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2 protocols using complete mini edta free inhibitor

1

Vesicle IP and Flotation Assays

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Vesicle IP and flotation assays were performed as previously described (Zhao et al., 2001 (link); Tanaka et al., 2016 (link)). WT and Kif1bβGFP/GFP adult mouse brains were homogenized with ∼5 ml Hepes-sucrose buffer (10 mM Hepes, pH 7.4, 320 mM sucrose, 5 mM MgSO4, 1 mM EGTA, and protease inhibitors [cOmplete mini EDTA-free inhibitor; Roche]) and cleared by centrifugation twice at 1,000 g for 10 min at 4°C. For IP, the supernatant (S1) was mixed with 50 µl magnetic beads (μMACS Protein A; 130-042-601; Miltenyi Biotec) and 2 µg anti-GFP antibody for 2 h at 4°C. The beads were washed, eluted, and sampled for IB. For the flotation assay, the supernatant was diluted in 60% Nycodenz at a volume ratio of 1:5 and subjected to step-gradient ultracentrifugation with Nycodenz (0, 10, 20, 30, 40, 50, and 60%; Progen Biotechnik) in OptiSeal tubes (11.2 ml; 362181; Beckman Coulter) using an Optima XL-100K Ultracentrifuge with an NVT 65 rotor (Beckman Coulter) at 65,000 rpm for 2.5 h at 4°C with both acceleration and deceleration in the slowest mode of 9. The effluent fractions were collected by piercing the bottom of the tube with a 22G needle (NN-2238R; Terumo) and placing in 1.5-ml tubes at 500 µl/tube, and the fractions were subjected to IB.
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2

Immunoprecipitation of Poly(ADP-ribose) Proteins

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At 48 h after transfection, HEK 293T cells were washed twice with PBS (phosphate-buffered saline) and lysed in IP buffer (50 mM Tris, pH 7.5, 150 mM NaCl, 0.2% Triton X-100) containing 1 μM ADP-HPD (Millipore) and cOmplete Mini EDTA-free inhibitor (Roche) for 20 min (with rotation at 4°C). The lysate was clarified by centrifugation at 4°C for 15 min at 18,800 ×g. A final concentration of 10 μg/mL cytochalasin B (Sigma) and 25 μM nocodazole (Sigma) were then added to the supernatant. Samples were then mixed with either anti-HA magnetic beads (Thermoscientific) or protein G magnetic beads (Thermoscientific) coupled with anti-pADPr (Abcam) (beads were pre-blocked with 1–2% BSA). After overnight incubation at 4°C, the beads were washed 4 times with IP buffer, re-suspended in SDS loading buffer, boiled for 5 min, electrophoresed on a Novex 4–20% Tris-Glycine mini-gel (Invitrogen), and then transferred onto PVDF membranes. Mouse anti-poly(ADP-ribose) polymer [10H] (1:1000; Abcam), mouse anti-HA [F-7] (1:3000; Santa Cruz), mouse anti-β-Actin [C4] (1:3000; Santa Cruz), and HRP-conjugated goat antibody to mouse (1:10,000; Azure Biosystems) were used for detection.
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