Use customized protein-based sensor to detect viral infection

Biological engineers from MIT have developed a modular system of proteins which can detect a particular DNA sequence in a cell and then give a response like cell death. According to the researchers, the system can be customized to detect any DNA sequence in a mammalian cell and kill cancer cells or cells infected with a virus.
"There is a range of applications for which this could be important," says James Collins, the Termeer Professor of Medical Engineering and Science in MIT's Department of Biological Engineering and Institute of Medical Engineering and Science (IMES). "This allows you to readily design constructs that enable a programmed cell to both detect DNA and act on that detection, with a report system and/or a respond system."
The technology is based on a type of DNA-binding proteins known as zinc fingers. These proteins can be designed to recognize any DNA sequence.
"The technologies are out there to engineer proteins to bind to virtually any DNA sequence that you want," says Shimyn Slomovic, an IMES postdoc and the paper's lead author. "This is used in many ways, but not so much for detection. We felt that there was a lot of potential in harnessing this designable DNA-binding technology for detection."
The researchers needed to link zinc fingers's DNA-binding capability with a consequence-either turning on a fluorescent protein to reveal that the target DNA is present or generating another type of action inside the cell. To create the new system, they exploited a type of protein known as an "intein" and split it into two pieces. The split protein pieces are called "exteins". They only become functional once the intein removes itself while rejoining the two halves.
They decided to divide an intein in two and then attach each portion to a split extein half and a zinc finger protein. The zinc finger proteins are engineered to recognize adjacent DNA sequences within the targeted gene, so if they both find their sequences, the inteins line up and are then cut out, allowing the extein halves to rejoin and form a functional protein. The extein protein is a transcription factor designed to turn on any gene the researchers want.
The researchers also deployed this system to kill cells by linking detection of the DNA target to production of an enzyme called NTR. This enzyme activates a harmless drug precursor called CB 1954, which the researchers added to the petri dish where the cells were growing. When activated by NTR, CB 1954 kills the cells.
There will be more versions in the future which bind to DNA sequences found in cancerous genes and then produce transcription factors that would activate the cells' own programmed cell death pathways. This protein-based sensor can be of great significance.
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