dna

43 Articles

Art Imitates DNA

February 1, 2020 by 8 Comments

It has recently been possible to pay a service a little bit of money and learn more about your own DNA. You might find out you really aren’t Italian after all or that you are more or less susceptible to some ailments. [Paul Klinger] had his DNA mapped and decided to make a sculpture representing his unique genetic code. The pictures are good, but the video below is even better.

The project requires a DNA sequencing, a 3D printer, and a Raspberry Pi Zero. Oh, you can probably guess you need a lot of RGB LEDs, too. Of course, the display doesn’t show the whole thing at one time — your DNA pattern scrolls across the double helix.

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Put The Power Of PCR In Your Pocket With This Open-Source Thermal Cycler

January 26, 2020 by 23 Comments

When the first thermal cyclers for the polymerase chain reaction came out in the 1980s, they were as expensive as a market driven by grant money could make them. Things haven’t got much better over the years, largely shutting STEM classes and biohackers out of the PCR market. That may be about to change, though, if the €99.00 PocketPCR thermal cycler takes hold.

PCR amplifies DNA in a three-step process: denaturation, which melts double-stranded DNA into single strands; annealing, which lets small pieces of primer DNA bind to either side of the region of interest; and elongation, where the enzyme DNA polymerase zips along the single strands starting at the primer to replicate the DNA. The cycle repeats and copies of the original DNA accumulate exponentially. Like any thermal cycler, [Urs Gaudenz]’s PocketPCR automates those temperature shifts, using a combination of PCB-mounted heating elements and a cooling fan. The coils rapidly heat a reaction block up to the 99°C denaturation temperature, the fan brings that down to the 68°C needed for annealing, and then the temperature ramps back up to 72°C  for elongation with thermostable DNA polymerase. PID loops keep the reaction temperature precisely controlled. The whole thing is, as the name suggests, small enough to fit in a pocket, and can either be purchased in kit form or scratch-built from the build files on GitHub.

We applaud [Urs]’ efforts to get the power of PCR into the hands of citizen scientists. Quick and dirty thermal cyclers are one thing, but Pocket PCR has a great fit and finish that makes it more accessible.

Thanks to [Abe Tusk] for the tip.

A Beginner’s Guide To X-Ray Crystallography

January 21, 2020 by 6 Comments

In graduate school, I had a seminar course where one of the sections was about X-ray crystallography. I was excited, because being able to discern the three-dimensional structure of macromolecules just by shining X-rays on them seemed like magic to me. And thanks to a lackluster professor, after the section it remained just as much of a mystery.

If only I’d had [Steve Mould] as a teacher back then. His latest video does an outstanding job explaining X-ray crystallography by scaling up the problem considerably, using the longer wavelength of light and a macroscopic target. He begins with a review of diffraction patterns, those alternating light and dark bands of constructive and destructive interference that result when light shines on two closely spaced slits — the famous “Double-Slit Experiment” that showed light behaves both as a particle and as a wave and provided our first glimpse of quantum mechanics. [Steve] then doubled down on the double-slit, placing another pair of slits in the path of the first. This revealed a grid of spots rather than alternating bands, with the angle between axes dependent on the angle of the slit pairs to each other.

Photograph 51, an X-ray crystallogram of the B-form of DNA, by Gosling and Franklin, 1952. Source: Wikipedia

 

To complete the demonstration, [Steve] then used diffraction to image the helical tungsten filament of an incandescent light bulb. Shining a laser through the helix resulted in a pattern bearing a striking resemblance to what’s probably the most famous X-ray crystallogram ever: [Rosalind Franklin]’s portrait of DNA. It all makes perfect sense, and it’s easy to see how the process works when scaled down both in terms of the target size and the wavelength of light used to probe it.

Hats off to [Steve] for making something that’s ordinarily complex so easily understandable, and for filling in a long-standing gap in my knowledge.

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A DNA-Based Computer Calculates Square Roots Up To 900

January 12, 2020 by 20 Comments

While DNA-based computing may not be taking over silicon quite so soon, there is progress in the works. In a paper published by Small, researchers from the University of Rochester demonstrate a molecular computing system capable of calculating square roots of integers up to 900. The computer is built from synthetic biochemical logic gates using hybridization, a process where two strands of DNA join to form double-stranded DNA, and strand displacement reactions.

