New Microscopic DNA Machines Could Deploy Drug Therapies Right Into Cells

Common medical treatments often allow drugs to indiscriminately target healthy tissues alongside unhealthy ones, leading to unpleasant or harmful side effects.

To minimize the negative side effects from drug treatments, scientists are continually seeking new ways to more precisely target diseased cells.

Researchers from the University of Chicago may have uncovered a new method for delivering chemical molecules (such as drugs) directly to diseased cells – without allowing any molecules to leak into the bloodstream, where they could damage healthy cells.

The researchers’ innovation relies on tiny, light-activated machines made of DNA: By loading microscopic DNA structures with chemical molecules, and then coating the structures with proteins designed to navigate them to the specific “addresses” of certain cells, the researchers were able to release the chemical molecules to targeted cells in a highly precise manner, on cue, simply by shining a light on the cells.

The university team has been working with DNA “nanomachines” for some time, and they’re not alone: Across the research community, many scientists are exploring how nanotechnology can be utilized to help doctors target specific cells in the most precise ways possible.

The field of nanotechnology uses technological systems many thousand times smaller than a human hair to manipulate molecules or atoms, such as those found in a diseased cell. By targeting cells at the molecular level, scientists can make drug treatment methods more localized – and ideally more effective, with fewer side effects.

(Recent advances on this front include a nanochip capable of “reprogramming” the function of diseased cells; and a nanodrill capable of killing cancer cells in seconds.)

The UChicago researchers initially set out to understand how certain types of cells – specifically, neurons and chemical neurosteroids – interact with each other in the body. But the DNA-based nanotechnology they created in order to carry out their study is now seen as having broader potential applications.

As detailed below, the team used DNA nanomachines as a highly controlled delivery method for carrying neurosteroid molecules into neurons and studying the effects.

Understanding cell function at a molecular level

Understanding the organic interactions among certain cells in the body is a difficult task for scientists: Inside the body, many cells communicate with each other in rapid, barely traceable chemical “whispers” – which happen too fast to accurately study.

Such is the case with neurons (aka nerve cells) and neurosteroids. In the brain, a neuron is an “excitable” cell that receives, processes, and transmits information in response to a number of electrical and chemical signals. The presence of neurosteroids has been known to rapidly alter the “excitability” of neurons.

“The moment you add a neurosteroid, the neuron’s already fired,” says UChicago chemistry professor Yamuna Krishnan, co-author of the study.

But understanding the chemical alteration that takes place has been next to impossible for researchers, due to how rapidly it happens.

A team led by UChicago chemistry professor Yamuna Krishnan sought to gain a blow-by-blow account of what happens in the cell as a neurosteroid “whispers” its chemical instructions to a neuron. Reaching that understanding required the researchers to:

• get the neurosteroids to the cell inside an airtight, self-contained package;
• release them on cue to disseminate in a way that would modify only neurons (and no other cells); and
• track how the “signaling dance” happens inside the neuron, ultimately making it fire.

Custom-built DNA machines provided the ideal delivery vehicle for meeting those requirements:

• Like a set of Legos, DNA exists as a standard set of interlocking pieces that can be built into various configurations. Krishnan’s lab made tiny structures of DNA into the icosahedral shape depicted above (like a 20-sided die). The structure was comprised of two halves clamped together – like an airtight capsule – around a “payload” of molecules of dehydroepiandrosterone (DHEA), a neurosteroid.
• The DNA machines could also be coated with bacterial proteins to navigate them to the exact molecular addresses of the neurons. (Scientists find these addresses by studying how viruses and bacteria home in on particular parts of the body.) “Gluing” these molecular addresses on to the DNA capsules ensured the DHEA interacted only with the exact cells meant to be studied.  
• The DNA structures could also be engineered to be “photoresponsive,” aka light-activated so that researchers would be able to give the structures a cue for when to release the neurosteroid. The researchers loaded their nanostructures with photoresponsive polymers that would trigger the capsules to release the payload of DHEA following exposure to light.

And since DNA is comprised of natural substances already in the body, the custom-built nanostructures could dissolve harmlessly once the DNA had served its molecule-carrying purpose.

Molecules ‘uncaged’ for studying their impact

The researchers carried out their experiments in tests on worms. As the study puts it, the “sequestration” of the DHEA neurosteroid molecules in the DNA nanomachines prevented the DHEA from activating the neurons prematurely.

Once the DNA machines had affixed themselves to the neurons and normal light was applied to them, the machines released the “photocaged” DHEA (as shown in the image below).

By “uncaging” the DNA in this targeted, precise manner, the researchers were able to measure the kinetics of the neurosteroids in previously elusive ways. The team’s technology could report on:

• the number of small molecules released after photoactivation;
• the exact location at which the uncaging of molecules occurred; and
• the timescale of “neuronal activation” by DHEA.

That neuronal activation exhibits itself in the gif below.

CREDIT: Krishnan Group via GIPHY

Since drug delivery wasn’t the initial goal of their research, the UChicago team hasn’t experimented with other drug-carrying molecules just yet. But since the neurosteroids stimulate neurons chemically (in a manner similar to the way therapeutic drugs affect cells), Krishnan says the technology could someday be used to deliver drugs or genetic treatments to certain parts of the body.

For now, the UC researchers’ technology exists as an exciting method for helping scientists better understand the body’s cells and how they interact.

“It’s really a molecular platform,” said Yamuna Krishnan, professor in chemistry and co-author of the study. “There are a host of research problems from cardiology to neurobiology that need a system like this to study very fast molecular phenomena, so it could be applied in a variety of ways.”

The original study “Cell-targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules” was published in the journal Nature Nanotechnology in August 2017. Full information is available here.