09 September 2013

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 previosly 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 known as “molecular combing,” has been used to image DNA that has been aligned on a substrate and labelled 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 convenient 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 tweeked 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.

Now read: Sorry, you will never ride, see or pet a cloned dinosaur

Research Paper: doi:10.1371/journal.pone.0069058 - “Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface”


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