DNA origami presenting the receptor binding domain of SARS-CoV-2 elicit robust protective immune response

Abstract

Effective and safe vaccines are invaluable tools in the arsenal to fight infectious diseases. The rapid spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the coronavirus disease 2019 pandemic has highlighted the need to develop methods for rapid and efficient vaccine development. DNA origami nanoparticles (DNA-NPs) presenting multiple antigens in prescribed nanoscale patterns have recently emerged as a safe, efficient, and easily scalable alternative for rational design of vaccines. Here, we are leveraging the unique properties of these DNA-NPs and demonstrate that precisely patterning ten copies of a reconstituted trimer of the receptor binding domain (RBD) of SARS-CoV-2 along with CpG adjuvants on the DNA-NPs is able to elicit a robust protective immunity against SARS-CoV-2 in a mouse model. Our results demonstrate the potential of our DNA-NP-based approach for developing safe and effective nanovaccines against infectious diseases with prolonged antibody response and effective protection in the context of a viral challenge.

Customized Scaffolds for Direct Assembly of Functionalized DNA Origami

“…Here, we designed the binding sequence to be complementary to a peptide nucleic acid (PNA) strand as this method allows the use of a shorter linker due to the higher affinity of PNA for DNA rather than DNA itself. We chose a recombinant protein G (PG) commonly used to bind and immobilize antibodies via their Fc domains . The PG has a free cysteine at its N-terminal that we used to conjugate with a PNA maleimide to form protein G-PNA (PG-PNA) as recently described .…”

“…The unmodified PB DNA-NPs and PB DNA-NPs containing scaffolds that were produced using 10, 20, and 35% phosphorothioate-modified linkage (henceforth referred to as “αThiol”) as well as the multifunctional PB (multi-V: 7.5% biotin, 15% NH2, 15% αThiol) were assembled in the presence of either only FAM (5′-donor)-modified staple strands or staple strands having both FAM and TAMRA (5′-acceptor) together (Table S4). FAM and TAMRA staple strands have been positioned to ensure a distance of approximately 3 nm between the donor and acceptor to maximize FRET efficiency as previously used . Following purification using 100 kDa Amicon columns as described in Section , fluorescently labeled DNA-NPs were incubated in PBS that had been complemented with 20% mouse serum.…”

“…16 This unique capability endows the DNA-NPs with unique properties and functions when compared to other nanoparticle materials, which has led to the development of several promising nanocarriers that could replace some of the more classical materials, such as liposomes and polymeric nanoparticles, that are traditionally used in various biomedical applications. 17,18 For instance, DNA origami is used for labelfree RNA detection, 19 triggered cargo release, 20,21 vaccine development, 22,23 immune cell stimulation, 24,25 cancer immunotherapy, 26,27 enzyme cascade reconstitution, 28 and analysis of dynamic molecular events. 29,30 The assembly of DNA-NPs is usually accomplished via slow annealing of a long single-stranded DNA (ssDNA) scaffold with several complementary short ssDNA oligonucleotides called "staple strands".…”

“…The DNA origami technique offers unprecedented precision for the design and assembly of discrete, biocompatible, and functional nanoarchitectures, ranging from 10 to a few hundred nanometers (nm) in size. − The unique addressability of DNA origami nanoparticles (DNA-NPs) also enables the organization of biomolecules (e.g., proteins, − peptides, and nucleic acids , ), fluorophores, , and metallic nanoparticles , with nanoscale precision and controlled stoichiometry . This unique capability endows the DNA-NPs with unique properties and functions when compared to other nanoparticle materials, which has led to the development of several promising nanocarriers that could replace some of the more classical materials, such as liposomes and polymeric nanoparticles, that are traditionally used in various biomedical applications. , For instance, DNA origami is used for label-free RNA detection, triggered cargo release, , vaccine development, , immune cell stimulation, , cancer immunotherapy, , enzyme cascade reconstitution, and analysis of dynamic molecular events. , …”

Functional DNA as a Molecular Tool in Regulating Immunoreceptor–Ligand Interactions

“…Of note, unlike protein scaffolds (virus-like particles, VLPs), the DNA-based scaffolds themselves, as thymus-independent antigens, induce only extrafollicular B-cell responses, thus avoiding scaffold-directed immunological memory that results in antibody dependent clearance of the vaccine platform. Almost at the same time, Oktay et al also demonstrated that precisely patterning ten copies of a reconstituted trimer of the RBD of SARS-CoV-2 along with CpG adjuvants on DNA origami was able to elicit a robust protective immunity against SARS-CoV-2 in mice . These works illustrated the potential of DNA nanotechnology for the construction of novel and highly effective subunit vaccines.…”