DNA-based circuits have already been shown to implement complex logic functions, but most existing circuits prior to the recent paper were unable to calculate square root operations. This required 4-bit binary numbers – the new prototype implements a 10-bit square root logic circuit, operating up to the decimal integer 900.

The computer uses 32 strands of DNA for storing and processing information. The process uses three modules, starting off with encoding a number on the DNA. Each combination is attached to a florescent marker, which changes signal during hybridization in the second module. The process for calculating the square root controls the signals, with the results deducted from the final color according to a threshold set in the third module.

We’re beginning to see the end of Moore’s Law approaching, with companies like Intel and AMD struggling to shrink transistors 10 nm wide. Nevertheless, with DNA molecules still about 10 time smaller than the best transistors today and DNA computing systems continuing to gain in sophistication, biochemical circuits could potentially be holding solutions to increasing the speed of computing beyond silicon computing.

Stealing DNA By Phone

April 24, 2019 by 8 Comments

Data exfiltration via side channel attacks can be a fascinating topic. It is easy to forget that there are so many different ways that electronic devices affect the physical world other than their intended purpose. And creative security researchers like to play around with these side-effects for ‘fun and profit’.

Engineers at the University of California have devised a way to analyse exactly what a DNA synthesizer is doing by recording the sound that the machine makes with a relatively low-budget microphone, such as the one on a smart phone. The recorded sound is then processed using algorithms trained to discern the different noises that a particular machine makes and translates the audio into the combination of DNA building blocks the synthesizer is generating.

Although they focused on a particular brand of DNA Synthesizers, in which the acoustics allowed them to spy on the building process, others might be vulnerable also.

In the case of the DNA synthesizer, acoustics revealed everything. Noises made by the machine differed depending on which DNA building block—the nucleotides Adenine (A), Guanine (G), Cytosine (C), or Thymine (T)—it was synthesizing. That made it easy for algorithms trained on that machine’s sound signatures to identify which nucleotides were being printed and in what order.

Acoustic snooping is not something new, several interesting techniques have been shown in the past that raise, arguably, more serious security concerns. Back in 2004, a neural network was used to analyse the sound produced by computer keyboards and keypads used on telephones and automated teller machines (ATMs) to recognize the keys being pressed.

You don’t have to rush and sound proof your DIY DNA Synthesizer room just yet as there are probably more practical ways to steal the genome of your alien-cat hybrid, but for multi-million dollar biotech companies with a equally well funded adversaries and a healthy paranoia about industrial espionage, this is an ear-opener.

We written about other data exfiltration methods and side channels and this one, realistic scenario or not, it’s another cool audio snooping proof of concept.

Forget Artificial Intelligence; Think Artificial Life

April 19, 2019 by 19 Comments

If you are a science fiction fan, you are probably aware of one of the genre’s oddest dichotomies. A lot of science fiction is concerned about if a robot, alien, or whatever is a person. However — sometimes in the same story — finding life is as easy as asking the science officer with a fancy tricorder. If you go to Mars and meet Marvin, it is pretty clear he’s alive, but faced with a bunch of organic molecules, the task is a bit harder. Now it is going to get harder still because Cornell scientists have created a material that has an artificial metabolism and checks quite a few boxes of what we associate with life. You can read the entire paper if you want more detail.

Three of the things people look for to classify something as alive is that it has a metabolism, self-arranges, and reproduces. There are other characteristics, depending on who you ask, but those three are pretty crucial.

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DNA Computers Are In The Lab Now

March 30, 2019 by 18 Comments

Although it isn’t very real-world practical, researchers at Cal Tech have produced a DNA-based programmable computer. Spectrum reports that the system executes programs using a set of instructions written in DNA using six bits. Like any programmable computer, this one can execute many programs, but so far they have run 21 different programs.

Using DNA for computation isn’t new — your body does it all the time. But, in general, DNA computers were akin to some logic gates that would do one set of things, not a general-purpose reprogrammable computer.

DNA has two parts composed of four different chemicals — you can think of each part as a ladder cut vertically down the middle with each “rung” being one of the four chemicals. Each part will try to pair up with a part that has a complementary set of rungs. The researchers created DNA strands to act like logic gates that have two inputs and two outputs. They combine five of these gates to create a layer with six inputs and six outputs. A program contains a stack of these six-bit layers.

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