Crosslinking Primary Antibody to Protein A/G resin using dimethylpimelimidate (DMP), for MS-Compatible Immunoprecipitation

(As an alternative to disuccinimidyl suberate (DSS) crosslinking)

Reagents:

  1. PBS
  2. Binding buffer: 0.2M sodium borate (adjust 0.2M Boric Acid to pH 9 with NaOH)
  3.  Crosslinking reagent: 20mM DMP (dimethylpimelimidate, Pierce # 21666) dissolved in 0.2M sodium borate – make immediately prior to use
  4. “Quenching” reagent: 0.2M ethanolamine (pH 8.0 in 50 mM Ammonium Bicarbonate)
  5. Acid Wash buffer: 0.58% v/v acetic acid with 150mM NaCl
  6. Lower stringency lysis buffer for wash: 150mM NaCl, 50mM Tris, 10mM EGTA, 0.2% NP40
  7. MS Wash buffer: 50mM ammonium bicarbonate
  8. Elution buffer: 0.25% Rapigest SF Surfactant in 50mM ammonium bicarbonate

Procedure:

Coupling antibody with agarose beads:

  1. Couple antibody/control IgG andProtein A/G beads (Pierce # 20421) in PBS:
    • Add 60ul (20 ug) X antibody to 30 ul Prot A/G beads in 1ml PBS
    • Add 50ul (20 ug) IgG rabbit to 30 ul Prot A/G beads in 1ml PBS (control)
    • Rock 2-3 hours or overnight at 4C
  2. Wash beads 3X with 1ml of 0.2M sodium borate pH 9 – after each wash, spin at 300-500g to pellet beads, gently remove supernatant
  3. Save small sample to run on gel to check efficiency (see step 15)

    Crosslinking:
     
  4. Make fresh DMP:
    • Let solid warm up to room temperature ~20min
    • Weigh out 0.0259 g DMP
    • Immediately add DMP to 5ml of 0.2M sodium borate (pH 9) to make 20mM DMP solution
  5. Immediately add 1ml 0.2M sodium borate + 20mM DMP to (1) beads + X Antibody; and (2) beads + Control IgG
  6. Rock at RT for 40min to perform antibody crosslinking
  7. Spin down and remove supernatant
  8. Wash beads once in 0.2M ethanolamine (pH 8.0) – this removes/quenches any residual DMP
  9. Resuspend in 1ml of 0.2M ethanolamine (pH 8.0)
  10. Rock at RT for 1-2 hours
  11. Save small sample to run on gel to check efficiency (see step 15)
  12. To remove uncoupled IgGs, wash with 3X 1mL 0.58% v/v acetic acid + 150mM NaCl
  13. Wash 3X with 1ml cold PBS - after each wash, spin at 300-500g to pellet beads, gently remove supernatant
  14. Save small sample to run on gel to check efficiency (see step 15)

    Check the efficiency of immobilization:
     
  15. Sample beads (1) before and (2) after crosslinking, and (3) after the acid wash – elute by boiling resin in 2x LDS loading buffer, then run SDS-PAGE/Coomassie stain . **Ensure equal volumes of beads are analyzed for each of these samples. For example, if you are going to take out 5 uL of beads for the check and then elute in 20 uL 2X LDS and load 10 uL for SDSPAGE, be sure to do it the same for all resin binding steps.
  16. Evaluate the results of the immobilization process prior to proceeding. (please share images with us!!)

    Proceed with IP:
     
  17. Quantity of input material will vary depending on the expression of the target protein/complex. Typically, between 0.5 and 5 mg input protein is utilized. Preclearing is recommended, by adding your lysate to ~25 uL of uncoupled Protein A/G resin, rock for 30 minutes, and reserve supernatant for IP.
  18. Add 1ml (~1-5 mg/mL protein) of precleared lysate to approximately 25 uL coupled resin. Use same resin quantity for all samples.
  19. Rock overnight at 4C (with end-over-end mixing, if possible)
  20. Save supernatant for WB analysis.
  21. Wash resin 3X with lysis buffer containing 150mM NaCl, 50mM Tris, 10mM EGTA, 0.2% NP40 (you may want to save these washes for troubleshooting purposes… a signal in WB at this step (but not step 20) would suggest target bound to antibody but was then washed away)
  22. Elute with 50-100ul of 2X LDS loading buffer, boil 5 min at 95C, pellet beads by centrifugation, take supernatant for SDSPAGE analysis (below). ***see step 23 for MS compatible elution protocol

    Recommended Setup for Coomassie gel (or WB analysis):
  • Ladder
  • 50ug lysate
  • X Beads pre-elution
  • X Beads post-elution
  • X Elution supernatant
  • IgG Rab Beads pre-elution
  • IgG Rab Beads post-elution
  • IgG Rab Elution supernatant

    *Stain with Invitrogen Colloidal Blue Staining kit (LC6025)
    *Alternative elution steps once IP has been optimized
  1. After step 21 wash, wash resin 3X with 1 mL 50mM ammonium bicarbonate

  2. Add 50-100ul of 0.2% Rapigest SF Surfactant (Waters Corporation) in 50mM Ammonium Bicarbonate.

  3. Boil @ 95C for 5min, pellet beads by centrifugation, take supernatant for delivery to Duke Proteomics Core Facility, or for SDS-PAGE analysis as above.