Harnessing DNA tricks to boost nanosensors

Researchers at the University of Pennsylvania have found a way to increase the sensitivity of diagnostic devices, in particular those used to monitor and treat HIV. The research was led by postdoctoral fellows Zhaoli Gao and Han Xia, with guidance from A.T. Charlie Johnson. 

In a new paper, published in Nano Letters, the researchers combined a trick of DNA engineering which involves an engineered piece of DNA called a hairpin, with biosensors, increasing the sensitivity of the sensors by a factor of 50,000 in less than an hour.

The biosensors the researchers are working with are made with graphene, a one-atom-thick material that is perfectly two-dimensional. Because of this, it can be used as an extremely sensitive way of detecting biological signals, measuring the current that flows through graphene surface in the presence of biomolecules. When DNA or RNA molecules bind to the graphene, it produces a big change in the conductivity of the atomically thin material, allowing the researchers to detect infections and to measure viral loads. 

In the past, the researchers used one sequence of single-stranded DNA, which would then bind to the target DNA molecule and produce a change in current. However, this technique only allowed the target molecule to bind at one site. The DNA hairpin used in the new technique has a curled structure that unfurls when the target molecule binds to it. 

When the hairpin pops open, other “helper” DNA that has been added to the system binds with the open hairpin and kicks the target molecule out, allowing it to continuously to bind with many different sites on the sensor, bringing the sensitivity to a range that could prove useful in future diagnostics. 

One possible application of this technique is in portable and inexpensive diagnostic devices capable of detecting an infectious agent in people simply and conveniently and with enough sensitivity to catch it before the level of infection becomes very large. 

“One example would be people with HIV who are being treated, either with current antiretroviral therapy, or with new approaches that are being developed” Johnson says. “If their treatment starts to fail and the level of virus starts to grow, it would be important to catch it quickly and when it's at a relatively low level. It might be possible to combine the sensor with some other sample handling methods so that people might be able to monitor their viral load themselves at home, as opposed to having to go to the doctor. It might even be possible to use it in low-resource settings, parts of the world that don’t have access to the technology needed for this kind of monitoring.”

Johnson says his group is collaborating with others, including David Issadore of the School of Engineering and Applied Science and Ronald Collman of the Perelman School of Medicine to move this technology in the direction of something useful for HIV and in other diagnostic tools. 

“This is a very significant increase in sensitivity that pushes the technique forward,” Johnson says. “In my group, we really like to see graphene sensors of this type do something useful, and we're looking in a number of different directions. This is a huge step forward in the area of diagnostic devices.”

A.T. Charlie Johnson is a professor of physics in the School of Arts and Sciences.

Zhaoli Gao is a postdoctoral fellow in the Department of Physics and Astronomy in the School of Arts and Sciences

Han Xia was a visiting postdoctoral fellow in the Perelman School of Medicine.

David Issadore is an assistant professor of bioengineering in the School of Engineering and Applied Science.

Ronald Collman is a professor in Penn’s Perelman School of Medicine and director of the Penn Center for AIDS Research.

This research was supported by a Gates Grand Challenges Exploration Grant from the Bill & Melinda Gates Foundation.