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Alexa fluor 488 nhs ester

Manufactured by Thermo Fisher Scientific
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Alexa Fluor 488 NHS Ester is a fluorescent labeling reagent. It is a succinimidyl ester derivative of the Alexa Fluor 488 dye, which is used for covalent labeling of proteins and other biomolecules containing primary amino groups.

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89 protocols using alexa fluor 488 nhs ester

1

Fluorescent Labeling of Proteins

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Four to seven micromolar solutions of NiV Gecto-40 Å-pAzF proteins were labeled with Click-iT DIBO-AF647 (Invitrogen) at a 2:1 dye:protein ratio. The dye and protein were incubated in 50 mM Hepes (pH 7.5) and 150 mM NaCl for 2 hours at room temperature. Ninety-five micromolar solutions of His8-ephrinB2-229 were labeled with N-hydroxysuccinimide (NHS) ester-Alexa Fluor 488 or NHS ester-AF647 (Thermo Fisher Scientific) at a 2:1 dye:protein ratio. The dye and protein were incubated in 50 mM Hepes (pH 7.5) and 150 mM NaCl for 1 hour at room temperature. A 23 μM solution of scFv5B3 was labeled with NHS ester-Alexa Fluor 488 (Thermo Fisher Scientific) at a 3:1 dye:protein ratio. The dye and protein were incubated in 50 mM Hepes (pH 7.5) and 150 mM NaCl for 1 hour at room temperature. Unbound dye was removed from all labeling reactions and buffer was exchanged to 50 mM tris (pH 7.5) and 150 mM NaCl with 0.5 ml of Zeba Spin 7 K molecular weight cut-off (MWCO) desalting columns (Thermo Fisher Scientific).
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2

FRET-based Binding Assay for 14-3-3θ

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The Site 2 and Sites 2,4 peptides were fluorescently labeled at the amidated C-terminus. Both peptides were labeled with the donor probe Alexa Fluor 488 NHS Ester, whereas the Site 2 peptide was additionally labeled with the acceptor probe Alexa Fluor 568 NHS Ester (Thermo Fisher Scientific). The labeling reaction was performed at 25 °C for 1 h in 20 mM MES pH 6.8 and 50 mM NaCl and at a peptide concentration of 5 mg mL−1 with a 2-fold molar excess of fluorescent dye. The labeling reaction was stopped with the addition of a 10-fold molar excess of hydroxylamine (Sigma-Aldrich Corporation). Labeled peptides were separated from any remaining unlabeled peptide using a Symmetry300 C18 reverse phase HPLC column (Waters Corporation, Milford, MA). The peptides were lyophilized, resuspended in 100 mM HEPES pH 7.5, and dialyzed against 25 mM HEPES pH 7.5, 50 mM NaCl and 1 mM MgCl2. The donor-labeled peptides were pre-incubated with 14-3-3θ at a 1:1 molar ratio (i.e., one peptide per 14-3-3θ dimer). The acceptor-labeled Site 2 peptide (at 5 μM concentration) was then titrated into the preformed complexes. The steady-state fluorescence emission spectra were recorded at 25 °C, with an excitation wavelength of 495 nm (5-nm slit width) and an emission wavelength of 520 nm (5-nm slit width).
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3

Inflammasome Activation Assay in THP-1 Cells

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The following reagents were purchased: phorbol 12-myristate 13-acetate (PMA) and CP-456773 sodium salt (CRID3) from Sigma-Aldrich (USA); Amicon Ultra 0.5 mL centrifugal filter MWCO 100 kDa, MF-Millipore membrane filters of 0.45 μm and 0.22 μm pore sizes from Millipore Sigma (USA); GM-CSF recombinant human protein, fetal bovine serum (FBS), penicillin-streptomycin, sodium pyruvate (100 mM), GlutaMAX supplement, RPMI 1640 medium, PBS buffer, Pierce LDH cytotoxicity assay kit, cytochalasin D (CytD), Alexa Fluor 488 NHS ester (succinimidyl ester), wheat germ agglutinin Alexa Fluor 555, DRAQ5 fluorescent probe solution (5 mM) and 4% formaldehyde from ThermoFisher Scientific (USA); acridine orange (AO) from Dojindo Laboratories (Kumamoto, Japan); VX765 and lipopolysaccharide (LPS) Escherichia coli O111:B4 from InvivoGen (USA); human IL1 beta assay kit from Cisbio Bioassays (France); CD14 microbeads (human) from Miltenyi Biotech (Germany); silica crystals (MIN-U-SIL-15) from US Silica (USA); μ-Slide 8 well ibiTreat from Martinsried (Germany); THP-1 cells from Japanese Collection of Research Bioresource Cell Bank (Japan); CHO-K1 cells and F-12K medium from ATCC (USA).
Human PBMCs were donated from University Hospital Bonn (Germany), and the operation and usage were approved by the local ethics committee in accordance with the Declaration of Helsinki.
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4

