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Tuesday, August 17, 2021

Programmable Virus Traps?

Here on the face of it quite a claim.  Human tests still years away. 

Programmable Trap Can Kill Viruses  By R. Colin Johnson  in CACM

Commissioned by CACM Staff, August 17, 2021

Using computational genetic engineering, researchers at the Technical University of Munich (TUM) say they have invented a method of killing any type of virus. The researchers say they have demonstrated their solution on previously incurable hepatitis-B viruses, and are next aiming at the coronavirus.

The deoxyribonucleic acid (DNA) origami base-pair key-in-lock method they devised yields sphere-like icosahedral shells that kill viruses by clamping around each virion (the complete, infective form of a virus outside a host cell) until it is dead, dead, dead.

"Computational methods are an integral part of our work, from the initial design phase to the data processing for the final cryogenic electron microscopy," explains Hendrik Dietz,   a professor of biomolecular nanotechnology at TUM. "In one way or another, all members of my team are using computer modeling."

Shawn Douglas, a professor of molecular engineering at the University of California at San Francisco, said the work by Dietz and his team "is a remarkable demonstration of the power and versatility of DNA origami hierarchical assembly by non-covalent shape complementarity, a method that was also pioneered by the Dietz Lab. These new icosahedral shells are beautiful and inspiring artifacts of molecular engineering. I am excited to see how the team and their collaborators can adapt this system for in vivo applications in the coming years." 

The method uses a combination of software engineering, computational chemistry, and complementary DNA base-pair key-in-lock scaffolding to create icosahedral "traps" that snap shut around a target virus, isolating it harmlessly from both infecting and duplicating, and resulting in its eventual death.

The genetic engineering involved in the process does not tamper with human DNA; instead, the researchers use the universal building blocks of DNA—synthetic versions of the nucleotides cytosine, guanine, adenine, and thymine. A "virus trap" composed of locked-in-place isometric triangles is constructed in a spherical shape. A specific combination of nucleotides is first modeled in simulation to be the correct size to handle the target virus, then constructed using synthetic DNA from scientific laboratory suppliers. A coating is then inserted into the shell's interior to trap the virus inside, and a cap is added to block its exit. In practice, the virus victim's blood is flooded with the traps, which safely capture the individual virions and destroy them.

Dietz' TUM lab used a battery of software to model, simulate, validate, construct, and test prototype traps, the first of which were designed for hepatitis-B. The virus traps were tested in vitro (in a test tube or elsewhere outside the body) and were observed to be capable of trapping a targeted virus through the use of single-particle cryo-electron microscopy, which harnesses computationally intensive machine learning algorithms, according to Dietz. Subsequent in vivo (within a living organism) testing on mice showed the DNA-origami traps were capable of targeting individual virions inside the body, disarming them without disrupting bodily functions, and finally destroying them with natural immunological mechanisms. Human trials, however, are years away.    ... '

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