Double Staining for ALK and TUNEL
For double staining, we first carried out TUNEL and then proceeded to standard immunocytochemistry using anti-ALK antibody. TUNEL was performed using the DeadEnd Fluorometric TUNEL System (Promega) with the following modifications. The NB-39-nu cells seeded on the 24-well plates that were treated with siRNAs were washed with PBS twice and fixed with 4% paraformaldehyde (methanol free) for 25 minutes at 4°C. The cells were rinsed with PBS twice and then permeabilized with 0.2% Triton X-100 solution in PBS for 5 minutes at room temperature. The cells were washed with PBS twice and covered with an equilibration buffer (from the kit) for 10 minutes at room temperature. The equilibration buffer was drained off, and a reaction buffer containing the equilibration buffer, nucleotide mix, and terminal deoxynucleotidyl transferase enzyme was added to the cells and incubated at 37°C for 1 hour, avoiding exposure to light. The cells were incubated for 15 minutes at room temperature with 2× standard saline citrate to stop the reaction. The cells were washed with PBS three times and then stained for ALK using immunofluorescence as follows. The cells were blocked with 2% bovine serum albumin (Boehringer Mannheim) for 30 minutes at room temperature. The blocking solution was drained off, and the cells were incubated with a 1:1000 dilution of αALK for 1 hour at room temperature. The cells were rinsed with PBS three times and incubated with a 1:40 dilution of rhodamine-conjugated goat anti-rabbit secondary antibody (Santa Cruz Biotechnology) for 30 minutes at room temperature. The cells were washed three times with PBS and mounted in glycerol-based 2.5% 1,4-diazabicyclo[2,2,2] octan. Confocal laser scanning analysis was carried out.
DNA Fragmentation Assay
To detect apoptotic DNA cleavage, DNA fragmentation assay was performed using an Apoptotic DNA Ladder kit (Chemicon International, Inc., Temecula, CA). The cells seeded on the 12-well plates that were treated with siRNAs as previously mentioned were collected in 1.5-ml microcentrifuge tubes. The cells were washed with PBS, centrifuged, and lysed with 20 μl of TE lysis buffer. The lysates were incubated with 5 μl of enzyme A (RNase A) at 37°C for 10 minutes and then at 55°C for 30 minutes after the addition of 5 μl of Enzyme B (Proteinase K). Afterward, 5 μl of ammonium acetate solution and 100 μl of absolute ethanol were added, and the samples were kept at −20°C for 10 minutes. The samples were centrifuged, and the pellets were washed with 70% ethanol. Then the DNA pellets were dissolved in 30 μl of DNA suspension buffer. DNA fragmentations were visualized by electrophoresis on 2% agarose gel containing ethidium bromide.