking the DNA at specific temperatures for the right amount of time. The DNA is first denatured, to split the helix into individual strands. Next, the temperature is lowered and primers are bound to the strands. Finally, another temperature is used to allow the polymerase to duplicate the DNA. This process is repeated to multiply the DNA.

The OpenPCR uses an Arduino to control a solid state relay. This relay provides power to two large resistors that act as heaters. A MAX31855 is used to read a thermocouple over SPI and provide feedback for the system. A computer fan is used to cool the device down.

A milled aluminium sample holder houses and heats the samples during cycling. The laser cut, t-slot construction case features some helix art, and houses all of the components. It will be interesting to see what applications this $85 PCR device can perform.

Via Adafruit

How to grow your own EL wire DNA helix lamp

el-wire-helix-lamp

[LucidMovement] was looking for some crystal-based artwork and just couldn’t seem to find anything that fit the bill, so he decided to build something himself.

The inspiration for his desk lamp came from something we’re all familiar with, a DNA double-helix. To grow the crystals he built a helix-shaped growing substrate out of nichrome and EL wires, submerging them in a warm alum solution. Once he had a nice set of crystals, he mounted it in an acrylic tube, filling the air space with clear silicone to seal off the display. He then mounted the silicone-filled tube on top of a rotating acrylic stand that he had cut for the project. The stand is made from several sheets of acrylic and contains both the gearing for movement as well as RGB LEDs to light the display from the bottom.

The lamp looks great when sitting idle, but when he powers it on it really shines (no pun intended). [LucidMovement] put a ton of work into the lamp, and offers up all sorts of tips, tricks, and considerations for anyone looking to build their own. Be sure to check out his writeup for plenty more details, and stick around to see a short video of the lamp in action.

[Read more...]

Genetic testing with Lego

From the dark recesses of the Internet circa 2009 comes the BioBrick-A-Bot, a liquid handling system for molecular biologists.

The 2009 iGEM competition was a student competition to build devices for synthetic biology. The BioBrick-A-Bot’s goal is to build a simple, low-cost liquid handling system that sucks liquids out of petri dishes and into vials.

Like most lab equipment, the commercial version of this tech is insanely expensive – about 10 grand for a commercial liquid handling robot. The BioBrick-A-Bot is made nearly entirely out of LEGO parts, so the cost of the entire system was brought down to about $700.

There are two main parts to the BioBrick-A-Bot. The Alpha module holds four pipette on a delta platform We’ve seen this type of robot built out of LEGO before, but moving liquids is new territory. The Phi module contains all the mechanics to suck microliters of liquid into a pipette and spit them out into vials.

The BioBrick-A-Bot didn’t win the 2009 iGEM competition (that honor was taken by students from Heidelberg Cambridge), but we’d take a LEGO robot any day of the week. Check out the demo after the break.

[Read more...]

Simulated annealing

annealing

Here’s an update on our earlier post about genetic programming. Altered Qualia has posted a new implementation of [Ron Alsing]‘s idea. It starts with 50 polygons and then randomly changes one parameter with each optimization step. If the the change results in fewer differences from the target image, it’s kept as the new best DNA. This search method is similar to simulated annealing. The image above is the result of 1500 good mutations out of 35900 possible. The implementation lets you choose any image, but smaller means the fitness calculation is faster. It’s written in JavaScript using the <canvas> environment. You’ll definitely get better performance using newer browser builds.

[Original image by R Stevens]

[via Waxy]

24C3 Hacking DNA

[Drew Endy]‘s Programming DNA talk was by far the most interesting talk we saw at Chaos Communication Congress. No, DNA doesn’t have much to do with computers, but he points out that hacking principles can be applied just the same. Right now engineers are reversing genetic code and compiling building blocks for creating completely arbitrary organisms. This talk was designed to bootstrap the hacking community so that we can start using and contributing standard biological parts to an open source collection of genetic functions.

You should definitely watch the video to get a good idea of where biohacking is at today. You can find a higher quality version of the video in the archives.

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