A paper published today in Nature Nanotechnology describes what may be the world’s tiniest ruler for measuring proteins. Called DNA Nanoswitch Calipers (DNC), this technology enables researchers to perform distance measurements on single peptides with high precision by applying small amounts of force. By rapidly making many distance measurements on the same molecule, DNC creates a unique “fingerprint” that can be used to identify it in subsequent experiments.
DNC is based on the underlying technology of the DNA nanoswitch, a single strand of DNA with molecular “handles” attached to it at multiple points along its length. When two of these handles bind to each other, they create a loop in the DNA strand, and the overall length of the strand is shortened. When force is applied to pull the handles apart, the strand extends back to its original length. The difference between the length of the strand in its looped and unlooped states reflects the size of the loop, and thus the distance between the handles.
The research team realized that they could take DNA nanoswitches one step further: if they instead engineered the handles to bind to a biomolecule, the handles could effectively “pinch” the molecule between themselves like the two tips of a caliper, rather than binding to each other. By measuring how the addition of the target molecule between the handles changed the overall length of the DNA nanoswitch in its looped vs. unlooped states, the team hypothesized that they could effectively measure the size of the molecule.
“We were actually somewhat surprised by how well this technique worked,” said co-first author Prakash Shrestha. “Optical tweezers have been around for decades and cycling DNA between a looped and unlooped state has been around for about 10 years, and we weren’t sure whether we could get sufficiently high-resolution measurements by combining those ideas. But it turned out that these fingerprints are very effective for identifying proteins.”