Monoclonal Antibody Purification and Peptide Synthesis

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Monoclonal antibodies were purified from hybridoma supernatant using a protein G affinity column (Thermo Fisher Scientific). Recombinant mouse TNF-α was purchased from Corning (Corning, NY). Synthetic peptides with fluorophore- and azide-modified amino acids (Table S2) were purchased from Thermo Fisher Scientific. AlexaFluor488-NHS ester was purchased from Thermo Fisher Scientific. Bovine liver catalase was purchased from Sigma (Saint Louis, MO).
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5

Purification and Labeling of Monoclonal Antibodies

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Hybridomas were AP3 (Newman et al., 1985 (link)), AP5 (Kekomaki et al., 1991 (link)), LIBS1 (Frelinger et al., 1990 (link)), MBC319.4 (Zhang et al., 2013 (link)), 12G10 (Mould et al., 1995 (link)), 9EG7 (Lenter et al., 1993 (link)), SG/19 (Miyake et al., 1992 (link)), HUTS4 and HUTS-21 (Luque et al., 1996 (link)) and mAb16 (Akiyama et al., 1989 (link)). IgG produced from hybridoma was purified by protein G. For Fab fragments, antibodies were digested with papain (500:1 IgG:papain) in PBS with 10 mM EDTA and 10 mM L-Cys at 37°C for 18 h. After buffer exchange with 50 mM Tris (pH 9), the Fab was purified by anion exchange chromatography (HiTrap Q HP, GE Healthcare), after which the fractions containing Fab were concentrated, flash frozen, and stored at −80°C for future use. Antibodies and Fabs were fluorescently labeled with Alexa Fluor 647 NHS Ester or Alexa Fluor 488 NHS Ester (ThermoFisher Scientific) in PBS.
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6

Transferrin Uptake in Muc1-Expressing Cells

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Human apo-Transferrin (Sigma) was diluted to 1 mg/mL in PBS and labeled with Alexa Fluor 488 NHS Ester (Thermo Fisher Scientific) per manufacturer’s protocol. Cells were prepared by plating and inducing wild-type (Control) and Muc1-42TR ΔCT-expressing MCF10A cells with 0.2 μg/mL of doxycycline (Santa Cruz) for 18 h. The 488-labled transferrin was diluted 1:1000 into fresh cell culture media with doxycycline (Santa Cruz) and incubated at 37°C, 5% CO2 with cells for 30 min or 60 min. Cells were then detached with 0.05% trypsin EDTA (Thermo Fisher Scientific). Cells were washed with ice cold 0.5% BSA in PBS. Fluorescent signal was measured using a BD Accuri C6 flow cytometer. Confocal images cells were also acquired using a Zeiss LSM i880.
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7

