OSM (Pronounced Awesome) Hardware Makes DNA In Space

April 27, 2017 by Michael Uttmark 21 Comments

OSM stands for Oligonucleotide Synthesizer designed for use in Microgravity, meaning that it’s a device that makes arbitrary DNA strands (of moderate length) in space. Cool eh? I’ve been working on this project for the last eight months with a wonderful team of fellow hackers as part of the Stanford Student Space Initiative, and I’d like to share what we’re doing, what we’ve already done, and where we’re going.

Why space? Well, first of all, space is cool. But more seriously, access to arbitrary DNA in space could accelerate research in a plethora of fields, and the ability to genetically engineer bacteria to produce substances (say on a martian colony) could mean the difference between death and a life-saving shot. In short, it’s hard to predict the exact DNA one might need for research or practical use before hand.

First, as Hackaday tends to be a little light on biology terminology, we need to get a little vocabulary out of the way to grease the ways of communication. If you have a Ph.D. in synthetic biology, you might want to skip this section. Otherwise, here are five quick terms that will make your brain bigger so stay with me!

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Enzymes From The Deep – The Polymerase

March 22, 2016 by Nava Whiteford 46 Comments

Our bodies rely on DNA to function, it’s often described as “the secret of life”. A computer program that describes how to make a man. However inaccurate these analogies might be, DNA is fundamental to life. In order for organisms to grown and replicate they therefore need to copy their DNA.

dna-replication — DNA structure and replication

Since the discovery of its structure in 1953, the approximate method used to copy DNA has been obvious. The information in DNA is encoded in 4 nucleotides (which in their short form we call A,T,G, and C). These couple with each other in pairs, forming 2 complimentary strands that mirror each other. This structure naturally lends itself to replication. The two strands can dissociate (under heat we call this melting), and new strands form around each single stranded template.

However, this replication process can’t happen all by itself, it requires assistance. And it wasn’t until we discovered an enzyme called the DNA polymerase that we understood how this worked. In conjunction with other enzymes, double stranded DNA is unwound into 2 single strands which are replicated by the polymerase.

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Store Digital Files For Eons In Silica-Encased DNA

February 21, 2015 by Theodora Fabio 58 Comments

If there’s one downside to digital storage, it’s the short lifespan. Despite technology’s best efforts, digital storage beyond 50 years is extremely difficult. [Robert Grass, et al.], researchers from the Swiss Federal Institute of Technology in Zurich, decided to address the issue with DNA. The same stuff that makes you “You” can also be used to store your entire library, and then some.

As the existence of cancer shows, DNA is not always replicated perfectly. A single mismatch, addition, or omission of a base pair can wreak havoc on an organism. [Grass, et al.] realized that for long-term storage capability, error-correction was necessary. They decided to use Reed-Solomon codes, which have been utilized in error-correction for many storage formats from CDs to QR codes to satellite communication. Starting with uncompressed digital text files of the Swiss Federal Charter from 1291 and the English translation of the Archimedes Palimpsest, they mapped every two bytes to three elements in a Galois field. Each element was then encoded to a specific codon, a triplet of nucleotides. In addition, two levels of redundancy were employed, creating outer- and inner- codes for error recovery. Since long DNA is very difficult to synthesize (and pricier), the final product was 4991 DNA segments of 158 nucleotides each (39 codons plus primers).

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THP Entry: Polymerase Chain Reaction, Cheaper Than A Hamburger

July 14, 2014 by Brian Benchoff 15 Comments

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.

The 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

September 9, 2012 by Eric Evenchick 12 Comments

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