Viral trapping by DNA origami shells

Hi there, Alba here! I will use today’s online lecture as an opportunity to explain to you how we in Dietz lab have created a DNA origami platform for virus trapping.

We are currently living in the COVID-19 pandemic, and we all have experienced at first-hand how viruses can impact and influence our daily life. As it stands, there have been over ten major viral disease epidemics or pandemics in human populations in the last two decades, and several small sporadic outbreaks. In fact, there are over 200 viral-vector borne human diseases, of which only nine are treatable with current antiviral drugs. Unfortunately, general-acting antiviral systems currently remain a largely elusive goal.

In Dietz lab we have developed a DNA origami platform that can capture and neutralize viruses of different sizes and complexities. These DNA origami structures are shell-like objects, with dimensions ranging from 90 to 300 nm, and are designed to self-assemble from triangular subunits (Fig. 1).

Fig. 1. Schematic representation of the DNA origami-based full shell-like objects.

For virus binding, our shell library must feature apertures that are sufficiently large to permit passage of viruses inside the shell cavity. These apertures are achieved with half-shell designs, which require the design and assembly of different triangular subunits with different edge-docking rules compared to the full-shell variant (Fig. 2).

Fig. 2. O and T=1 half-shell designs.

The inside of the triangular subunits that form the shells can be modified with protruding single-stranded DNA oligos, that can act as handles for incorporation of virus binding moieties (e.g. antibodies, aptamers, polysaccharides, etc.), which then create a coating inside the shells (see Fig. 3). The characteristics of such modifications will determine the target virus. Because of the versatile design approach, our shell library can be used to capture and engulf any virus as long as we have the appropriate binder.

Fig. 3. Functionalization of the single-stranded DNA handles protruding from the triangle’s interior with virus binding moieties (e.g. antibodies, aptamers, etc.).

As an example, the O and T=1 half-shells were functionalized with antibodies for trapping hepatitis B virus (HBV) core particles. Figure 4A shows a cryo-electron microscopy (EM) 3D reconstruction of two O shells coordinating an HBV core particle. The virus particle is indicated with the red arrow, and the antibodies binding moieties with the blue arrow. An HBV core particle was also trapped with a single half T=1 shell (see Fig. 4B for a cryo-EM reconstruction). Negative stain TEM micrographs demonstrate that up to three virus particles could be engulfed by a single half T=1 shell (Fig. 4C).

Fig. 5. Trapping of hepatitis B virus (HBV) core particles. (A) Left: Two-dimensional EM class-averages. Middle: Cryo-EM reconstruction of two octahedral half-shells coordinating a trapped hepatitis-B virus particle. The density around the HBV core particle stems from the antibodies connecting the HBV core particles to the octahedral shell. Red arrows: HBV core particle. Blue arrows: antibodies connecting the shell to the HBV core particle. (B) Same as in (A) for the T=1 half-shell. (C) Negative stain TEM images of T=1 shells engulfing up to three HBV core particles (adapted from Sigl et al.).

When viruses are trapped inside the shells, all virus interactions with host cells are blocked, therefore preventing infection. Even if lots of work are still needed before the implementation of our system as a therapeutic, we envision that the viral load of a host can be considerably reduced in acute infections by irreversibly capturing the virus particles in our shells, and potentially helping a patient to recover faster.

References

Sigl, C. et al. Programmable icosahedral shell system for virus trapping. Nat. Mater. 20, 1281–1289 (2021).