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Data analysis software 10

Manufactured by Molecular Devices

Data Analysis software 10.0 is a comprehensive data analysis tool designed to efficiently process and interpret experimental data. It provides a suite of robust algorithms and visualization capabilities to support researchers in their data analysis workflow. The software's core function is to facilitate the organization, analysis, and presentation of scientific data from various experimental techniques.

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3 protocols using data analysis software 10

1

SARS-CoV-2 RBD-ACE2 Binding Kinetics

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RBD-ACE2 binding measurements were performed as described before73 (link) using an Octet® RED96 system (ForteBio) with integrated data acquisition software 10.0. Streptavidin (SA) biosensors (Sartorius #18-5019) were pre-hydrated in 1X Kinetics Buffer (Sartorius #18-1105) and were then loaded with biotinylated human ACE2/ACEH recombinant protein (Acrobiosystems #AC2-H82E6) for up to 0.5-1 nm thickness. The ACE2 loaded SA biosensors were then dipped in RBD or its mutants in the concentration of 0.07-50 μg/mL in 1X Kinetics Buffer for 600 s for association, followed by being immersed in 1X Kinetics Buffer alone for another 600 s for dissociation. All steps were conducted at 26°C with constant shaking at 1,000 RPM. Collected data were analyzed using ForteBio Data Analysis software 10.0. The Kon and Koff values were determined using a built-in 1:1 global curve-fitting model and the Kd values were calculated. In antibody blocking experiments, diluted human sera were pre-incubated with 10 μg/mL of RBD or its mutants at 37°C for 60 min before being applied to ACE2-loaded SA biosensors as described above.
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2

Quantifying RBD-mAb Binding Kinetics

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RBD-mAb binding was assessed using an Octet® RED96 system (ForteBio) with integrated data acquisition software 10.0. Streptavidin (SA) biosensors (Sartorius #18-5019) were saturated with biotinylated original RBD recombinant protein (Acrobiosystems #SPD-C82E9) in 1X Kinetics Buffer (Sartorius #18-1105). The RBD loaded SA biosensors were then dipped in 3-fold serially diluted mAbs with the initial concentration of 15 μg/ml in 1X Kinetics Buffer for up to 300 s for association, followed by immersion in 1X Kinetics Buffer alone for another 300–600 s for dissociation. In epitope binning experiments, the RBD loaded SA biosensors were dipped in 17B10 mAb (50 μg/ml in 1X Kinetics Buffer) for 600 s. After briefly washing in 1X Kinetics buffer for 60 s, the loaded biosensors were dipped in competing mAbs (50 μg/ml in 1X Kinetics Buffer) for another 600 s. Any binding shift indicates competing mAb targets a different epitope from 17B10. A spike-specific rabbit polyclonal Ab29 (link) was used as the positive control. All steps were conducted at 26°C with constant shaking at 1,000 RPM. Collected data were analyzed using a built-in 1:2 global curve-fitting model and the Kd values were calculated using ForteBio Data Analysis software 10.0.
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3

BLI Analysis of TET2-IOX1 Binding

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BLI is a label-free technique that monitors light intensity interference to analyze biomolecular interactions. In our study, we immobilized his-tagged TET2 (ab271754, Abcam, USA) on a Ni-NTA sensor (18-5101, Fortebio, Pall Life Sciences, Menlo Park, USA) at the concentration of 20 μg/ml in PBS. IOX1 was reconstituted with DMSO and further diluted with 1% DMSO-PBST. The concentrations of IOX1 were 15 μM, 7.5 μM, 3.75 μM, 1.88 μM, and 0.9375 μM. The baseline was established for 60s, then the sensor with or without immobilized TET2 was immersed into wells containing serial concentrations of IOX1 to obtain the association signal. Then dissociation curve was obtained by dipping the sensor back into PBST buffer. With FortéBio's Data Analysis software 10.0, the equilibrium dissociation constant (KD) was evaluated.
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