Scientists create DNA tracking tags, might soon be used to track protesters as well as animals. A global identification system will also be used to identify new species into the fold.
According to the tale of Caesar’s last breath, each breath we draw probably contains a few of the molecules that escaped with his last. That assumes of course, that those 1022molecules were more-or-less uniformly mixed with the 1044 molecules in the atmosphere. When acting blind, as with the simple inert molecules in the air, this great thermal mill only homogenizes. But if purposed with more versatile actors, it becomes the universal constructor that knits order into every cell in our bodies, molecule by molecule. When instead of gases, the molecules are snippets of DNA — barcodes if you will — they can be used to discreetly, and unambiguously, mark almost anything. With the right molecular touch, it is possible to determine where something first came from, and where it has been.
Researchers at the University of Aveiro in Portugal are developing DNA barcode tags that can be harmlessly applied to a wide variety of products, even foods or liquids. Each tag is a unique combination of DNA base pairs that attach to most surfaces, and can later be collected, amplified, and sequenced. The power of this technique lies in the uncountable micro-matings that take place in the DNA solution where the primary goal is to determine like from unlike. Every known sequencing method has some margin of error, and the chance of false positives or false negatives exists whenever the signal to noise ratio is too low.
The general concept has been around for some time, particularly as used by biologists to track and identify species. One major project, known simply as the barcode of life, now has over 200,000 animals cataloged in a searchable database. Since things like animals already come pre-barcoded, all one need do is find some region in their DNA that tends to mutate fast enough over time so that each species can be expected to show enough variation. Usually, a 600-spot region in a mitochondrial gene known as cytochrome oxidase is used. These oxidases are essential enzymes which perform functions like degrading caffeine, and many other drugs, into products that can be removed by the body.
The most imaginative use for DNA barcodes is to trace neurons, and their activities, within the brain. The original BRAIN Initiative, before its initial aspirations were chopped back, called for something even more dramatic — growing barcodes that stored vast amounts of information in real time. In other words, molecular ticker tapes built into every neuron. DNA sequencing pioneer George Church holds the patent for a so-called nucleic acid memory device.
This concept uses a specially constructed DNA polymerase (an enzyme which copies DNA) to directly transmute voltages appearing across the membranes of cells into DNA base pair patterns. By using several ticker tapes to create a sufficient level of redundancy, an arbitrary degree of accuracy can be achieved, all within the existing energy budget of the cell.
Some of these concepts will undoubtedly be harder to implement than others. A simple DNA paint might be something we could buy at the store or make at home with little effort. DNA may be everywhere right now, but compared to what soon may come, we could literally end up swimming in the stuff.
Molecular threading: A powerful tool for DNA sequencing
Familiar to us as building blocks of life, DNA molecules have also proven themselves as versatile building blocks for a wide variety of new nanostructures. While solution-phase chemistry lets millions of parallel DNA reactions be performed simultaneously in a beaker, manipulating single molecules of DNA is still a formidable challenge. A new technique, known as molecular threading, now lets researchers grab onto a single gnarled strand of DNA in solution, draw it out into thin air, and neatly fix it to a substrate where it can be accessed.
The process was developed several years ago by Halcyon Molecular and has attracted significant funding from illustrious investors including Elon Musk and Peter Thiel. The intellectual property is now owned by Aeon Biowares, a company which develops, among other things, heavy metal labels to visualize large biomolecules like DNA. Exotic DNA structures and devices, including things like 3D DNA origami, have many potential applications. Right now, though, the most practical application is sequencing.
We have previously reviewed several new technologies for sequencing which can potentially make the process a whole lot easier and faster. None of these techniques — not even the fiendishly intricate ion-pore sequencing — compares with the idea of actually watching a translating DNA strand with a transmission electron microscope. This possibility was first envisioned back in 1959 by Richard Feynman, and has yet to be fully realized. An older technique is known as “molecular combing,” has been used to image DNA that has been aligned on a substrate and labeled with heavy metals. This method, however, still has several shortcomings.
The power of the new molecular threading technique is that individual strands of DNA can be essentially hand-pulled out of a tiny drop, and neatly arrayed in perfectly straight lines on a variety of conventional materials. The researchers do this using some standard tools that have been available for years to fabricate fine glass electrodes for recording neurons, or to artificially inseminate eggs. By heating and pulling a fine glass needle into a sharp tip, and coating it with a hydrophobic material (PMMA), they were able to manipulate a delicate strand like you would a string with your hand.
To be competitive for sequencing, the threading rate will likely need to be increased beyond that of their initial experiments. The team reports a speed of 10hz, apparently the rate at which the individual base pairs are drawn from the droplet. Using faster piezo manipulators should increase this speed, although ultimately they will come up against the physical limits of the DNA strand itself — presumably the rate at which various viscous and surface tension forces relax at the interface area. They have also constructed parallel arrays, typically with 50 to 100 threads each, that will provide much-needed speed for the process. The team was able to thread both single-stranded and double-stranded DNA from a variety of different sources.
As their open source research paper indicates, the team has filed several patents related to the technique, and other applications besides sequencing may be forthcoming. One area of nanofabrication they describe would be precision nanowire arrays that could be tweaked to have favorable electrical, optical, or catalytic properties when suitably modified. If successfully commercialized, molecular threading will be a powerful new tool for building new kinds of DNA machines.
Source: Extreme Tech