Cheap and Easy Magnetic DNA Separation Method Needs Your Help

When you consider that almost every single cell in your body has more than a meter of DNA coiled up inside its nucleus, it seems like it should be pretty easy to get some to study. But with all the other cellular gunk in a crude preparation, DNA can be quite hard to isolate. That’s where this cheap and easy magnetic DNA separation method comes in. If it can be optimized and tested with some help from the citizen science community.

Commercial DNA separation methods generally involve mixing silica beads into crude cell fractions; the DNA preferentially binds to the silica, making it possible to mechanically separate it from the rest of the cellular junk. But rather than using a centrifuge to isolate the DNA, [Justin] from The Thought Emporium figured that magnets might do a better job. It’s not a new idea — biotech companies offer magnetic separation beads commercially, but at too steep a price for [Justin]’s budget. His hack comes from making magnetite particles from common iron compounds like PCB etchant and moss killer, and household ammonia cleaner. The magnetite particles are then coated with sodium silicate solution, also known as waterglass. The silica coating should allow the beads to bind to DNA, with the magnetic core taking care of separation.

[Justin] was in the process of testing his method when he lost access to the needed instruments, so he’s appealing to the larger science community for help optimizing his technique. Based on his track record of success in fields ranging from satellite tracking to graphene production, we’ll bet he’ll nail this one too.

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Living Logic: Biological Circuits for the Electrically Minded

Did you know you can build fundamental circuits using biological methods? These aren’t your average circuits, but they work just like common electrical components. We talk alot about normal silicon and copper circuits ‘roud here, but it’s time to get our hands wet and see what we can do with the power of life!

In 1703, Gottfried Wilhelm Leibniz published his Explication de l’Arithmétique Binaire (translated). Inspired by the I Ching, an ancient Chinese classic, Leibniz established that the principles of arithmetic and logic could be combined and represented by just 1s and 0s. Two hundred years later in 1907, Lee De Forest’s “Audion” is used as an AND gate. Forty years later in 1947, Brattain and H. R. Moore demonstrate their “PNP point-contact germanium transistor” in Bell Labs (often given as the birth date of the transistor). Six years later in 1953, the world’s first transistor computer was created by the University of Manchester. Today, 13,086,801,423,016,741,282,5001 transistors have built a world of progressing connectivity, automation and analysis.

While we will never know how Fu Hsi, Leibniz, Forest or Moore felt as they lay the foundation of the digital world we know today, we’re not completely out of luck: we’re in the midst’s of our own growing revolution, but this one’s centered around biotechnology. In 1961, Jacob and Monod discovered the lac system: a biological analog to the PNP transistor presented in Bell Labs fourteen years earlier. In 2000, Gardner, Cantor, and Collins created a genetic toggle switch controlled by heat and a synthetic fluid bio-analog2. Today, AND, OR, NOR, NAND, and XOR gates (among others) have been successfully demonstrated in academic labs around the world.

But wait a moment. Revolution you say? Electrical transistors went from invention to computers in 6 years, and biological transistors went from invention to toggle button in 40? I’m going to get to the challenges facing biological circuits in time, but suffice it to say that working with living things that want to be fed and (seem to) like to die comes with its own set of challenges that aren’t relevant when working with inanimate and uncaring transistors. But, in the spirit of hacking, let’s dive right in. Continue reading “Living Logic: Biological Circuits for the Electrically Minded”

Synthetic Biology Creates Living Computers

Most people have at least a fuzzy idea of what DNA is. Ask about RNA, though, and unless you are talking to a biologist, you are likely to get even more handwaving. We hackers might have to reread our biology text books, though, since researchers have built logic gates using RNA.

Sometimes we read these university press releases and realize that the result isn’t very practical. But in this case, the Arizona State University study shows how AND, OR, and NOT gates are possible and shows practical applications with four-input AND gates and six-input OR gates using living cells. The key is a construct known as an RNA toehold switch (see video below). Although this was worked out in 2012, this recent study shows how to apply it practically.

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Get into Biohacking on the Cheap with this Electrophoresis Rig

If you want to get into electronics, it’s pretty straightforward: read up a little, buy a breadboard and some parts, and go to town. Getting into molecular biology as a hobby, however, presents some challenges. The knowledge is all out there, true, but finding the equipment can be a problem, and what’s out there tends to be fiendishly expensive.

So many would-be biohackers end up making their own equipment, like this DIY gel electrophoresis rig. Electrophoresis sorts macromolecules like DNA or proteins by size using an electric field. For DNA, a slab of agarose gel is immersed in a buffer solution and a current through the tank moves the DNA through the gel. The shorter the DNA fragment, the easier it can wiggle through the pores in the gel, and the faster it migrates down the gel. [abizar]’s first attempt at a DIY gel rig involved a lot of plastic cutting and solvent welding, so he simplified the process by using the little plastic drawers from an old parts cabinet. With nichrome and platinum wires for electrodes for the modified ATX power supply, it’s just the right size and shape for the gel, which is cast in a separate mold. The video below shows the whole build, and while [abizar] doesn’t offer much detail on recipes or techniques, there are plenty of videos online to guide you.

Need more apparatus to deck out your lab? We’ve got you covered there too.

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OSM (Pronounced Awesome) Hardware Makes DNA in Space

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

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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DNA Lamp Adds Some Science To Your Room

Lava lamps had their time, but that time is over. Perhaps a spinning, glowing, DNA helix style lamp will take their place?

Inspired by the ever mesmerizing DNA helix, a member of the eLab hackerspace decided to try making it into a lamp. It’s almost entirely 3D printed, with the helix made out of glow in the dark filament.  A series of UV LEDs fade in and out as a small geared motor from a microwave turntable spin the helix round and around.

[João Duarte] designed the assembly using TinkerCAD and has shared all the files on the Instructable in case you want to make one yourself. It is a lot of printing though, so you might want to recruit your own hackerspace’s 3D printer to do some of the work. He ended up using his own Prusa i3 as well as the LulzBot TAZ4 from the space to speed things up.

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