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4 6 diamidino 2 phenylindole (dapi)

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DAPI is a fluorescent dye used for nucleic acid staining. It binds strongly to the adenine-thymine (A-T) rich regions in DNA. DAPI is commonly used in microscopy and flow cytometry applications to visualize and quantify cellular nuclei.

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20 protocols using 4 6 diamidino 2 phenylindole (dapi)

1

Exosomes Modulate PMVEC DNA Damage

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PKH26 labeled ADSCs exosomes were added into PMVECs. After co-culture for 12 h, the PMVECs were stained with DAPI (Bio-rad). Immunofluorescence signals were visualized with secondary antibodies by FSX100 microscope (Olympus). The 8OHdG immunofluorescence analysis was performed to assess DNA damage of PMVECs in CLP treated mice as described previously. To identify DNA damage in PMVECs, lung tissues were detected using monoclonal mouse DAPI (Bio-rad), CD31 (Bio-rad), 8OHdG (Abcam), HO-1(CST), 4HNE(Bioss), GPX4 (Abmart) and Nrf2(Abmart) antibodies according to manufacturer's instructions. Immunofluorescence signals were visualized with secondary antibodies by FSX100 microscope (Olympus).
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2

Immunofluorescence Staining Protocol

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Following each experimental procedure, cells were collected via centrifugation and subjected to two rounds of washing with 1 x PBS. Cells were then fixed and permeabilized using a combination of 4% paraformaldehyde (Sigma-Aldrich/Merck) and 0.1% Triton X-100 (Sigma-Aldrich/Merck). After blocking with 5% BSA (BIO-RAD) in 1 X PBS at room temperature for 1 h, cells were incubated with appropriate primary antibodies at room temperature for 2 h, followed by incubation with species specific Alexa Fluor secondary antibody (Thermo Fisher Scientific Inc.) at room temperature for 1 h. Nuclei were counterstained with 4’, 6’,-diamidino-2-phenylindole (DAPI; BIO-RAD) at room temperature for 30 minutes. Cells were then washed three times with 1 x PBS and mounted using an antifade mounting media (Sigma-Aldrich/Merck). The images were captured using a Zeiss AXIO Observer.Z1 Inverted Fluorescence microscope (Zeiss), and subsequently analysed using ZEN software (Zeiss). The list of primary and secondary antibodies used in immunofluorescence analyses are given in Table 1.
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3

Visualizing α-Synuclein Pathology in HEK293T

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Two days after transduction with or without α-syn PFF, HEK293T cells expressing EGFP-PFFNBs were fixed with 4% paraformaldehyde. The fixed cells were permeabilized using 0.1% Triton-X, followed by blocking with 5% BSA in PBS. Cells were stained with rabbit anti-p129S primary antibody (1:1000 dilution, Abcam, Cat no. ab51253) and DAPI (1:1,000, Bio-Rad, Cat no. 1351303) for 1 h at RT. The secondary stainings were performed with anti-rabbit IgG-AlexaFluor 568 (1:2000 dilution, Thermo Fisher Scientific, Cat no. A11036) for 1 h at RT.
Confocal imaging was performed on a Nikon Eclipse Ti2 inverted confocal microscope with 60X oil-immersion objectives, outfitted with Yokogawa CSU-X1 5000RPM spinning disk confocal head and ORCA-Flash 4.0 LT + sCMOS camera. The following combinations of laser excitation and emission filters were used for corresponding fluorophores: DAPI (405 nm excitation; 455/50 emission), EGFP (488 nm excitation; 525/36 emission), Alexa Fluor 568 (568 nm excitation; 605/52 emission). Region with high pS129 signal were chosen as region of interest (ROI), then the Pearson correlation analysis was performed using Nikon NIS-Elements software.
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4

