Structural DNA nanotechnology arrays devices to capture molecular building blocks

To use programmable nanomechanical manipulating devices to maneuver molecular building blocks it would be very helpful to array two or more devices in a molecularly precise arrangement with respect to each other. Structural DNA nanotechnology has now achieved this milestone with the demonstration that two independently controlled nanomechanical devices can be positioned on a two-dimensional DNA grid so that they can cooperate to capture between them one of four DNA building blocks, determined by which of two possible states each device is set to. Thus the identity of the building block captured by the two devices can be dynamically programmed by programming the setting of each of the two devices. From New York University, via AAAS EurekAlert “Chemists create two-armed nanorobotic device to maneuver world’s tiniest particles“:

Chemists at New York University and China’s Nanjing University have developed a two-armed nanorobotic device that can manipulate molecules within a device built from DNA. The device is described in the latest issue of the journal Nature Nanotechnology [abstract].

“The aim of nanotechnology is to put specific atomic and molecular species where we want them and when we want them there,” said NYU Chemistry Professor Nadrian Seeman, one of the co-authors. “This is a programmable unit that allows researchers to capture and maneuver patterns on a scale that is unprecedented.”

The device is approximately 150 x 50 x 8 nanometers. A nanometer is one billionth of a meter. Put another way, if a nanometer were the size of a normal apple, measuring approximately 10 centimeters in diameter, a normal apple, enlarged proportionally, would be roughly the size of the earth.

The creation enhances Seeman’s earlier work—a single nanorobotic arm, completed in 2006, marking the first time scientists had been able to employ a functional nanotechnology device within a DNA array.

The new, two-armed device employs DNA origami, a method unveiled in 2006 that uses a few hundred short DNA strands to direct a very long DNA strand to form structures that adopt any desired shape. These shapes, approximately 100 nanometers in diameter, are eight times larger and three times more complex than what could be created within a simple crystalline DNA array.

As with Seeman’s previous creation, the two-armed nanorobotic device enables the creation of new DNA structures, thereby potentially serving as a factory for assembling the building blocks of new materials. With this capability, it has the potential to develop new synthetic fibers, advance the encryption of information, and improve DNA-scaffolded computer assembly.

In the two-armed nanorobotic device, the arms face each other, ready to capture molecules that make up a DNA sequence. Using set strands that bind to its molecules, the arms are then able to change the structure of the device. This changes the sticky ends available to capture a new pattern component.

The researchers note that the device performs with 100 percent accuracy. Earlier trials revealed that it captured targeted molecules only 60 to 80 percent of the time. But by heating the device in the presence of the correct species, they found that the arms captured the targeted molecules 100 percent of the time.

They confirmed their results by atomic force microscopy (AFM), which permits features that are a few billionths of a meter to be visualized.

Nadrian Seeman was awarded the Feynman Prize in Nanotechnology in 1995. His subsequent pioneering achievements in structural DNA nanotechnology included the development in 2002 of the PX-JX₂ devices used as nanomanipulators in this work. The scaffolded DNA origami that was essential to provide a large enough array to accommodate two PX-JX₂ devices was invented by Paul W.K. Rothemund, co-winner of the 2006 Foresight Institute Feynman Prizes in both the theory and experimental categories. Because the DNA origami substrate holds the two different PX-JX₂ devices in a specific orientation with respect to each other, and because each device has two unique binding sites that can be arranged in either of two possible configurations, the two devices can be set to four possible configurations of the four binding sites. Depending on which of the four configurations is programmed, the two devices will capture the one of four DNA tiles that presents the complementary configuration of binding sites—either a straight rod tile, or a diamond tile, or a triangle tile pointing to the notched side of the DNA origami substrate, or a triangle pointing away from the notched side of the DNA origami substrate. Because the settings of the two devices can be independently programmed, the configuration of the binding sites can be dynamically programmed and thus the pattern of the DNA tile positioned on the DNA origami substrate can be dynamically patterned. The authors note that “there is no apparent limitation on the ability of the target tile to carry a cargo … This ability would allow a given addressable two-dimensional DNA surface to be programmed dynamically for a variety of purposes…”. The authors further note that the principal current limitation of the method is the difficulty of constructing DNA origami tiles larger than 5000 to 10,000 square nanometers, and the difficulty of combining multiple origami tiles to make larger areas. (Credit: KurzweilAI.net and ScienceDaily.)
—Jim