SDS-PAGE Protein Gels

Sample Prep - Marina Protocol

For 5GB1 whole cell protein SDS-PAGE

• Grow cells to ~ OD 1.0

- For calculation purposes, you ideally want 1 ml of cells at an OD of 1.0

- If your samples are not at 1.0, increase or decrease volume to compensate (eg: If OD is only 0.747, use 1.34 ml)

• Weigh eppindorf tube

- Need to subtract tube weight to determine wet cell weight (WCW) of sample -- don't forget this step!

• Harvest appropriate sample volume and pellet cells

- RT benchtop centrifugation at 14K RPM; 2-3 minutes should be more than sufficient

• Dry the pellet as completely as possible by decanting and then pipetting off any remaining liquid
• Weigh dried pellet and eppindorf tube, subtract out tube weight and record WCW

At this point, pellet can be frozen and the following steps can be performed at a later date

• Mix Laemmli sample buffer using the following recipe:

500 ul BioRad 4x Laemmli buffer

450 ul dH2O

50 ul 2-mercaptoethanol

• Add 100 ul of buffer to pellet and vortex to ensure cells and Laemmli buffer are well mixed
• Incubate sample for 5 minutes at 95-100°C

Samples are ready to be loaded into gel as described below

Consolidated/Pictorial Protocol

SDS-PAGE sample prep and loading

Running the Gel

• Bio-Rad Mini-Cell Setup
  • If only 1 gel, use buffer dam to replace second gel
• Position the gels with the shorter plate facing inward!
• Apply pressure on gel holder and gels as you close the tabs to seal the center compartment.

Mini-cell Gel holder

• Fill central compartment with running buffer
  • should fill sample wells
• Pour more into the outer compartment to specified line
• Load gel
  • Make sure you will be able to determine the orientation of your gel after it is stained. Asymmetry is good!
• Make sure to color/charge-match the cords to the power unit as the electrodes in the gel holder to the contacts in the lid.
• Run @ 60 V for ~15 min, then 200 V for ~ 20+ min.
  • Note: ladder looks blurry while running through the stacking gel; don't be alarmed unless it still looks blurry in the resolving gel.
  • Can skip the 60V step if you don't need a gorgeous gel
  • Amanda runs 20 min at 200V, then checks frequently to make sure the protein doesn't run off the gel.

Storing Samples After Use

• Amanda was taught to flash-freeze (liquid N₂) samples and store them at -80^oC. Janet loves liquid N2 (particularly dumping it on the ground after use) so I follow along without question.
• Ladder is stored at -80oC. An aliquot of PageRuler Prestained that sat out at room temp for 1 week looked perfect in a gel, so don't worry about that ladder's stability.