Immunostaining of Phospho-Tau and Antioxidant Proteins

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Deparaffinization and antigen retrieval of the brain tissue sections were performed as previously described.30 (link) After washing with phosphate-buffered saline (PBS), sections were blocked in 0.1% Triton X-100 (Sigma-Aldrich), 2% normal goat serum (Thermo Fisher Scientific, MA, USA) and 1% bovine serum albumin (Sigma-Aldrich) in PBS for 1 h at room temperature. Sections were then incubated with primary antibodies diluted in blocking buffer overnight at +4°C. After 3 × 10 min washes in 0.1% Triton X-100 in PBS, they were incubated with secondary antibodies and DAPI (2-(4-Amidinophenyl)-1H-indole-6-carboxamidine) for 1 h at room temperature followed by 3 × 10 min washes in Triton X-100 in PBS. The following dilutions and antibodies were used: 1:100 mouse anti-phospho-tau (Thr212, Ser214) (MN1060; Thermo Fisher Scientific), 1:100 rabbit anti-TRX-1 (MA532569; Thermo Fisher Scientific), 1:100 rabbit anti-AGT (MA529010; Thermo Fisher Scientific), 1:500 Alexa Fluor fluorescently conjugated secondary goat anti-rabbit and anti-mouse antibodies (Thermo Fisher Scientific) and 1:100 DAPI (1351303; Bio-Rad, USA). To quench the autofluorescence of lipofuscin, sections were washed for 5 min in PBS and incubated with 0.1% w/w Sudan Black B (199664; Sigma-Aldrich) in 70% ethanol. Prior to mounting, sections were washed with Triton X-100 in PBS 2 × 10 min and 10 min with PBS.
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5

Confocal Microscopy Imaging of Transfected Cells

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Cells used for confocal microscopy imaging were transfected as described above in 12 -well plates on poly-L-lysine treated #1.5 round coverslip glass (Thermo Fisher Scientific, Waltham, MA). Nuclei were labeled with DAPI (Bio-Rad, Hercules, CA), the plasma membrane was labeled with wheat germ agglutinin (WGA)-Alexa Fluor 647 conjugate (Invitrogen, Carlsbad, CA) and the ER was labeled by cotransfecting cells with pDsRed2-ER (Takara Bio USA, Mountain View, CA), as described previously26 (link). Confocal microscopy was performed on a SP8 confocal microscope (Leica, Buffalo Grove, IL) equipped with a 100x/1.4-NA oil objective, as described previously6 . Microscopy images presented were obtained with a 5× zoom factor. Colocalization analysis of different fluorescent species in confocal microscopy images was conducted using the Coloc 2 plugin in Fiji (version 2.1.0/1.53c)27 (link). Costes threshold regression was used and the Pearson’s correlation coefficient (r) recorded as an indicator of colocalization.
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6

Multicolor Confocal Microscopy Labeling

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Confocal microscopy and sample preparation was performed as described previously [26 (link), 33 (link)]. Briefly, nuclei were labeled with DAPI (Biorad, Hercules, CA), the plasma membrane was labeled with WGA-Alexa Fluor 647 conjugate (Invitrogen, Carlsbad, CA) and the ER was labeled by cotransfecting cells with pDsRed2-ER (Clontech, Mountain Valley, CA), as described previously [33 (link)]. Confocal microscopy was performed on a SP8 confocal microscope (Leica, Buffalo Grove, IL) equipped with a 100x/1.4-NA oil objective. DAPI was detected by exciting samples with a 405 nm diode laser and collecting the emission signal at 415 – 450 nm. Fluorescence from mTq2 was detected by exciting samples at 458 nm using an Argon laser and collecting the emission signal at 465 – 500 nm. Images were collected sequentially. YFP was detected by exciting samples at 514 nm using a tunable white light laser and collecting the emission signal at 520 – 570 nm. DsRed2-ER was detected by exciting samples at 558 nm using a tunable white laser and collecting the emission signal at 570 – 600 nm. WGA-Alexa Fluor 647 was detected by exciting samples at 650 nm using a tunable white light laser and collecting the emission signal at 675 – 680 nm.
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7

Immunofluorescence Visualization of Cellular Targets

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Cells were fixed, permeabilized and blocked as previously published [12 (link)] and incubated overnight at 4 °C with primary Abs. Then, cells were incubated for 2 h in the dark with the secondary Abs. Nuclei were counterstained with DAPI (Bio-Rad) for 15 min. Slides were visualized at 64X magnification as previously described [12 (link)]. A minimum of 200 cells per condition was analyzed using the ImageJ program.
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8

