A newly developed DNA “cage” allows scientists to more easily and quickly identify specific portions of a DNA strand. The cage — which traps a single DNA strand — acts as a tiny test tube in which scientists can perform biochemical experiments to determine whether the strand contains a particular gene sequence, according to a new study by University researchers.
The device was developed by Derek Stein, associate professor of physics and engineering, and Xu Liu ScM’11 PhD’14, who led the project during his time at Brown. The traps use nanopores, tiny holes in the cage, that can function as sensors, Stein said.
Some researchers see nanopores as ideal devices for investigating reactions between a polymer and other molecules, but previously there was no way to perform an experiment on the DNA that had passed through the nanopore, said Daniel Branton, professor of biology at Harvard, who was not involved in the study. This new device makes it possible for investigators to use nanopores to study reactions that would not have been observable otherwise, he added.
To trap a DNA strand, the researchers place a nanopore in two reservoirs of salt water and apply a voltage to the water, Stein said. This hole is so small that it forces the DNA strand to pass through head to tail, unfolding any potential tangles. The small size of the nanopore also allows it to serve as a sensor — if the DNA passes through, it will block a significant portion of the current that was sent, Stein said. Scientists can then measure this current to determine if the DNA strand has indeed gone through the hole, he added.
Once the strand is inside the cage, scientists can perform biochemical experiments to reveal the presence or absence of specific DNA sequences. This method can be particularly useful for identifying specific genes or mutations in the strand, Stein said. The DNA can be mixed together with a probe that will bond to a sequence of interest. Examination of the binding between the DNA molecule and the probe can reveal whether a target sequence is present. This little test tube allows for researchers to examine the molecule both before and after the experiment, which was not possible prior to the study.
The device can also be used to learn more about enzymes and other molecules, Liu said. Scientists can use a known sequence of a DNA strand to learn more about enzymes and other chemicals by observing how those enzymes react to the DNA molecule.
The alternative to this technique, a full sequencing of a DNA molecule, usually requires more lab work and more expensive equipment, Stein said. The development of these little test tubes offers a faster and more portable option — one that any scientists with nanopore experience can easily create, he added.
“They laid out very clearly how to make the cage,” Branton said. “It’s a very simple, straightforward procedure.”
Stein said he hopes the nanopore cage will become commonplace in labs. Though the DNA cage is easy to reproduce, specialized researchers may not want to create one on their own, he said. The easiest way to achieve more widespread use of the device is for a company to turn it into a product that could be bought off the shelf, he added.
Liu, who is working at the nanopore startup Two Pore Guys, is helping to develop the technology to commercialize it and “change this from an academic process to an industry process,” he said. This process includes changing steps in their procedures to make structures at a lower cost and finding ways to automate the whole system, he said. Currently, interested researchers “need to go to a lab bench to assemble the cage and perform the experiment … but customers do not want to do this,” he added.