image of a Click-iT® EdU Imaging Kit

DNA synthesis–based cell proliferation assay

In this assay the modified thymidine analogue EdU (5-ethynyl-2′-deoxyuridine, a nucleoside analog of thymidine) is efficiently incorporated into newly synthesized DNA and fluorescently labeled with a bright, photostable Alexa Fluor® dye in a fast, highly specific, mild click reaction.

This protocol can be used for:

  • Detecting DNA synthesis using a fluorescence microscope

This protocol should not be used for:

You will need the following for this protocol:


Prepare stock solutions

  1. Allow vials to warm to room temperature
  2. Add 2 mL DMSO (Component C) or an aqueous solution to Component A to make a 10 mM EdU stock solution. Store at –20°C
  3. Make 1X Click-iT® EdU reaction buffer by transferring the solution (4 mL) in the Component D bottle to 36 mL of deionized water. Store any remaining solution at 2–8˚C
  4. Make 10X Click-iT® EdU buffer additive by adding 2 mL deionized water to Component F and mixing until fully dissolved. Store at –20°C
  5. Dilute Hoechst® 33342 (Component G) 1:2,000 in PBS to obtain a 1X solution

Label cells with EdU

  1. Plate cells on coverslips and incubate overnight
  2. Dilute 10 µL of 10 mM EdU stock solution in 5 mL of prewarmed tissue culture medium to make a 20 µM EdU labeling solution (enough for 10 coverslips)
  3. Remove half of the medium from cells
  4. Replace with an equal volume of EdU labeling solution (final concentration of 10 µM)
  5. Incubate cells under appropriate growth conditions for two hours. NOTE: the choice of incubation time depends on the cell growth rate; thus optimization may be required
  6. Proceed immediately to fixation and permeabilization

Fix and permeabilize cells

  1. Transfer each coverslip into one well of a 6-well plate
  2. Add 1 mL of 3.7% formaldehyde in PBS to each well
  3. Incubate for 15 minutes at room temperature
  4. Remove formaldehyde and wash twice with 1 mL of 3% BSA in PBS
  5. Remove wash solution and add 1 mL of 0.5% Triton® X-100 in PBS to each well
  6. Incubate for 20 minutes at room temperature


Protocol tips

  • For in vivo experiments, additional EdU can be purchased separately (Cat. Nos. A10044, E10187)
  • Fixation/permeabilization reagents such as methanol and saponin can be used instead of the included Triton® X-100

Image of cells labeled with Click-iT® Plus EdU Alexa Fluor® 647 Imaging Kit
ERK2 A375 GFP expressing cells labeled with Click-iT® Plus EdU Alexa Fluor® 647 Imaging Kit (pink), Proliferating cells have pink nuclei. Non-proliferating cells have blue nuclei.

Detect EdU

  1. Make 1X Click-iT® EdU buffer additive by diluting the 10X solution created above 1:10 in deionized water. Prepare this solution fresh and use the solution on the same day.
  2. Prepare Click-iT® Plus reaction cocktail according to the table below. IMPORTANT: add the ingredients in the order listed in the table. 

  3. Reaction components*
    Number of coverslips
      1 2 4 5 10 25 50
    1X Click-iT® reaction buffer 440 µL 880 µL 1.84 mL 2.25 mL 4.4 mL 10.9 mL 21.9 mL
    Copper protectant 10 µL 20 µL 40 µL 50 µL 100 µL 250 µL 500 µL
    Alexa Fluor® picolyl azide (Component B)  1.2 µL 2.5 µL 5 µL 6 µL 12.5 µL 31 µL 62 µL
    1X Click-iT® EdU buffer additive 50 µL 100 µL 200 µL 250 µL 500 µL 1.25 mL 2.5 mL
    Total volume 500 µL 1 mL 2 mL 2.5 mL 5 mL 12.5 mL 25 mL
    *Note: Add the ingredients in the order listed in the table.
  4. Remove permeabilization buffer from cells and wash twice with 1 mL of 3% BSA in PBS
  5. Remove the wash solution
  6. Add 0.5 mL of Click-iT® Plus reaction cocktail to each well. Rock the plate briefly to ensure even distribution of reaction cocktail
  7. Incubate the plate for 30 minutes at room temperature, protected from light
  8. Remove the reaction cocktail and wash each well once with 1 mL of 3% BSA in PBS

Stain DNA

  1. Wash each well with 1 mL of PBS. Remove the wash solution
  2. Add 1 mL of 1X Hoechst® 33342 solution per well
  3. Incubate for 30 minutes at room temperature, protected from light
  4. Remove the Hoechst® 33342 solution
  5. Wash each well twice with 1 mL of PBS
  6. Remove the wash solution
  7. OPTIONAL: Perform antibody labeling of the samples at this time, following the recommendations from the manufacturer of the primary and secondary antibody. Note: protected samples from light during these incubations.


  1. Cells labeled with Click-iT® Plus EdU are compatible with all methods of slide preparation including wet mount or prepared mounting media
  2. Image cells with appropriate filters listed below
  Hoechst® 33342 Alexa Fluor® 488 Alexa Fluor® 555 Alexa Fluor® 594 Alexa Fluor® 647
Excitation/Emission (in nm) 350/461 495/519 555/565 590/615 650/670
Standard filter set DAPI FITC RFP TRITC Cy®5