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MoS2 Pushes Graphene Aside for Fast DNA Sequencing [Chemical Engineering Progress](Chemical Engineering Progress Via Acquire Media NewsEdge) Like a blueprint of a complex building or computer code, sequenced DNA provides an intricate sketch of a person's inner workings. Mapping the DNA of individuals could lead to personalized medicine, early diagnosis of diseases, and a better understanding of the human body. While techniques are available to read DNA, one big challenge is the high cost and timeconsuming nature of these techniques. Researchers at the Univ. of Illinois at Urbana-Champaign (UIUC) have found that the material molybdenum sulfide (MoS-,) sequences DNA more accurately, quickly, and inexpensively than any other method to date. "One of the big areas in science is to sequence the human genome for under $ 1,000 - the so-called genome-at-home," says Narayana Aluru, a professor of mechanical science and engineering at UIUC. "There is now a hunt to find the right material,'' he says. "We've used MoS, for other problems, and we thought, 'Why don't we try it and see how it does for DNA sequencing?"' The traditional method for sequencing DNAi.e., determining the order of each of the four DNA bases (guanine [G], adenine [A], thymine [T], and cytosine [C]) - involves several steps, the first of which is preparing (copying and splitting) the DNA for analysis. The DNA is copied many times by polymer chain reaction (PCR) amplification, and then split into four batches. A small amount of modified base is added to each batch - modified T is added to one batch, A to the second, G to the third, and C to the fourth. The DNA chains are then tagged with fluorescent molecules, one dye for each of the four ending bases. Next, electrophoresis is used to separate the DNA chains into pieces that differ in length by only one base. Once the DNA has been prepared for analysis, a mixture containing DNA from all four batches is placed at one end of a gel. An electric current is applied to the electrodes at both ends of the gel, which causes the DNA chains to move through the gel. The time it takes each piece of DNA to reach the end of the gel is proportional to the length of that chain - longer chains take longer to move from one end to the other. The chains pass through a laser that causes the dye molecules to fluoresce. The computer detects the dye molecule, which identifies the corresponding base. These readings of raw sequence data are then transformed like a jigsaw puzzle into a complete DNA chain. Although progress has been made to speed up this method, it is still time consuming and expensive. Nanoporesequencing techniques, on the other hand, are much faster and less expensive because they do not require PCR amplification, dye labeling, or optical instruments to identify the base labels. Instead of chopping the DNA into small pieces, an intact DNA chain can be processed through a tiny hole in a thin sheet of material. An applied electric field drives the DNA chain through the pore. As each base passes through the pore, it disrupts the current in a way that is characteristic of that particular base, as each base has a slightly different size and shape. The DNA chain moves through the pore at speeds of about 107 bases/sec. Several materials have been used for nanopore-based sequencing. The problem with those materials, though, is that they are too thick. Even very thin pieces of most materials are thicker than one DNA base structure, making it almost impossible to accurately determine the order of the bases in the chain. To address this issue, many researchers have turned to graphene, which consists of a single layer of carbon atoms. Although it is thin enough to allow only one base to pass through at a time, graphene has another drawback: DNA molecules stick to it. The interaction between the DNA and the graphene creates electronic noise, thereby marring the signal. Just like graphene, MoS, is also a single layer of atoms, which means it is thin enough to thread one DNA base through at a time. Unlike graphene, however, MoS, does not interact with DNA in the same way and the bases move through the nanopore unimpeded. The UIUC scientists performed molecular dynamics (MD) simulations to compare the nucleotide-sensing ability of a MoS, nanopore to that of graphene. The simulations revealed four distinct current signals from DNA passing through a nanopore in MoS" one for each of the four bases. Other systems, including graphene, generate only two signals - one for A/T and one for C/G - and extensive computational analysis is required to distinguish A from T and C from G. "MoS, is a competitor of graphene in terms of transistors, but we showed here a new functionality of this material - that it is capable of biosensing," says Amir Barati Farimani, a graduate student of mechanical science and engineering at UIUC. Barati Farimani and his team also performed MD simulations to determine the signal-to-noise ratio of MoS, and graphene nanopores. The results: MoS, has a signal-tonoise ratio of 15, which compares to 3.32 for graphene. According to the researchers, the best signal-to-noise ratio of any nanopore studied to date is about 10. "The ultimate goal of this research is to make some kind of home-based or personal DNA sequencing device," says Barati Farimani. "We are on the path to get there by finding the technologies that can quickly, cheaply, and accurately identify the human genome," he continues. "Having a map of your DNA can help to prevent or detect diseases in the earliest stages of development." The UIUC team is now evaluating the performance of composites, in which MoS, is combined with other materials. (c) 2014 American Institute of Chemical Engineers |