denv1 ns1 v1  (Native Antigen Inc)

Journal: Nature Communications

Article Title: Expanded genetic alphabet increases structural and chemical diversity of six-letter DNA for high-affinity protein-targeting aptamers

doi: 10.1038/s41467-025-67486-x

Figure Lengend Snippet: A Unnatural bases in XenoAptamers. The Ds−diol-Px pair is utilized in PCR as a third base pair in the ExSELEX process. B Secondary structures of three XenoAptamers targeting DENV1-NS1-v1 (AptD1), DENV1-NS1-v1 and -v2 (AptD1c), and DENV2-NS1 (AptD2). C Binding analysis of anti-DENV1-NS1-XenoAptamers with the NS1 variants (DENV1-NS1-v1 and v2) by an electrophoretic mobility shift assay (EMSA) in the presence of 3 M urea at 30°C. The experiment was performed once. D EMSA-based binding analysis of AptD2 derivatives containing substituted Pa'35 variant bases. The experiment was performed in duplicate. E K D values of AptD2 and its derivatives, AptD2-Pa′ and AptD2-Pa′ (diol), determined by SPR.

Article Snippet: Recombinant DENV-NS1 proteins with a C-terminal poly-histidine-tag were obtained from the Native Antigen Company (DENV2-NS1 and DENV1-NS1-v1) or produced in-house using a conventional CHO cell expression system (DENV1-NS1-v2) as described previously .

Techniques: Binding Assay, Electrophoretic Mobility Shift Assay, Variant Assay

Journal: Nature Communications

Article Title: Expanded genetic alphabet increases structural and chemical diversity of six-letter DNA for high-affinity protein-targeting aptamers

doi: 10.1038/s41467-025-67486-x

Figure Lengend Snippet: A–C Cryo-EM density maps of AptD1 with DENV1-NS1-v1 (hexamer) ( A ), AptD1c with DENV1-NS1-v2 (tetramer) ( B ), and AptD2 with DENV2-NS1 (dimer) ( C ). D–F Cryo-EM structures of XenoAptamers with their respective NS1 proteins. In the figures, only one XenoAptamer and one dimer of NS1 are shown. G – I The electrostatic surface potential models of NS1 show the XenoAptamers’ recognition of the positively charged surfaces of NS1 proteins ( G–I ). J–L Cryo-EM structures of XenoAptamers, in which the unnatural bases Ds and Pa′ are shown in yellow and black, respectively.

Article Snippet: Recombinant DENV-NS1 proteins with a C-terminal poly-histidine-tag were obtained from the Native Antigen Company (DENV2-NS1 and DENV1-NS1-v1) or produced in-house using a conventional CHO cell expression system (DENV1-NS1-v2) as described previously .

Techniques: Cryo-EM Sample Prep

Journal: Nature Communications

Article Title: Expanded genetic alphabet increases structural and chemical diversity of six-letter DNA for high-affinity protein-targeting aptamers

doi: 10.1038/s41467-025-67486-x

Figure Lengend Snippet: A , B The overall structure of DENV1-NS1-v1 is complexed with AptD1 (green). In the XenoAptamer structures, the unnatural Ds bases are shown in yellow. One protomer of NS1 protein is colored dark blue (β-roll domain), orange (connector subdomain), yellow (wing domain), and pink (β-ladder domain), while the other is shown in light colors. The residues interacting with AptD1 are highlighted in red. C–E DENV1-NS1-v1 recognition of AptD1 in the positively-charged cleft ( C , D ) and at the outer surface ( E ).

Article Snippet: Recombinant DENV-NS1 proteins with a C-terminal poly-histidine-tag were obtained from the Native Antigen Company (DENV2-NS1 and DENV1-NS1-v1) or produced in-house using a conventional CHO cell expression system (DENV1-NS1-v2) as described previously .

Techniques:

Journal: Nature Communications

Article Title: Expanded genetic alphabet increases structural and chemical diversity of six-letter DNA for high-affinity protein-targeting aptamers

doi: 10.1038/s41467-025-67486-x

Figure Lengend Snippet: A , B Overall structure ( A ) and cleft-focused structure ( B ) of DENV1-NS1-v2 with AptD1c (green). In the XenoAptamer structures, the unnatural bases Ds are shown in yellow. One protomer of NS1 protein is colored dark blue (β-roll domain), orange (connector subdomain), yellow (wing domain), and pink (β-ladder domain), while the other is shown in light colors. The residues interacting with AptD1 are highlighted in red. ( C–H ) DENV1-NS1-v1 recognition of AptD1c in the positively-charged cleft ( C–F ) and at the outer surface ( G , H ).

Article Snippet: Recombinant DENV-NS1 proteins with a C-terminal poly-histidine-tag were obtained from the Native Antigen Company (DENV2-NS1 and DENV1-NS1-v1) or produced in-house using a conventional CHO cell expression system (DENV1-NS1-v2) as described previously .

Techniques:

Journal: Science translational medicine

Article Title: Antibody Fc characteristics and effector functions correlate with protection from symptomatic dengue virus type 3 infection

doi: 10.1126/scitranslmed.abm3151

Figure Lengend Snippet: A) Pre- inapparent (blue) and pre-symptomatic (orange) secondary DENV3 infection plasma samples were collected for systems serology. Neutralization (Neut) (B) and inhibition enzyme-linked immunosorbent assay (iELISA) binding antibody titers (C) were determined. (D-E) Heatmap showing the antigen-specific antibody isotype and Fc-receptor binding (D), as well as Fc effector functions (E) of antibodies against envelope (E) and non-structural 1 (NS1) proteins of DENV1–4 and ZIKV. Antibody isotype and Fc receptor binding were measured by a Luminex-based assay and are shown as median fluorescence intensity (MFI). Heatmaps show univariate analysis for biophysical (D) and Fc effector function (E) profiling of polyclonal antibodies against envelope (E) and non-structural 1 (NS1) proteins of DENV1–4 and ZIKV. Fc effector functions investigated were: Antibody-dependent cellular phagocytosis (ADCP), neutrophil phagocytosis (ADNP), complement deposition (ADCD) in the presence of guinea pig complement, and NK cell activation (ADNKA). The values were z-scored across all samples, and the tiles indicate the difference in median z-score within the group. Asterisks indicate Benjamini-Hochberg adjusted p-values for Mann-Whitney U tests (*p<0.05, **p<0.01, ***p<0.001). “-“ indicates that this combination of antigen and antibody feature was not measured. MIP1b: macrophage inflammatory protein 1β; IFNg: Interferon-γ (gamma). B, C, and D were performed in technical duplicates. For effector functions in ‘E’, data represents an average from primary neutrophils or NK cells from two donors (ADNP and ADNKA) or average of technical duplicates (ADCP and ADCD).

Article Snippet: Recombinant envelope (E) and nonstructural protein 1 (NS1) from DENV1–4 and ZIKV were commercially acquired from Meridian Life Sciences (USA) and Native Antigen (UK), respectively, and used for biophysical and Fc effector function assays.

Techniques: Infection, Clinical Proteomics, Neutralization, Inhibition, Enzyme-linked Immunosorbent Assay, Binding Assay, Luminex, Fluorescence, Activation Assay, MANN-WHITNEY