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9 protocols using ez link micro sulfo nhs lc biotinylation kit

1

Recombinant SARS-CoV-2 Spike RBD Protein Production

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Human ACE2 protein was ordered from Sino Biological (Beijing, China). Recombinant SARS-CoV-2 spike RBD proteins with His-tag from wild-type virus (wt RBD) as well as the delta variant (delta RBD) were produced by ISAR Bioscience (Planegg, Germany) with the wt RBD being taken from the S protein nucleotide sequence of the SARS-CoV-2 Wuhan Hu-1 genome (GenBank accession number MN908947, positions 22517 to 23183), while the delta RBD contained the following mutations: L452R and T478K. Details on the procedures were published before [45 (link), 46 (link)]. Shortly, CHO cells were transfected with plasmid vectors containing the DNA sequences for the RBD proteins with an added His-tag and subsequently grown at 37 °C. The supernatants were centrifuged and filtered and subsequently purified using HisTrap columns. Protein content after elution was determined by OD280 measurement and the relevant fractions were dialyzed.
The biotinylation of wt RBD and human ACE2 was done using the EZ-Link Micro Sulfo-NHS-LC biotinylation kit (Thermo Scientific #21935 or #A39257) with 20-fold molar excess according to the standard procedure instruction, followed by removal of excess biotin by dialysis against 1 L PBS for 16 h at 4 °C, using Slide-A-Lyzer™ Dialysis Cassettes, 7 K MWCO, 0.5 mL (Thermo Scientific #66373).
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2

Antibody Effector Function Assay

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Assays for antibody effector functions were adapted from previously established protocols.20 (link) Post–challenge NHP sera were inactivated by gamma-irradiation (4 MRad)18 (link) and removed from the maximum containment laboratory according to RML SOPs approved by the RML IBC. Recombinant MARV-Angola GPdTM (IBT Bioservices) was tethered to Fluospheres NutrAvidin-Microspheres yellow-green or red (Thermo Fisher Scientific, Waltham, MA) using the EZ-link Micro Sulfo-NHS-LC-Biotinylation kit (Thermo Fisher Scientific).
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3

Quantitative Serum Myl3 Assay for Rats

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Myl3 was quantitated in rat serum on a custom assay by MPI Research (Mattawan, MI). Samples (5μL) were analyzed in duplicate on Gyrolab™ Bioaffy 1000 CDs (Gyros, Uppsala, Sweden) using the Gyrolab xP workstation with a biotinylated (EZ Link™ Micro Sulfo-NHS-LC biotinylation kit, Thermo Scientific) capture antibody (BiosPacific, Emeryville, CA) and a fluorescently labeled (Alexa Fluor®647 labeling kit, Invitrogen) detection antibody (Abcam, Cambridge, UK). Prior to analysis, samples were diluted 1:4 in Rexxip A buffer (Gyros). Concentrations were interpolated from a 7-point standard curve using a recombinant; his-tagged rat specific myl3 expressed in-house (Eli Lilly and Company, Indianapolis, IN) as a calibrator and fit with a 5-parameter logistic curve. Capture antibody was diluted in PBS + 0.01% Tween 20, detection antibody was diluted in Rexxip F buffer (Gyros), and standards were diluted in Rexxip A. Prior to sample analysis, the performance of the assay was characterized using positive controls (assay calibrator spiked into rat serum) at six different concentrations (approximately mid-way between each standard concentration) ran on 3 different CDs on 3 different days to assess precision and accuracy. Myl3 was quantifiable from 0.05 ng/mL to 200 ng/mL with <12.5 %CV and −5 to −12% relative error.
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4

Ribosome Interaction Assay with RACK1

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Ribosome interaction experiments were performed as described previously (32 (link)). Briefly, 96-well plates (Nunc) were coated overnight at 4°C with 50 μg/well of RACK1-downregulated HeLa cell lysate diluted in 50 μl of PBS. The coating solution was removed, and nonspecific sites were blocked for 1 h at room temperature with 5% BSA in PBS. Plates were washed with 200 μl/well PBS–0.05% Tween 20. Previously purified recombinant proteins (MBP, wild-type RACK1-MBP, or R36D K38E mutant RACK1-MBP) were biotinylated by using the EZ-Link Micro Sulfo-NHS-LC biotinylation kit (Thermo Scientific) according to the manufacturer's instructions. The biotinylated recombinant proteins were added at 0.5 μg per well in 50 μl PBS. The recombinant proteins were incubated on the coated total cell extract for 2 h at room temperature. After washing with PBS–0.05% Tween 20, HRP-conjugated streptavidin in PBS–0.05% Tween 20 was added to wells for 30 min at room temperature in a final volume of 50 μl. After washes, 3,3′,5,5′-tetramethylbenzidine (TMB) was used according to the manufacturer's protocol (Sigma-Aldrich) to detect streptavidin peroxidase activity. HCl at 1 N was used as the stop solution. The absorbance at 450 nm was read on an Infinite F200 multiwell plate reader (Tecan).
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5

