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(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.

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

(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).

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