Grad students receive national attention

Nanotechnology research published in July by two Illinois grad students has recently received a lot of attention. MechSE Ph.D. students Amir Barati Farimani and Kyoungmin Min, working under MechSE professor Narayana Aluru, have been studying DNA sequencing, specifically single base recognition. They researched an alternative material to be used for single base recognition and found that it is potentially the best possible material so far.

Single base recognition means to identify the individual bases that make up a DNA strand. DNA sequencing is the study of the order in which these bases make up each strand. These sequences can tell a lot about each person’s body, such as what diseases they’re susceptible to and what cancers they’re the most prone to.

"Understanding this unique map is key for knowing how a person’s body functions," Barati Farimani said.

The bases are each 1-2 nanometers long, and therefore can’t be seen under a normal microscope. The research has been performed by molecular dynamic simulation and density functional theory (completed simulated). The goal of their research was to find a more successful way to read each individual base.

In the last 14 years, one of the most efficient methods that has been proposed is to run the DNA strands through nanopores in a piece of material so that each base can be distinguished by the ionic current associated with it. The pores are about two nanometers in diameter. The DNA and material are put in water and salt with an applied electric field. The DNA is negatively charged, which causes it to move through the pores. Ions in the water are also moving through the pores, and when the DNA bases pass through, they block the ions. Since the bases differ slightly in size, they will each block a different amount of ions from flowing through the pore as they pass through it. So on a graph plotting ionic current vs. time, there will be spikes where the bases blocked the pores, and from the current reading the identity of the individual base that passed through the pore can be read.

The problem with this method is that the pores are 5-8 nanometers thick, meaning that multiple bases will fit inside at the same time.

“The current is mixed, so you can’t identify each base individually,” Barati Farimani said.

The original solution found for this problem was to use graphene as the material that contained the pores, because graphene is only 0.34 nanometers thick. However, around 2010 it was discovered that the DNA strands would stick to the side of the graphene material and wouldn’t pass easily through the pores.

Barati Farimani and Min have been exploring an alternative solution since 2011, which is to use a different material called MoS2 (molybdenum disulfide). 

"We’ve used MoS2 for other problems, and we thought, why don’t we try it and see how it does for DNA sequencing?" Aluru explained.

Using simulations, they have found that DNA doesn’t stick to MoS2 – the bases pass smoothly through the pore. In addition, it could be possible for single base recognition due to the single-layer nature of MoS2. It has been said that graphene is the most optimistic material for DNA sensing, but their conclusion is that MoS2 is better, and could be the best material ever thus far.

Their research was published in ACS Nano and recently featured in Nature Nanotechnology. It was also published in numerous other news sites such as the Illinois NewsBureau, Science Daily, NSF, Air Force Office of Scientific Research, and Medgadget.

"We are happy that our work is actually highlighted in Nature Nanotechnology and other media outlets," Barati Farimani said.

As for the next step in their research, they are now looking into other uses for MoS2. MoS2 has multiple functionalities and would also make a good alternative to the silicon base used in semiconductors. The new question is: which application is the best use of MoS2?