MIT engineers have developed a modular system of proteins that can detect a particular DNA sequence in a cell and then trigger a desired response, including killing cancer cells or cells infected with a virus.
The technology is based on a type of DNA-binding proteins known as zinc fingers. These proteins can be designed to recognise any DNA sequence.
“The technologies are out there to engineer proteins to bind to virtually any DNA sequence that you want,” said Shimyn Slomovic, a postdoc at Massachusetts Institute of Technology’s Institute of Medical Engineering and Science (IMES) and the paper’s lead author.
“We felt that there was a lot of potential in harnessing this designable DNA-binding technology for detection,” Slomovic said.
To create their new system, the researchers needed to link zinc fingers’ 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.
The researchers achieved this by exploiting a type of protein known as an “intein” – a short protein that can be inserted into a larger protein, splitting it into two pieces.
The split protein pieces, known as “exteins,” only become functional once the intein removes itself while rejoining the two halves. The researchers 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 recognise 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.
In the study, researchers linked green fluorescent protein (GFP) production to the zinc fingers’ recognition of a DNA sequence from an adenovirus, so that any cell infected with this virus would glow green.
The researchers can programme the system to produce proteins that alert immune cells to fight the infection, instead of GFP.
“Since this is modular, you can potentially evoke any response that you want. You could programme the cell to kill itself, or to secrete proteins that would allow the immune system to identify it as an enemy cell so the immune system would take care of it,” Slomovic said.
The MIT 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.
Future versions of the system could be designed to bind to DNA sequences found in cancerous genes and then produce transcription factors that would activate the cells’ own programmed cell death pathways.