DNA Funtime: How to Stretch DNA and Put It Anywhere You Want (sort of)

Ever since the days of Watson and Crick—and Franklin, but we won’t get into that right now—we’ve known that double-stranded DNA’s favorite shape is that of a helix. DNA also comes single-stranded and as a random coil, but regardless, as a type of strand, it stands to reason that if tension could somehow be applied to it, it could be elongated or “stretched.”

Why mess with the shape of DNA strands, single, double, random, or otherwise? Actually, when stretched out in all its glory, scientists hope that they may be able to do many things: map patterns in the DNA sequence, characterize chromosomal abnormalities, and possibly even directly read the genetic or epigenetic information right off its back…bone.

Stretching DNA is very tricky, as you might imagine, and requires fairly complicated (and slow) techniques that often create limitations. Particularly, once you’ve stretched the DNA, you’d like to set it down on a surface somewhere to have a look at it. To do this, scientists often need to use a liquid or solid “carrier,” like a pH-controlled solution, to get the DNA in contact with the depositing surface. However, problems can arise if the surface is fragile or otherwise incompatible with the carrier.

In an epic race to try to stretch DNA the fastest, cheapest, and best, scientists have been wracking their brains to come up with new ways in which this can be done. One of these is illustrated in a recently published PLOS ONE study, titled “Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface,” where Harvard researchers developed a new method of stretching DNA that allows the strands to be deposited on many types of surfaces in a precise manner.

The authors call this technique molecular threading, and the method is as follows: stick a special-coated glass microneedle into a DNA-containing droplet of solution, pull it out, and suspend the DNA segment in air until you are ready to put it down on the dry surface below (illustrated in the figure above and the video here).  This works because when you are pulling the DNA out of the droplet, there is an air-liquid interface between the droplet and the air that has the ever-so-convenient property known as surface tension. In a desperate fight to keep the droplet’s shape, the droplet molecules “hold on” to the pulled DNA molecule and create a restoring force that allows the molecule to be suspended in air. As the needle is lowered to the surface, the DNA molecule makes contact with it, and the substrate has enough weak forces to overcome the surface tension, so the DNA sticks to it. And, because threading stretches DNA in air rather than in liquid, the extended thread can be placed onto water-soluble, dry, or fragile surfaces. Voilà!

The researchers gadgeted out the apparatus so that they could monitor this high-throughput process in real-time, take pictures, introduce alternate positioning and angling, and make very precise needle movements. In addition, they made efforts to prevent droplet evaporation and make the straightest DNA strands that they could. The scientists took a look at their handiwork by introducing a fluorescent dye to the DNA and imaging the threads with both fluorescence and electron microscopy; the results of the fluorescence imaging can be seen as bright green lines (individual DNA strands!) in the image below.

As with any technique, there are caveats and limitations, including the occasional multi-thread extraction and missing thread, but all in all, the authors believe that this technique produces cleaner, straighter, and more reproducible strands than other techniques, like molecular combing, and it also allows them to deposit more molecules closer together. Of course, more work is needed to improve the set up and understand exactly what is going on during stretching.

If you are interested in geeking out further on this topic, please check out the awesome instrument and method pics in the article here.

Citation: Payne AC, Andregg M, Kemmish K, Hamalainen M, Bowell C, et al. (2013) Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface. PLoS ONE 8(7): e69058. doi:10.1371/journal.pone.0069058

Image and Video Credits: Figure 1, Figure 2, and Video S1 from the article