Immunostaining of Phospho-Tau and Antioxidant Proteins

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Deparaffinization and antigen retrieval of the brain tissue sections were performed as previously described.30 (link) After washing with phosphate-buffered saline (PBS), sections were blocked in 0.1% Triton X-100 (Sigma-Aldrich), 2% normal goat serum (Thermo Fisher Scientific, MA, USA) and 1% bovine serum albumin (Sigma-Aldrich) in PBS for 1 h at room temperature. Sections were then incubated with primary antibodies diluted in blocking buffer overnight at +4°C. After 3 × 10 min washes in 0.1% Triton X-100 in PBS, they were incubated with secondary antibodies and DAPI (2-(4-Amidinophenyl)-1H-indole-6-carboxamidine) for 1 h at room temperature followed by 3 × 10 min washes in Triton X-100 in PBS. The following dilutions and antibodies were used: 1:100 mouse anti-phospho-tau (Thr212, Ser214) (MN1060; Thermo Fisher Scientific), 1:100 rabbit anti-TRX-1 (MA532569; Thermo Fisher Scientific), 1:100 rabbit anti-AGT (MA529010; Thermo Fisher Scientific), 1:500 Alexa Fluor fluorescently conjugated secondary goat anti-rabbit and anti-mouse antibodies (Thermo Fisher Scientific) and 1:100 DAPI (1351303; Bio-Rad, USA). To quench the autofluorescence of lipofuscin, sections were washed for 5 min in PBS and incubated with 0.1% w/w Sudan Black B (199664; Sigma-Aldrich) in 70% ethanol. Prior to mounting, sections were washed with Triton X-100 in PBS 2 × 10 min and 10 min with PBS.
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9

Immunofluorescence Staining of U2OS and HeLa Cells

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U2OS and HeLa cells were grown on coverslips up to 50% confluence. The cells were washed with chilled PBS and fixed with 4% paraformaldehyde in PBS. The cells were permeabilized with 0.15 v/v% Triton-X 100 for 3 min. Nonspecific sites were blocked with 2% bovine serum albumin (Sigma-Aldrich) in PBS for 45 min. Fixed cells were stained with the following antibodies (for 3 h at 37 °C): β-Tubulin (1:100, Sigma-Aldrich), DBC1 (1:100, Cell signaling), and HA (1:100, Invitrogen). Primary antibodies were visualized by secondary antibodies conjugated to Alexa fluor 488 and Alexa fluor 594 (1:5000, Jackson ImmunoResearch) at 37 °C for 1 h. The cells were stained with DAPI (BioRad) for 10 min. Pictures were taken with an inverted fluorescence microscope (Axio Observer, Colibri7, Carl Zeiss MicroImaging, Inc) using filters for DAPI, GFP and mRF12, X20, X63, and DIC Apotome.2 oil objectives. The pictures were generated with ZEN 2.3 pro (Zeiss).
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10

Immunohistochemical Analysis of Pancreatic Islets

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Mice were transcardially perfused and the pancreas was processed as described previously12 (link). Mounted 16 μm-thick sections were incubated with primary antibodies in a humidified chamber at 4 °C overnight (rabbit anti-glucagon antibody, 1:1,000, BioGenex, Fremont, CA, USA) and guinea pig anti-insulin antibody (1:200, Bio-Yeda, Rehovot, Israel). After washing in PBS (0.01 M) they were incubated with secondary antibodies for 90 min at room temperature (donkey Cy3-conjugated anti-rabbit IgG and donkey FITC-conjugated anti-guinea pig IgG, 1:150 and 1:40 respectively, Jackson Immunoresearch Europe, Suffolk, United Kingdom). Sections were finally incubated with DAPI (1:10,000, Bio-Rad, Hercules, CA, USA) diluted in PBS for 15 min at room temperature and mounted using 2.5% DABCO in glycerol (Sigma-Aldrich, ST. Louis, MO, USA) and stored at −20 °C in darkness. Another set of sections was used for H&E staining (Histolab, Gothenburg, Sweden) and mounted with VectaMount permanent mounting medium (Vector Laboratories Inc., Burlingame, CA, USA). For the detection of apoptotic β cells, sections were processed as according to the commercial kit used (Click-iT Plus TUNEL assay, Thermo Scientific, Waltham, MA) and co-labeled with insulin.
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