Quantifying SARS-CoV-2 Antibody Responses

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The recombinant SARS-CoV-2 prefusion stabilized S protein and RBD were biotinylated using an EZ-Link Micro Sulfo-NHS-LC Biotinylation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Probes were generated by coupling biotinylated proteins to fluorophore-conjugated streptavidin (SA) molecules for detection by flow cytometry (SA-BV421, SA-APC, and SA-PE, BioLegend). Isolated PBMCs were stained by a panel of antibodies listed in Table S3 as well as S protein and RBD probes (S-APC, S-PE, and RBD-BV421, 100 ng each). The samples were analyzed on a BD Aria III Fusion cell sorter (weeks 6 and 30) or a BD LSRFortessa flow cytometer (all other time points). At weeks 6 and 30, memory B cells (CD3 CD11c CD14 CD16 CD123 HLA-DR+ CD20+ IgM IgG+) double-positive for S protein binding were single cell sorted into 96-well plates and frozen immediately on dry ice for subsequent B cell receptor (BCR) amplification. Data were analyzed using FlowJo v.10.7.1 (FlowJo).
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6

Biotinylation and Sulfonation of Antibodies

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For biotinylation
of antibody EP1536Y, 40 μL of a 0.90 mg/mL solution of the antibody
was incubated with 1.61 μL of 11 mM Sulfo-NHS-biotin (50-fold
molar excess) on ice for 2 h according to the manufacturer’s
protocol (EZ-Link Micro Sulfo-NHS-LC-biotinylation kit, Thermo Fisher
Scientific). Excess free biotin was removed using a 0.5 mL of 7 kDa
MWCO Zeba spin desalting column (Thermo Fisher Scientific). 200 μL
of ultrapure water (purified using a Milli-Q system, Millipore, Burlington,
MA) was added as a stacker volume for elution of the biotinylated
EP1536Y antibody. 40 μL of 1.167-mg/mL solution of antibody
MJFR1 was biotinylated using the same biotinylation kit. Biotinylation
levels were evaluated using a fluorescence biotin quantitation kit
(Thermo Fisher Scientific). For sulfonation, 40 μL of a 0.90
mg/mL of EP1536Y solution was incubated with Sulfo-TAG NHS-ester (MSD)
according to the manufacturer’s instructions. The protein concentration
of all antibody conjugates was determined using a Pierce BCA assay
kit (Thermo Fisher Scientific). The antibody solutions were aliquoted
and stored at 4 °C until use.
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7

Biotinylation of Broadly Neutralizing Antibodies

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All bNAbs (3BNC117 (CD4bs), 10–1074 (V3-loop), PG16 (V1V2-loop), 35O22 (gp120-gp41 interface), 10E8 (MPER gp41) were biotinylated with EZ-Link Micro Sulfo-NHS-LC-Biotinylation Kit (Thermo Fisher). Briefly, a total of 2.5 μg bNAb mix of equal quantities was biotinylated with a 30-fold molar excess of Sulfo-NHS-LC-Biotin in 500 μL volume for 60 min at room temperature (RT). To remove excess Biotin, biotinylated bNAbs were purified over a Zeba Spin Desalting Column. Biotinylated bNAbs were stored at 4°C until further use.
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8

SARS-CoV-2 Spike Protein Binding Assay

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To generate the protein probes, the recombinant WA-1 S-2P and RBD proteins were biotinylated using the EZ-Link Micro Sulfo-NHS-LC Biotinylation Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions [20 (link)]. Streptavidin-conjugated fluorophores (SA-PE, SA-APC or SA-BV421) and biotinylated proteins were coupled at a 4:1 molar ratio. The cryopreserved PBMCs were thawed and stained with 100 ng of the fluorescent protein probes for 20 min at 4 °C, followed by staining with 7-aminoactinomycin D (7-AAD, Thermo Fisher, Waltham, MA, USA) and a panel of antibodies, IgM PerCP-Cy5.5 (G20-127, BD, Franklin Lakes, NJ, USA), IgD FITC (polyclonal, Southern Biotech, Birmingham, AL, USA), CD3 BV510 (SP34-2, BD), CD14 BV510 (M5E2, BioLegend, San Diego, CA, USA), CD16 BV510 (3G8, BD), CD20 BV605 (2H7, BioLegend, San Diego, CA, USA), HLA-DR BV650 (L243, BioLegend, San Diego, CA, USA) and IgG BV786 (G18-145, BD, Franklin Lakes, NJ, USA), for another 20 min at 4 °C. After staining, the cells were washed with FACS buffer (PBS supplemented with 2% heat-inactivated fetal calf serum) and fixed with 1% formaldehyde solution. The samples were acquired using a BD LSRFortessa cell analyzer (BD, Franklin Lakes, NJ, USA). The data were analyzed using FlowJo software v.10.7.1 (FlowJo, Ashland, OR, USA).
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9

Biotinylation of Lipopolysaccharide

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10 mg LPSBV was biotinylated with EZ-Link Micro Sulfo-NHS-LC-Biotinylation Kit (Thermo Scientific), according to the manufacturer’s protocol, using PBS as a solvent. To remove PBS, an exhaustive dialysis against distilled water was performed. The biotinylated LPSBV (bioLPSBV) was then collected and lyophilized. For in vitro experiments, lyophilized bioLPSBV was dissolved in distilled water in concentrations not higher than 1 mg mL−1.
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