DNA origami vaccines program antigen-focused germinal centers

Priming rare subdominant precursor B cells in germinal centers (GCs) is a central goal of vaccination to generate broadly neutralizing antibodies (bnAbs) against HIV. Multivalent immunogen display on protein nanoparticle scaffolds can promote such responses, but it also generates scaffold- specific B cells that could theoretically limit bnAb precursor expansion in GCs. We rationally designed DNA origami–based virus–like particles (DNA- VLPs) displaying a germline- targeting HIV envelope protein immunogen, which elicited no scaffold-specific antibody responses. Compared with a state- of- the- art clinical protein nanoparticle, these DNA- VLPs increased the expansion of epitope-specific GC B cells relative to off-target B cells and enhanced expansion of bnAb- lineage B cells in a humanized mouse model of CD4 binding site priming. Thus, minimizing off-target responses enhances bnAb priming and indicate DNA- VLPs are a promising vaccine platform.
, For complete methods, please see accompanying article (Romanov et. al. 2026.)
DNA-VLP synthesis and characterization
DNA-VLPs were assembled as previously described(53). All designs were generated using DAEDALUS(53) (d40 VLP) or ATHENA(49) (d30 VLP) with staples manually adjusted in Tiamat software(87) to have outward nick positions (2 per edge). To fold origami, 30 nM of scaffold was mixed with 5–10x excess of each oligonucleotide staple in TAE buffer with 12 mM MgCl2 and thermally annealed as follows: 95°C for 5 min, 80–75°C at 1°C per 5 min, 75–30°C at 1°C per 15 min, and 30–25°C at 1°C per 10 min. DNA-VLPs**** were purified into PBS using Amicon Ultra 100 kDa centrifugal filters (Millipore Sigma, cat #UFC810024) spun at 2000g and stored at 4 °C. Purity and dispersity of DNA-VLPs were validated by AGE (1.6% agarose, TAE buffer with 12 mM MgCl2, SYBR Safe, 65V for 150 min) and dynamic light scattering. For antigen conjugation, DNA-VLPs were concentrated to >1 μM and reacted with at..., , # Data from: DNA origami vaccines program antigen-focused germinal centers

Dataset DOI: [10.5061/dryad.n2z34tn7k](10.5061/dryad.n2z34tn7k)

Full article author llist: Anna Romanov, Grant A. Knappe, Larance Ronsard, Christopher A. Cottrell, Yiming J. Zhang, Heikyung Suh, Lauren Duhamel, Marjan Omer, Asheley P. Chapman, Katie Spivakovsky, Patrick Skog, Claudia T. Finn, Jeong Hyun Lee, Oleksandr Kalyuzhniy, Alessia Liguori, Molly F. Parsons, Vanessa R. Lewis, Josue Canales, Boris Reizis, Ryan D. Tingle, Torben Schiffner, William R. Schief, Daniel Lingwood, Mark Bathe, Darrell J. Irvine

Contacts:
Anna Romanov (first author): [[e-mail]](mailto:[e-mail])
Darrell J. Irvine (corresponding author): [[e-mail]](mailto:[e-mail])
Mark Bathe (corresponding author): [[e-mail]](mailto:[e-mail])

Date of data collection: 2021–2025

Location of data collection: MIT Biological Engineering, MIT Nano, MIT BioMicro Center, Koch Institute for Integra...,