Salk scientists use DNA origami to track molecular movements

Scientists often describe life as a series of chemical reactions. Dr. Pallav Kosuri describes life as movement. Chemical reactions are how you drive a car a movement Of atoms, proteins, cells and bodies without movement, nothing life.

“If you don’t know how something moves, you don’t know what it does,” Kosuri says. “And if you want to understand the function of molecules, manipulate them and change them, understanding their physical motions is just as important as understanding their chemical reactions. The difference is: we have a comprehensive catalog of chemical reactions, while the mechanical side is still the Wild West.”

Kosori’s lab is poised to change that. They started with DNA origamia method that uses DNA building blocks to create custom, self-assembled nanostructures with a range of applications, such as drug delivery, lab-on-a-chip devices, and now foundational biological discovery. Then they evolved Orbita method that uses DNA origami to build fluorescent nanostructures to visualize molecular movements.

Technical limitations have long made it difficult or impossible to measure molecular motion over long periods. Fluorescence microscopy is a powerful technique, but observation times are limited by the amount of time the fluorescent markers remain bright over time, always darkening.

Their most recent work published in Cell reporting methods August 13, 2026 ORBIT overcame this challenge with ORBIT’s new “dye cycling” strategy that constantly replenishes fluorescent markers, extending the measurement time window from seconds to hours. This allowed them to measure the turnover of a single RNA polymerase molecule as it “reads” DNA with base-pair precision and over unprecedented timescales. The new method could provide important mechanistic insights into how genes are transcribed in cells.

What is DNA origami?

The DNA contained within every cell in our body is the result of billions of years of evolution and improvement. The structure of DNA depends on complementarity nucleic acids, They are represented briefly by A, T, C, and G DNA The “letter” has a partner that it interlocks with (A with T; C with G) to create the iconic ladder-like double helix we know.

The unique ability of DNA strands to bind and assemble with each other inspired an idea decades ago: What if we used the innate architectural elements of DNA to build structures other than the double helix?

DNA origami structures build themselves, their structure being encoded in their structure. “This is essential to our ability to achieve near-atomic accuracy in our designs.”

Pallav Kosuri, Ph.D., is lead author of the paper and an assistant professor at Salk

In the top-down construction approach, tens of nanometers are limited as the best possible resolution. But because DNA origami self-assembles, the structures can be built from the bottom up instead, allowing much smaller resolutions while maintaining precision and customization.

“You can design 3D structures with higher precision and accuracy than commercial manufacturing methods, and without any machine, just put the components together and let them combine to form something on the nanometer scale, or even smaller,” Kosuri continues. “It’s quick to replicate, cheap, biodegradable, and really fun to work with.”

Why study molecular movements?

Kosuri’s lab has become a leader in DNA origami research — so much so that it was enlisted by engineer and educator Mark Robert to build the world’s smallest Nerf gun entirely out of DNA. The two filmed an educational video that went viral on YouTube and has now been watched by more than 80 million viewers around the world. While the Kosuri lab greatly appreciated the opportunity to showcase the possibilities of DNA design, they are now turning their attention to detecting molecular motion using these same techniques.

Proteins that interact with DNA, such as RNA polymerase, He should They rotate due to the helical structure of DNA. RNA polymerase copies genetic information from DNA into RNA, providing the instructions that the cellular machinery uses to build proteins necessary to maintain cellular life and health.

Transcription of DNA by RNA polymerase is essential for development and daily activity Every cell. So why don’t we study the motion of this master molecular machine?

“Well, we simply can’t see the motion,” Kosuri says. “The circular radius of DNA is 100 times smaller than the wavelength of visible light.” “But instead of measuring that, we thought we could assemble a DNA origami rotor He is visible, then attach it to a DNA strand, and then measure the motion of the rotor instead.”

What is Orbit?

Orbit does just that; It is a method developed by Kosuri that uses fluorescently labeled DNA origami rotors to track the rotation of DNA as it rotates during its interaction with RNA polymerase. Thanks to the precise and specific nature of DNA origami, the method maintains single base pair resolution, allowing scientists to measure rotation as the RNA polymerase traverses each base pair, from AT to CG and so on.

“It’s as simple as attaching a larger object to a smaller object,” Kosuri says. “Now, when the smaller object rotates, we can see the larger object rotating, and record that in a standard microscope.”

A DNA origami rotor attached to a DNA strand looks a lot like a wine opener — a long stem of a key attached to a large, X-shaped handle marked with a fluorescent dye. Once the spike stem is attached to RNA polymerase, the large, fluorescent, X-shaped knob amplifies the movement of the base spike DNA, so scientists can see and measure the rotation.

“ORBIT had the potential to be a powerful way to study RNA polymerase and other proteins that interact with DNA,” says first author Amanda Walker, PhD, who recently completed her PhD in Kosuri’s lab. “But, like other fluorescence tracking methods, ORBIT’s observation times are limited by photobleaching of fluorescent tags on the DNA origami rotor. This is what inspired ORBIT to cycle the dye.”

What is ORBIT for dye recycling?

Fluorescent signs become chemically damaged over time as they emit light. For Kosuri and Walker, this means that Orbit can only track the movement of a few base pairs before the shine fades. The dye cycle provides a solution to this problem.

Instead of attaching a single fluorescent tag to a DNA origami rotor, the dye cycling strategy keeps the fluorescent probes constantly replenished throughout the monitoring process. In other words, the rotorcraft continues to be refueled mid-flight.

“Coupling dye cycling with ORBIT allowed us to overcome the limitations of photobleaching and track RNA polymerase transcription over long timescales while maintaining single base pair resolution,” says Wacker. “We were able to use ORBIT to cycle the dye to track DNA cycles during transcription 10 minutes“.

ORBIT was originally only able to capture a few seconds of movement. While the study shows a solid 10 minutes of effective use of ORBIT for dye rotation, Kosuri shares that ORBIT for dye rotation has since been used in his lab to capture motion for hours. This method has removed a major barrier in fluorescence microscopy methods.

What can the ORBIT dye course teach us?

Dye cycling ORBIT will be an essential tool for exploring this mechanical aspect of biomolecules as the Kosuri Laboratory continues to lead in DNA origami research. Studying the basic rotational movements that underlie gene expression will deepen scientific understanding of the genome, its products, and how cells function or malfunction.

“The only reason the mechanical aspect is a mystery is because we can’t see it,” Kosuri adds. “This method makes it possible to see movements at a fundamental molecular level, and therefore, I believe this method can be used to understand the large, unexplored universe of structural movements that occur in biology.”