Self-replicating Anti-viral Molecular Machines

Augmanity, a research company based in Rehovot, Israel, has synthesized molecular machines, made from nucleic acids, which are capable of digesting viral RNA and utilizing it to assemble additional copies of itself inside living cells.

The machine’s body plan combines several parts that build upon the target RNA, assembling an immobile, DNA:RNA 4-way junction, which contains a single gene encoding a hammerhead ribozyme (HHR). Full assembly of the machine’s body from its parts enables the subsequent elongation of the gene and transcription of HHR molecules, followed by HHR-mediated digestion of the target molecule. This digestion converts the target to a building block suitable for participation in the assembly of more copies of the machine, mimicking biological heterotrophy.

Above – Images of the prototype automaton attached to DNA rectangles.

The work was led by Ido Bachelet. In 2014, Ido had developed nanobots that could open and close based on molecular sensing. This was going to be the basis for nano-surgery. They had made billions of the devices and would inject them into patients. The company that made the nanobots was bought by Pfizer. There has been no reports on the progress toward nanosurgery from Pfizer. Now, Ido Bachelet appears to have left Pfizer and is working on more advanced nanorobots based upon DNA and RNA.

Augmanity researchers describe the general design of a prototypical machine, characterize its activity cycle and kinetics, and show that it can be efficiently and safely delivered into live cells. As a proof of principle, we constructed a machine that targets the Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) GP64 gene, and show that it effectively suppresses viral propagation in a cell population, exhibiting predator/prey-like dynamics with the infecting virus. In addition, the machine significantly reduced viral infection, stress signaling, and innate immune activation inside virus-infected animals. This preliminary design could control the behavior of antisense therapies for a range of applications, particularly against dynamic targets such as viruses and cancer.

The discovery and synthesis of the immobile DNA junction by Seeman, nearly 4 decades ago, emerged as a cornerstone of DNA nanotechnology, an expanding field with unique technological potential. The immobile junction enabled, for the first time, programming and control of the spatial positioning of matter at a single DNA base resolution, or approximately 3.5 angstroms.

In this work, a preliminary working prototype of such a system is reported. They describe a machine, or automaton, assembled from DNA and RNA, which incorporates structural and functional principles of DNA nanotechnology. The automaton is designed as an immobile, DNA:RNA 4-way junction assembled from 3 parts, and contains a single gene which encodes a hammerhead ribozyme (HHR). Full assembly of the automaton’s body from its parts enables the subsequent transcription of HHR molecules and HHR-mediated digestion of the target molecule. This digestion renders the target suitable for participation in the assembly of more copies of the automaton, essentially mimicking biological heterotrophy. The starting material for self-replication, and for the subsequent “lifecycle” of the automaton, is a small seed population of fully-assembled machines, and a non-limiting amount of the separate DNA parts required for the assembly of new copies of the machine.

The automaton they describe here was inspired by pathogenic viruses and viroids, and is designed to be delivered into and operate inside living, virus-infected cells. Inside the cells, the automaton’s goal is to counter viral infection by utilizing viral RNA as “food”.

The design reported here is modular, and can be adapted rapidly to counter new targets, for example viruses once their genome has been sequenced. In addition, it could lead to new types of biologically-inspired, programmable agents for a range of therapeutic applications. Interestingly, this machine highlights complex anatomy and a hypothetical, rudimentary mechanism for predation, plausible features of molecular life forms from the RNA world.

DNA origami folding. Previously-described DNA rectangles8 were re-designed using caDNAno33 to include 6 edge staples comprising the automaton S strand on its 3’ to enable rectangle-based assembly.

SOURCES – Biorxiv – An antiviral self-replicating molecular heterotroph
Written by Brian Wang,