Fluorescent Probes for α4β1 and Fn3 Integrin Binding

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FITC-labeled α4β1-specific probe, 4-((N′-2-methylphenyl)ureido)-phenylacetyl-L-leucyl-L-aspartyl-L-valyl-L-prolyl-L-alanyl-L-alanyl-L-lysine (FITC-LDVP) and its unlabeled version (LDVP), were from Tocris Bioscience (Avonmouth, Bristol, UK). Human VCAM D1D2 (mature residues F1 to T202) were expressed and purified from HEK 293S GnTI−/− cell line supernatants by affinity chromatography and gel filtration (Yu et al., 2013 (link)). VCAM D1D2 was fluorescently labeled with Alexa Fluor 488 NHS Ester (Thermo Fisher Scientific). Human Fn39-10 S1417C mutant (mature residues G1326 to T1509) and its synergy and RGD site (R1374A&P1376A&R1379A&S1417C&Δ1493-1496) mutated inactive version were expressed in Escherichia coli and purified as described (Li et al., 2017 (link); Takagi et al., 2001 (link)). Fn39-10 S1417C mutant was fluorescently labeled with Alexa Fluor 488 C5 maleimide (Thermo Fisher Scientific) at residue Cys-1417. Both Fn39-10 S1417C mutant and its inactive version were biotinylated with Maleimide-PEG11-Biotin at residue 1417 (Thermo Fisher Scientific) in PBS.
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8

Synaptosomes Oligomer Binding Assay

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Synaptosomes were treated with AβO and/or TauO for binding challenges, and the binding percentages were evaluated with flow cytometry. After assessing that the binding of AβO and/or TauO was comparable among the single human cases (Supplementary method 2), we decided to pool together an equal number of synaptosomes isolated from each subject for practical purpose. We incubated 2 million of synaptosomes for 1 h at RT without oligomers (control) as well as with AβO tagged with HyLite Fluor 647 or/and TauO tagged with Alexa Fluor™ 488 NHS Ester (Thermo Fisher Scientific) at concentrations of 0–0.5–1–2.5–5–10 μM. Synaptosomes were then pelleted, washed three times with HBK buffer, and resuspended in HBK. Oligomer fluorescence positivity was acquired by a Guava EasyCyte 8 flow cytometer (EMD Millipore) and analyzed using Incyte software (EMD Millipore).
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9

Quantifying Cellular Uptake of Fluorescent Probes

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CLC or BSA (10735078001; Sigma‐Aldrich) was labeled with Alexa Fluor™ 488 NHS Ester (Thermo Fisher Scientific) or Alexa Fluor™ 594 NHS Ester (Thermo Fisher Scientific) and incubated with 4T1 cells for 2 h at 37°C. After five washes with PBS buffer, 4T1 cells were stained with lysosomal staining kit (ab112137; Abcam). 4T1 cells were fixed with 4% paraformaldehyde (Electron Microscopy Sciences), and diamidino‐2‐phenylindole (DAPI) (VECTASHIELD, Vector Laboratories) was used to counterstain the cell nuclei. The cells were visualized using an EVOS™ FL Auto 2 Imaging System (Thermo Fisher Scientific). After splitting each color channel, the area with fluorescence was measured for each color channel with Image J (National Institutes of Health; Bethesda, MD). The percent of uptake of CLC was calculated by dividing with measured area from DAPI channel.
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10

Pharmacokinetics of Exendin Conjugates

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Exendin, 54.6 kDa EG9, 55.6 kDa EG3 and 71.6 kDa EG3 exendin-C-POEGMA conjugates were fluorescently labeled with Alexa Fluor® 488 NHS ester (Thermo Fisher Scientific) via their solvent accessible primary amines on lysine residues and the N-terminus, according to manufacturer’s protocol. Unreacted free fluorophore was removed using a ZebaSpin desalting column (Thermo Fisher Scientific). Mice were randomly divided into four groups (n=3). Animals were weighed before injection. Each group of mice received a single s.c. injection of one of the labeled samples at 75 nmol/kg (45 nmol/kg fluorophore). 10 μL of blood samples were collected from the tail vein into 100 μL of a heparin solution (1kU/ml in PBS, Sigma Aldrich) at 40 s, 40 min, 2.5 h, 4.5 h, 8 h, 24 h, 48 h, 72 h, 96 h and 120 h after injection. Blood samples were centrifuged at 4 °C and 20,000 ×g for 10 min to extract the plasma for fluorescence reading at excitation 485 nm and emission 535 nm on a Victor multilabel plate reader (Perkin Elmer). Plasma concentrations of constructs as a function of time were fitted using a non-compartmental analysis (PK Solutions 2.0, Summit Research Services) that characterizes the absorption and elimination phases of the profiles to derive the pharmacokinetic parameters.
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