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: Nucleic acids research

Article Title: CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells.

doi: 10.1093/nar/gkac049

Figure Lengend Snippet: Figure 2. Nuclear localization and genome integration of nanostructured DNA. (A) Schematic of experimental approach: 0.5 pmol of each template either was transfected with 500 ng Cas9 nuclease expression plasmid along with 150 ng of sgRNA expressing plasmid or electroporated with 57.2 nmol of Cas9 RNPs. Genomic integration was assessed via flow cytometry after 7 days. (B) (i) Flow cytometry data measuring mNeonGreen+ cells (GFP+) show that looped templates are more efficiently incorporated into the genome compared to unstructured and 18-helix nanostructures. (ii) Flow cytometry of electroporated cells shows similar values across unstructured, looped and 18-helix nanostructures. (C) Aggregated flow cytometry data show that looped templates perform best for both transfection and electroporation. Error bars represent standard deviations (SDs) from three experiments, **P < 0.01, one-way ANOVA. (D) PCR using primers flanking the insertion site confirms mNeonGreen insertion at the target site (right triangle). (E) AFM images of the 18-helix nanostructure before and after electroporation. Scale bar: 100 nm.

Article Snippet: Nanostructured DNA comprising a human gene enhances human primary cell HDR compared to unstructured dsDNA. (A) Schematic of knock-in strategy of a 3.5-kb HDR template encoding IL2RA–GFP fusion and mCherry driven by an EF1a promoter. (B) oxDNA simulations and AFM images of four distinct versions of 18-helix DNA nanostructured HDR templates, including 50% Staples, Only Top, Open and Complex.

Techniques: Transfection, Expressing, Plasmid Preparation, Flow Cytometry, Electroporation

Journal: Nucleic acids research

Article Title: CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells.

doi: 10.1093/nar/gkac049

Figure Lengend Snippet: Figure 4. Nanostructured DNA comprising a human gene enhances human primary cell HDR compared to unstructured dsDNA. (A) Schematic of knock-in strategy of a 3.5-kb HDR template encoding IL2RA–GFP fusion and mCherry driven by an EF1a promoter. (B) oxDNA simulations and AFM images of four distinct versions of 18-helix DNA nanostructured HDR templates, including 50% Staples, Only Top, Open and Complex. Scale bar: 100 nm. (C) Unstructured ssDNA and 18-helix nanostructure templates show increased knock-in efficiency compared to dsDNA. Error bars represent SDs from duplicate experiments. (D) Live cell count shows that unstructured ssDNA and 18-helix nanostructured templates display lower toxicity compared to dsDNA. Error bars represent SDs from duplicate experiments.

Article Snippet: Nanostructured DNA comprising a human gene enhances human primary cell HDR compared to unstructured dsDNA. (A) Schematic of knock-in strategy of a 3.5-kb HDR template encoding IL2RA–GFP fusion and mCherry driven by an EF1a promoter. (B) oxDNA simulations and AFM images of four distinct versions of 18-helix DNA nanostructured HDR templates, including 50% Staples, Only Top, Open and Complex.

Techniques: Knock-In, Cell Counting

Journal: Nucleic acids research

Article Title: CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells.

doi: 10.1093/nar/gkac049

Figure Lengend Snippet: Figure 5. VLPs enable intracellular delivery of nanostructured DNA. (A) Schematic of experimental setup where successful incorporation of HDR tem- plates results in mNeonGreen+ cells. (B) Knock-in efficiencies of unstructured, looped and 18-helix nanostructures show comparable values for delivery using electroporation. Error bars represent SDs from duplicate experiments. (C) Cas9-VLP delivery shows that 18-helix nanostructured templates display a 2.5-fold higher knock-in efficiency compared to unstructured and looped templates. Error bars represent SDs from duplicate experiments, **P < 0.01, one-way ANOVA.

Article Snippet: Nanostructured DNA comprising a human gene enhances human primary cell HDR compared to unstructured dsDNA. (A) Schematic of knock-in strategy of a 3.5-kb HDR template encoding IL2RA–GFP fusion and mCherry driven by an EF1a promoter. (B) oxDNA simulations and AFM images of four distinct versions of 18-helix DNA nanostructured HDR templates, including 50% Staples, Only Top, Open and Complex.

Techniques: Knock-In, Electroporation

Journal: Progress in Biomaterials

Article Title: Graphene-tethered 5-fluorouracil-loaded ZnO nanocomposites for pH-responsive enhanced efficacy in drug delivery on MCF-7 cells

doi: 10.1007/s40204-022-00184-9

Figure Lengend Snippet: Comparison of present nanocomposite drug delivery system (DDS) against literature reported DDS with ZnO, graphene for 5-fluorouracil and superiority on the basis of special characteristics

Article Snippet: Hence, this nanocomposite drug delivery system is best alternative to other reported drug delivery nanomaterials and nanocomposites for apoptosis of cancer cells as per Table . table ft1 table-wrap mode="anchored" t5 Table 3 caption a7 Sr. no. Nanohybrids components and drug-loaded delivery system Selective anticancer activity and characteristics of nanomaterials References 1 ZnO nanoparticles DNA leakage in lung cancer cells, cell–particle interaction but low apoptosis Haider et al. ( 2020 ) 2 Curcumin-loaded ZnO nanocomposite Efficient drug treatment on breast cancer cells but limited apoptosis Sawant and Bamane ( 2017 ) 3 Reduced graphene oxide-5-FU nanocomposite Sustained release and drug delivery on MCF-7 cells but low release with alginate beads Adilakshmi et al. ( 2021 ) 4 Graphene oxide–ZnO nanocomposites Enhanced drug release and good drug loading, limited efficiency of apoptosis Afzal1 et al. ( 2020 ) 5 5-FU loaded on Zeolite ZIF and ZnO core nanocomposites Controlled release with good biocompatibility, but moderate efficiency and require heat treatment Xiao et al. ( 2020 ) 6 Present work: graphene-tethered ZnO nanohybrids for 5-FU anticancer delivery Highest apoptosis of cancer cells, easy drug delivery through graphene, good biocompatibility and sustained drug release at acidic pH Present work Open in a separate window Comparison of present nanocomposite drug delivery system (DDS) against literature reported DDS with ZnO, graphene for 5-fluorouracil and superiority on the basis of special characteristics

Techniques: Activity Assay