SDS-PAGE Protein Gels

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(New page: === Consolidated/Pictorial Protocol === SDS casting protocol =='''Sample Prep - Marina Protocol'''== '''''For 5GB1 SDS-PA...)
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=== Consolidated/Pictorial Protocol ===
 
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[[image:SDS-PAGE casting procedure.jpg|thumb|upright=3.0|center|SDS casting protocol]]
 
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=='''Sample Prep - Marina Protocol'''==
=='''Sample Prep - Marina Protocol'''==
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'''''For 5GB1 SDS-PAGE total protein concentration estimation'''''
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'''''For 5GB1 whole cell protein SDS-PAGE'''''
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# Grow cells to ~ OD 1.0
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*Grow cells to ~ OD 1.0
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:For calculation purposes, you ideally want 1 ml of cells at an OD of 1.0  
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:- For calculation purposes, you ideally want 1 ml of cells at an OD of 1.0  
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: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)
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:- 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)
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# Weigh eppindorf tube
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*Weigh eppindorf tube
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:Need to subtract tube weight to determine wet cell weight (WCW) of sample -- don't forget this step!
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:- Need to subtract tube weight to determine wet cell weight (WCW) of sample -- don't forget this step!
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# Harvest appropriate sample volume and pellet cells
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*Harvest appropriate sample volume and pellet cells
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:RT benchtop centrifugation at 14K RPM; 2-3 minutes should be more than sufficient
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:- RT benchtop centrifugation at 14K RPM; 2-3 minutes should be more than sufficient
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#Dry the pellet as completely as possible by decanting and then pipetting off any remaining liquid
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*Dry the pellet as completely as possible by decanting and then pipetting off any remaining liquid
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# Weigh dried pellet and eppindorf tube, subtract out tube weight and record WCW
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*Weigh dried pellet and eppindorf tube, subtract out tube weight and record WCW
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'''''At this point, pellet can be frozen and the following steps can be performed at a later date'''''
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*Mix Laemmli sample buffer using the following recipe:
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::500 ul BioRad 4x Laemmli buffer
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::450 ul dH2O
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::50 ul 2-mercaptoethanol
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*Add 100 ul of buffer to pellet and vortex to ensure cells and Laemmli buffer are well mixed
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*Incubate sample for 5 minutes at 95-100°C
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'''''Samples are ready to be loaded into gel as described below'''''
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Revision as of 18:10, 20 May 2013

Contents

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
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
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 -80oC. 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.
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