Journal: bioRxiv

Article Title: Resolving antibody avidity through nanoscale antigen patterning

doi: 10.64898/2026.04.18.719169

Figure Lengend Snippet: (A) Schematic representation of the PANMAP pipeline. 1) the surface of a plate is coated with the antigen-patterned nanostructures resulting in a homogenous distribution of the antigen. 2) HRP-conjugated antibodies against the antigen of interest bind to the nanopatterns until equilibrium is reached. Thanks to the controlled antigen spatial distribution, the binding mode of the antibodies is also homogeneous. 3) The bound antibodies are detected by measuring the absorbance of the HRP product. (B) Output of the PANMAP pipeline: a detailed breakdown of constituent binding states comprising the ensemble as a function of antibody solution concentrations (top), and the affinity dependent on antigen separation distance (bottom). (C) ChimeraX illustration of an IgG antibody. PDB ID: 1IGT. (D) Schematic representation of binding state progression with antigen separation distance increase.

Article Snippet: These are made by the DNA origami method for the self-assembly of three-dimensional DNA nanostructures, based on the hybridization of short oligonucleotides (staples) to their complementary regions in a long circular DNA molecule (scaffold) ( ; ; Rothemund et al., 2006).

Techniques: Binding Assay

Journal: bioRxiv

Article Title: Resolving antibody avidity through nanoscale antigen patterning

doi: 10.64898/2026.04.18.719169

Figure Lengend Snippet: (A) Cryo-EM density map of the rod DNA origami with corresponding achieved resolutions. (B) TEM micrograph showing a field of view of empty DNA nanostructures. Scale bar 140 nm. (C) Agarose gel electrophoresis of the antigen-coated nanopatterns after incubation with an excess of low affinity (top) or high affinity (bottom) α-digoxigenin antibodies. L: DNA ladder, S: scaffold, E: empty nanostructure 1ag: 1-antigen nanostructure, 4-35: 2-antigen nanostructures with separations of 4nm, 7nm, 8nm, 10nm, 14nm, 16nm, 21nm and 35nm. (D) Representation of the possible antibody states comprising the electrophoretic bands from the gels in (C). 14: 14 nm 2-antigen nanopattern, 16: 16 nm 2-antigen nanopattern, 21: 21 nm 2-antigen nanopattern. (E) On the left, TEM 3D class average reconstructions of antibody-bound DNA nanopatterns with 1 antigen (top), 2 antigens separated by 14 nm (middle) or 2 antigens separated by 35 nm (bottom), from different perspectives. ChimeraX illustration of the antibody configurations observed on the TEM three-dimensional reconstructions (right).

Article Snippet: These are made by the DNA origami method for the self-assembly of three-dimensional DNA nanostructures, based on the hybridization of short oligonucleotides (staples) to their complementary regions in a long circular DNA molecule (scaffold) ( ; ; Rothemund et al., 2006).

Techniques: Cryo-EM Sample Prep, Agarose Gel Electrophoresis, Incubation

Journal: bioRxiv

Article Title: Predicting DNA origami stability in physiological media by machine learning

doi: 10.1101/2025.07.18.665506

Figure Lengend Snippet: Starting, from left to right, the assembly of DNA origami nanostructures, in three different shapes (rods, icosahedrons and rectangles); their exposure to temperature, pH, MgCl 2 concentration, incubation time and DNase I concentration values; analysis of their stability by dynamic light scattering and generation of the ML model.

Article Snippet: The final concentration of the DNA origami nanostructures was determined via the NanoDrop UV-Vis spectrophotometer (Thermo Fisher Scientific) by measuring the absorption at a wavelength of 260 nm.

Techniques: Concentration Assay, Incubation

Journal: bioRxiv

Article Title: Predicting DNA origami stability in physiological media by machine learning

doi: 10.1101/2025.07.18.665506

Figure Lengend Snippet: ( A ) Schematic representation of the components and formation of DNA origami nanostructures. ( B ) 3D rendered representation of the icosahedrons, rectangles and rods, and their corresponding AFM images (scale bar = 200 nm; heigh values in nm). ( C ) DLS characterization of the three origami shapes. D) GE of purified and unpurified origami shapes, where 1 is M13 scaffold, 2 unpurified icosahedrons, 3 purified icosahedrons, 4 unpurified rectangles, 5 purified rectangles, 6 p7560 scaffold, 7 unpurified rods and 8 purified rods. Sc refers to the scaffold, St to staples and DO to DNA origami.

Article Snippet: The final concentration of the DNA origami nanostructures was determined via the NanoDrop UV-Vis spectrophotometer (Thermo Fisher Scientific) by measuring the absorption at a wavelength of 260 nm.

Techniques: Purification

Journal: bioRxiv

Article Title: Predicting DNA origami stability in physiological media by machine learning

doi: 10.1101/2025.07.18.665506

Figure Lengend Snippet: ( A ) Schematic representation of the change of diffusion coefficient, as measured by DLS, upon destabilization of the DNA nanostructure. The relationship between the radius and diffusion coefficient is provided to aid understanding. D is diffusion coefficient, k B Boltzmann’s constant, T temperature and μ solvent viscosity. ( B ) Diffusion coefficient values measured via DLS for each shape at different experimental conditions (temperature, MgCl 2 concentration, incubation time, pH and DNase I concentration). Error bars represent the standard error of the mean. All p-values were computed from the unpaired t-test with unequal variance with respect to the diffusion coefficient at 4°C; *p-value ≤ 0.05; **p-value ≤ 0.01, ***p-value ≤ 0.001, ****p-value ≤ 0.0001. ( C ) Representative AFM height images corresponding to the control (4°C) and two unstable conditions (60°C and 0.2 U/mL of DNase I) depict the different ways in which loss of structural stability occurs, leading to different diffusion coefficient values (scale bar = 100 nm).

Article Snippet: The final concentration of the DNA origami nanostructures was determined via the NanoDrop UV-Vis spectrophotometer (Thermo Fisher Scientific) by measuring the absorption at a wavelength of 260 nm.

Techniques: Diffusion-based Assay, Solvent, Viscosity, Concentration Assay, Incubation, Control