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Self-powered RNA nanomachine

An artist’s impression of Yokobayashi’s nanomachine. A trigger molecule of RNA causes the nanomachine to change its shape and provide a fluorescent light signal. The trigger molecule is able to act on many nanomachines, allowing amplification of the light signal. Once fully developed, the technology could be used to identify disease states in patients. For more illustrations from @skeppuccino

Scientists at the Okinawa Institute of Science and Technology Graduate University (OIST) have created a nanomachine that can detect RNA sequences and signal their presence with fluorescent light. The technology, discussed in Nucleic Acids Research, could be used to identify RNAs that signal disease states in patients.

The nanomachine, dubbed an “RNA molecular transformer”, is a synthetic RNA molecule that toggles between two states. Upon binding its target RNA, the transformer changes its shape, and this new conformation signals the target’s presence by emitting fluorescent light. This act of shapeshifting also releases the target molecule, leaving it free to transform other nanomachines, amplifying the signal.

Previous studies have created RNA sensors that are similar to the nanomachine, but these sensors needed multiple molecules to work, making them difficult to prepare and use. Here, the researchers were able to combine the actions of many strands into a single RNA molecule.

“Nucleic acids such as RNA and DNA are a fascinating class of molecules for their sheer variety of functions,” explains Professor Yohei Yokobayashi, the study’s lead author. “But what we wanted to do was push beyond what already exist in nature, to explore the possibility of designing molecules that integrate multiple functions.”

Rise of the (nano)machines

In nature, RNAs have diverse functions. They regulate gene expression, recognize specific molecules, and catalyze reactions. Here, Yokobayashi and his colleagues Dr. Shungo Kobori and Dr. Yoko Nomura synthesized RNAs with novel functions. In particular, the team wanted to create a piece of RNA that would change its shape only in in the presence of a specific target.

The synthetic RNAs exist in what is called a branch-like structure. Such structures aren’t thermodynamically stable. They are said to be “frustrated”, which means they can exist in this state for a long time. However, they shift into more thermodynamically stable, rod-like structures, when provided with sufficient energy. For some RNAs, the energy required is high — needing heat or a catalyst — whereas other RNAs can shift structures spontaneously.

Yokobayashi’s team wanted to design an RNA that shifted into its thermodynamically stable form only when they provided the correct trigger — a specific sequence of target RNA. If the molecule were to shift without the trigger, this would provide a fluorescent light signal at an incorrect time, rendering it useless in any medical application.

After exploring many synthetic RNAs the researchers found one that emitted a huge burst of light only when the trigger was introduced.

“In this initial phase, we were driven by intellectual curiosity, to demonstrate that creating such a machine was even possible,” explains Yokobayashi. “But eventually we want to shift into in vivo environments with more relevant medical applications, as well as building additional complexity into these molecules.”

In the future, researchers could deliver nanomachines into living cells using viral vectors encoding the molecule. In this way, the cell’s own machinery could be used to create the nanomachines. They could then act as a diagnostic device by sensing specific molecules associated with different disease states.

Until then, Yokobayashi is keen to explore how much complexity can be built into these molecules, pushing the barriers of what is possible in these elegant, tiny machines.

Okinawa Institute of Science and Technology Graduate University (OIST)

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