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codon-optimized spike protein nucleotide sequence  (Thermo Fisher)


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    Structured Review

    Thermo Fisher codon-optimized spike protein nucleotide sequence
    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 <t>S</t> <t>protein</t> 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.
    Codon Optimized Spike Protein Nucleotide Sequence, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/codon-optimized spike protein nucleotide sequence/product/Thermo Fisher
    Average 90 stars, based on 1 article reviews
    codon-optimized spike protein nucleotide sequence - by Bioz Stars, 2026-05
    90/100 stars

    Images

    1) Product Images from "Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that clamp the spike at its base"

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

    Journal: Nature Communications

    doi: 10.1038/s41467-025-60250-1

    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.
    Figure Legend 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.

    Techniques Used: Labeling, Binding Assay, Mutagenesis



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    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 <t>S</t> <t>protein</t> 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.
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    Image Search Results


    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.

    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