DNA origami

DNA Origami Nanovaccine Demonstrates Full Protection Against SARS-CoV-2 in Mice

A study recently published in Communications Biology (Nature Portfolio) by Esra Oktay, Farhang Alem, Keziah Hernandez, Michael Girgis, Christopher Green, Divita Mathur, Igor L. Medintz, Aarthi Narayanan, and Rémí Veneziano introduces an innovative DNA origami–based nanovaccine platform targeting the receptor-binding domain (RBD) of SARS-CoV-2. Their findings highlight the potential of rationally engineered DNA nanoparticles to elicit strong and durable immune protection.

The researchers designed wireframe DNA origami nanoparticles (DNA-NPs) functionalized with ten trimerized RBD antigens and CpG oligonucleotides as adjuvants. Trimer assembly was achieved by peptide nucleic acid (PNA)–mediated conjugation of protein G to RBD-Fc, enabling precise orientation on DNA-NP overhangs. Biophysical characterization employed dynamic light scattering, Förster resonance energy transfer (FRET)–based stability assays, and quantitative fluorescence labeling. Structural confirmation was obtained via atomic force microscopy (AFM). For high-resolution AFM imaging, the team employed NanoWorld® USC-F0.3-k0.3 ultra-short cantilevers, chosen for their 300 kHz resonance frequency, ~0.3 N/m force constant, and <10 nm tip radius. These probes provided enhanced stability and resolution, enabling accurate nanoscale visualization of the vaccine constructs. In murine models, the fully assembled RBD-DNA-NP with CpG provided complete protection following viral challenge. Vaccinated mice exhibited no weight loss or mortality, in stark contrast to control groups that received unconjugated components, bare origami scaffolds, or RBD alone—several of which experienced significant morbidity or mortality. Immunological assays revealed sustained neutralizing antibody activity two months post-immunization, with robust titers of RBD-specific IgG, IgM, and IgA, underscoring the durability of the immune response. This work demonstrates that DNA origami nanostructures can serve as an adaptable and effective vaccine delivery platform. By integrating precise antigen display with adjuvant loading, the approach provides a promising blueprint for next-generation nanovaccines. The use of advanced AFM probes, such as the NanoWorld® USC-F0.3-k0.3, further underscores the importance of high-precision nanometrology tools in validating nanoscale biomedical designs.
a Hydrodynamic diameter measurement of DNA-NPs with DLS. b Atomic force microscopy imaging of DNA-NPs formation and conjugation with 3-mer RBDs (scale bar: 20 nm). c Fluorescence-intensity based determination of PG and RBD stoichiometry on DNA origami NP. i) Tryptophan fluorescence emission was used to determine the total number of PG loaded on the surface of the DNA-NPs. ii) Second, the stoichiometry of RBD on NP was quantified via measuring the emission of Cy5 dyes conjugated to the RBD antigens. The bar graph represents the total coverage percentage for the PG (green bar) and the 3-mer RBD (orange bar) on the DNA-NP surface normalized to the number of conjugation sites available. Data are shown as the mean ± SD (n = 3 independent experiments).

This article contains images reused from Jia et al., Nature Communications 14, 1394 (2023), licensed under CC BY 4.0.

Cryopreservation of DNA Origami Nanostructures

Although DNA origami nanostructures have found their way into numerous fields of fundamental and applied research, they often suffer from rather limited stability when subjected to environments that differ from the employed assembly conditions, that is, suspended in Mg2+-containing buffer at moderate temperatures.*

In the article “Cryopreservation of DNA Origami Nanostructures” Yang Xin, Charlotte Kielar, Siqi Zhu, Christoph Sikeler, Xiaodan Xu, Christin Möser, Guido Grundmeier, Tim Liedl, Amelie Heuer-Jungemann, David M. Smith and Adrian Keller investigate means for efficient cryopreservation of 2D and 3D DNA origami nanostructures and, in particular, the effect of repeated freezing and thawing. It is found that, while the 2D DNA origami nanostructures maintain their structural integrity over at least 32 freeze–thaw cycles, ice crystal formation makes the DNA origami gradually more sensitive toward harsh sample treatment conditions. *

The cryoprotectants glycerol and trehalose are found to efficiently protect the DNA origami nanostructures against freeze damage at concentrations between 0.2 × 10−3and 200 × 10−3m and without any negative effects on DNA origami shape. This work thus provides a basis for the long-term storage of DNA origami nanostructures, which is an important prerequisite for various technological and medical applications. *

NanoWorld Ultra-Short Cantilevers for High-Speed AFM USC-F0.3-k0.3 were used for the AFM imaging in liquid of the DNA origami sample described in this article.

