DNA Forklifts

Pretty cool, using DNA to move single molecules around.

Manipulating nanoscale objects is a very hot research area these days, but no one’s quite sure whether it should be called physics or chemistry. The single-atom stuff (like the famous 1989 spelling of I-B-M using an early scanning tunneling microscope tip) would probably be the former, while moving whole molecules around would probably be the latter.

Now we’re to the point where you might consider it biology, since several recent papers describe ingenious uses of DNA as nanoscale pliers and Velcro. A report in Science from a group in Munich, demonstrates a nanoscale depot on a chip, formed by short DNA strands bound to its surface. Various molecules are tagged with complementary single strands of DNA. When you bring the two close enough, they hybridize, winding together spontaneously into a small double helix, which Velcros each molecule down to a defined position.

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The second key to the work is that each of the molecules has a second, different DNA strand bonded to its other side. This one is complementary to a single strand attached to the tip of an atomic force microscope, so when that moves in close enough, those two hybridize as well. For the moment, the target is bound front and back.

But here's the trick: the two DNA helices are engineered so that the double helix on the bottom opens base-by-base, like a zipper, while the one on the AFM tip shears off all at once. That gives them different strengths, so when you pull up on the AFM tip, you can see the force profile of the "zipper" strand giving way as the attached molecule pulls free. Now it's dangling from the tip of the AFM, its newly freed DNA strand waving in the, uh, nano-breeze, I guess.

This was now moved to another portion of the chip, where more DNA strands awaited. These, like the tip strands, where also in the stonger "shear" geometry, but these were even longer, with more residues to wrap up with that free DNA strand on the molecule of interest. Lowering the two into proximity caused them to hybridize, and now pulling up on the tip caused the tip strand to unwind instead, leaving the molecule stuck on the new location on the chip. The AFM tip could then be sent back to the depot to pick up another molecule, and so on. (The illustration, courtesy of Science for nonprofit use, will give you the idea). The fluorescent molecules they used could then be imaged on the chip, confirming that they'd been arranged as expected.

Wait until scientists figure out how proteins fold. Then we'll be able to engineer DNA strands that code for nanoscale turbines or whatever you can dream up of. And clone that DNA into bacteria and make limitess nanobots!