Nuclear Extraction Method


Hypotonic Buffer Solution

  • 20 mM Tris-HCl, pH 7.4
  • 10 mM NaCl
  • 3 mM MgCl2

Phosphate Buffered Saline (Cat. No. 20012050)
Microfuge Tubes
NP-40 Detergent (10%)
Invitrogen Cell Lysis Buffer (Cell Extraction Buffer) (Cat. No. FNN0011)
PMSF (1 mM)
Protease Inhibitor Cocktail, (Cat. No. 78429)
Invitrogen Quant-iT Protein Assay Kit (Cat. No. Q33210)


Cell Extraction Buffer

  • 10 mM Tris, pH 7.4
  • 2 mM Na3VO4
  • 100 mM NaCl
  • 1% Triton X-100
  • 1 mM EDTA
  • 10% glycerol
  • 1 mM EGTA
  • 0.1% SDS
  • 1 mM NaF
  • 0.5% deoxycholate
  • 20 mM Na4P2O7

This Cell Extraction Buffer may be apportioned into 1X aliquots in microcentrifuge tubes and stored at –20°C until ready for use. Thaw on ice prior to extracting cells.

The Cell Extraction Buffer must be supplemented with 1 mM PMSF (not included) and Protease Inhibitor Cocktail (not included) just prior to use to make Complete Cell Extraction Buffer. Addition of the Protease Inhibitor Cocktail and PMSF is necessary to inhibit proteolysis in cell extracts. For the PMSF addition, we recommend making a 0.3 M stock in DMSO, and adding sufficient volume for a final concentration of 1 mM (i.e., 17 μL per 5 mL Cell Extraction Buffer). PMSF is very unstable and must be added just prior to use, even if added previously. For the Protease Inhibitor Cocktail addition, we recommend Halt Protease Inhibitor Cocktail (Cat. No. 78429), reconstituted according to 1X, and adding 50 μL per 5 mL Cell Extraction Buffer. The stability of protease inhibitor-supplemented Cell Extraction Buffer is 24 hours at 4°C.


This protocol has been successfully applied to several cell lines of human origin. Researchers should optimize the cell extraction procedures for their own applications.

1. Collect cells (5 x 106) in PBS by centrifugation (non-adherent) or scraping from culture flasks (adherent).
2. Wash cells twice with cold PBS.
3. Remove and discard the supernatant and collect the cell pellet.
4. Transfer the cells into a prechilled microcentrifuge tube.
5. Gently resuspend cells in 500 μL 1X Hypotonic Buffer by pipetting up and down several times. Incubate on ice for 15 minutes.
6. Add 25 μL detergent (10% NP-40) and vortex for 10 seconds at highest setting.
7. Centrifuge the homogenate for 10 minutes at 3,000 rpm at 4°C.
8. Transfer and save the supernatant. This supernatant contains the cytoplasmic fraction. The pellet is the nuclear fraction.
9. Resuspend nuclear pellet in 50 μL complete Cell Extraction Buffer for 30 minutes on ice with vortexing at 10 minute internals.
10. Centrifuge for 30 minutes at 14,000 x g at 4°C. Transfer supernatant (nuclear fraction) to a clean microcentrifuge tube.
11. Aliquot and store at –80°C. The nuclear extracts are ready for assay.
12. Quantitate protein concentration using the Quant-iT Protein Assay Kit (Cat. No. Q33210).

Ordering information

BioSource C-070276 1107 1-Jan-2007