Figure 2 from “Cryopreservation of DNA Origami Nanostructures” by Yang Xin et al.:

AFM images of triangular DNA origami nanostructures after 32 freeze–thaw cycles measured a) in air and b) in liquid. AFM images of triangular DNA origami nanostructures assembled from scaffold and staple strands that were subjected to 32 freeze–thaw cycles measured c) in air and d) in liquid. Images have a size of 1.5 × 1.5 μm2 and height scales are 2.3 nm. — Figure 2 from “*Cryopreservation of DNA Origami Nanostructures*” by Yang Xin et al.:

AFM images of triangular DNA origami nanostructures after 32 freeze–thaw cycles measured a) in air and b) in liquid. AFM images of triangular DNA origami nanostructures assembled from scaffold and staple strands that were subjected to 32 freeze–thaw cycles measured c) in air and d) in liquid. Images have a size of 1.5 × 1.5 μm2 and height scales are 2.3 nm.

*Yang Xin, Charlotte Kielar, Siqi Zhu, Christoph Sikeler, Xiaodan Xu, Christin Möser, Guido Grundmeier, Tim Liedl, Amelie Heuer-Jungemann, David M. Smith and Adrian Keller
Cryopreservation of DNA Origami Nanostructures
Small 2020, 16, 1905959
DOI: 10.1002/smll.20190595

Please follow this external link to read the full article: https://onlinelibrary.wiley.com/doi/pdf/10.1002/smll.201905959

Open Access The article “ Cryopreservation of DNA Origami Nanostructures “ by Yang Xin, Charlotte Kielar, Siqi Zhu, Christoph Sikeler, Xiaodan Xu, Christin Möser, Guido Grundmeier, Tim Liedl, Amelie Heuer-Jungemann, David M. Smith and Adrian Keller is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability

DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions.*

In their article “Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability” Charlotte Kielar, Yang Xin, Xiaodan Xu, Siqi Zhu, Nelli Gorin , Guido Grundmeier, Christin Möser, David M. Smith and Adrian Keller investigate the effect of long-term storage of the employed staple strands on DNA origami assembly and stability.*

Atomic force microscopy (AFM) under liquid and dry conditions was employed to characterize the structural integrity of Rothemund triangles assembled from different staple sets that have been stored at −20 °C for up to 43 months.*

NanoWorld Ultra-Short Cantilevers USC-F0.3-k0.3 were the AFM probes that were used for the AFM measurements under liquid conditions.*

Figure 1. from “*Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability*” by Charlotte Kielar et al.
(a) Schematic illustration of the Rothemund triangle DNA origami. AFM images of DNA origami triangles assembled from staple sets aged for (b) 2–7 months, (c) 11–16 months, (d) 22–27 months, and (e) 38–43 months. Measurements were performed either in liquid (left column) or dry conditions after gently dipping the sample into water (central column) or after harsh rinsing (right column). Scale bars represent 250 nm. Height scales are given in the individual images. The insets show zooms of individual DNA origami triangles.

*Charlotte Kielar, Yang Xin, Xiaodan Xu, Siqi Zhu, Nelli Gorin , Guido Grundmeier, Christin Möser, David M. Smith and Adrian Keller
Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability
Molecules 2019, 24(14), 2577
doi: https://doi.org/10.3390/molecules24142577

Please follow this external link to the full article: https://www.mdpi.com/1420-3049/24/14/2577/htm

Open Access: The article « Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability » by Charlotte Kielar, Yang Xin, Xiaodan Xu, Siqi Zhu, Nelli Gorin , Guido Grundmeier, Christin Möser, David M. Smith and Adrian Keller is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.