Synthetic biology has gone through a sequence-specific revolution recently, with CRISPR-cas leading the charge of systems that can detect any DNA sequence of interest. But these techniques have a key limitation: they can only respond locally with one action – cutting, activating, or repressing – at that particular DNA molecule.
This is like giving Paul Revere a big fat telescope so he can see with exquisite detail who is coming to his party, but he can only respond by meeting them with dry towels if they happen to be coming by sea. This wouldn’t make Paul a very good sentinel, so a new study shows how to equip him with a cell phone so he can spread the message and activate specific plans based on who’s coming.
Giving DNA-Sensors a Cell Phone
To do this, Shimyn Slomovic and Jim Collins at MIT used zinc-finger (ZF) proteins, which recognize specific DNA sequences, with a very clever use of the SceVMA intein. Inteins are peptide sequences that cut themselves out of the middle of a protein and then splice the two ends back together. Interestingly, the SceVMA intein works even if it’s cut in half, as long as the two halves get close enough together. If there are peptides dangling off each half of the intein, the splicing reaction cuts them off and glues them together, making a new fused protein.
To tie this back to DNA recognition, Shimyn fused the two intein halves to ZFs that would bind right next to each other on a target sequence, thus activating splicing. The business ends of the intein halves were fused to a third ZF domain and an activator domain, respectively. So without target DNA, we would have:
When ZF1 and ZF2 bind next to each other on the target DNA, they activate the intein, which splices and releases a new ZF3-Activator protein, which can go spread the word and activate a pre-programmed response.
Making the Zinc-Finger Cell Phone Smart
As proofs of principle, the team transfected the system into mammalian cells and showed they could turn on either GFP or a cell death gene in response to invasion by specific plasmid or virus DNA.
This probably isn’t ready for thwarting invasions just yet, but there are a lot of cool places it could go, including:
- Identifying transfected or infected cells
- Identifying successfully genome-edited cells
- Finding live cells with specific mutations
- Studying long-range DNA looping in live cells
One of the most interesting synthetic biology applications would be using this to induce gene expression with short dsDNA sequences. Current sequence recognition lets us turn any gene on or off, but specific inducers would let us control when.
Ok, we’ve detected this study and carried the message on to you, now activate your response circuit and go check out the paper in Nature Methods, 2015.