codon-optimized spike sequences  (GenScript corporation)

Journal: Nature Communications

Article Title: Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that clamp the spike at its base

doi: 10.1038/s41467-025-60250-1

Figure Lengend Snippet: a left: model of full-length prefusion S (6VSB_1_1_2 ) with superimposition of the R3DC23 – HR2 complex, all shown in molecular surface representation, with N-glycans in stick representation. R3DC23 VHHs are colored in orange, labeled S protein regions: cytoplasmic domain (red; CP), transmembrane domain (gray; TM), heptad repeat 2 (blue; HR2), S2 stem helix (deep pink; SH), heptad repeat 1 (lemon, HR1), central helix and connector domain (pink; CH-CD), the S1 regions encompassing the N-terminal domain (NTD) and receptor binding domain (RBD) (light blue). Right: model of the proteolytically processed postfusion S2 subunit (7E9T ), color coded as in prefusion spike. b Side and axial view (inset) of the R3DC23 – HR2 complex (sand and blue, respectively) superimposed with prefusion HR2 coiled-coil (light blue). In R3DC23, CDR1, 2, and 3 are colored magenta, yellow, and cyan, respectively. The HR2-binding epitope spanning D1192 – Y1206 is shown in stick representation. c Close-up of boxed region, encompassing a single VHH and two HR2 copies (i and ii) forming the adjoined binding epitope. Escape mutant positions are labeled in red. d Axial view of HR1-HR2 (lemon and blue) region of postfusion S protein, superimposed with R3DC23 in the HR2 complex (gray). e The amino acids involved in interactions between R3DC23 and two HR2 helices as observed in the crystal of the R3DC23-HR2 complex are indicated in red.

Article Snippet: For the pCG1-SARS-2-BA.2 Sdel18 expression vector, a codon-optimized spike protein nucleotide sequence containing the BA.2 mutations (T19I, ΔL14-P26, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K) and flanking BamH I and Sal I restriction sites was ordered at GeneArt (Thermo Fischer Scientific) and cloned in the pCG1 vector as a Bam HI/ Sal I fragment.

Techniques: Labeling, Binding Assay, Mutagenesis

Journal: iScience

Article Title: Immunogenicity of a third dose with mRNA-vaccines in the ChAdOx1-S/BNT162b2 vaccination regimen against SARS-CoV-2 variants

doi: 10.1016/j.isci.2024.110728

Figure Lengend Snippet:

Article Snippet: Codon-optimized spike DNA sequences for D614G, B.1.617.2, BA.1, BA.4/BA.5, BQ.1.1, XBB.1.5/XBB.1.9, BA.2.86, and JN.1 SARS-CoV-2 variants , GeneArt Gene Synthesis (ThermoFisher) , N/A.

Techniques: Recombinant, Luciferase, Software

Journal: Biomaterials Research

Article Title: Development of a screening platform to discover natural products active against SARS-CoV-2 infection using lung organoid models

doi: 10.1186/s40824-023-00357-y

Figure Lengend Snippet: Infectivity tested using compounds of K-4 and M-4 (10 μM) against pseudotyped virus (PV) of SARS-CoV-2 Delta ( A , B ) or Omicron ( C , D ) variant with 10 μM dose of Lopinavir ( E ) as a positive control drug. Values indicate means ± SEM. ( n = 3, *** p < 0.001, **** < 0.0001 vs. control group)

Article Snippet: The SARS-CoV-2-related sequences were codon-optimized for human expression and purchased from Sino Biological (Beijing, China).

Techniques: Infection, Variant Assay, Positive Control

Journal: Biomaterials Research

Article Title: Development of a screening platform to discover natural products active against SARS-CoV-2 infection using lung organoid models

doi: 10.1186/s40824-023-00357-y

Figure Lengend Snippet: Transcriptome analysis and the cell type analysis in control (GFP) or pseudovirus of SARS-CoV-2 Omicron variant infected in human LOs ( n = 3). A Volcano plot of differentially expressed genes (DEGs) of PV-infected LO samples compared with control samples. Horizontal and vertical dashed blue lines indicate p -value < 0.05 and fold change = 4, respectively. Red dots indicate significant ( p -value < 0.05) DEGs. B Top 25 genes of significantly up- or downregulated DEGs. C Heatmap of enrichment with lung-related cell types in PV-infected LOs by referring to the CellMarker database. D Lung cell-specific markers whole-stained using LOs. LOs were fixed and analyzed with various cell-type markers through immunofluorescence and visualized through confocal microscopy. Scale bar: 20 μm

Article Snippet: The SARS-CoV-2-related sequences were codon-optimized for human expression and purchased from Sino Biological (Beijing, China).

Techniques: Variant Assay, Infection, Staining, Immunofluorescence, Confocal Microscopy

Journal: Biomaterials Research

Article Title: Development of a screening platform to discover natural products active against SARS-CoV-2 infection using lung organoid models

doi: 10.1186/s40824-023-00357-y

Figure Lengend Snippet: The anti-infective potential of K-4 ( A ) or M-4 ( B ) in the lung organoids infected with pseudotyped virus (PV) of SARS-CoV-2 Omicron variant. Values indicate means ± SEM. ( n = 3, **** < 0.0001 vs. control group)

Article Snippet: The SARS-CoV-2-related sequences were codon-optimized for human expression and purchased from Sino Biological (Beijing, China).

Techniques: Infection, Variant Assay