20.109(S18): Prep notes for M1
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M1D1
- restriction enzymes and buffers
- filtered pipet tips
M1D2
prior to laboratory:
- prepare 1% agarose gels, 1 per 2 teams
- subculture BL21(DE3) pRSETb_FKBP12 1:10 into 50 mL LB containing 100μg / mL amp and 34 μg / mL cam, 1 per team
per team:
- 25 μL 6x loading dye
- 520 μL 0.1 M IPTG
M2D3
prior to laboratory:
- prepare dialysis buffer, X mL per team
per team:
- lysis buffer reagents
- 170 μL 1 M Tris, pH = 7
- 470 μL 1 M NaCl
- 770 μL 40% glycerol
- 5 μL 1 M DTT
- 35 μL 10 mM AEBSF
- 1.8 mL sterile H2O
- 250 μL slurry (Ni-NTA resin) in 2 mL microcentrifuge tube
- 2.5 mL 1X PBS
- 40 μL 1 M MgCl2
- 12 μL DNase
- 2 mL 1X PBS containing 10 mM imidazole
- 3.5 mL 1X PBS containing 250 mM imidazole
M2D4
prior to laboratory:
- boil stained and unstained molecular weight standards, if required
- prepare electrophoresis buffer, 1 chamber volume per 2 teams
per team:
- 20 μL Laemmli buffer
- 50 mL coomassie stain
- BSA reagents
- 110 μL albumin
- 1.3 mL 1X PBS
- 17 mL BCA Reagent A
- 400 μL BCA Reagent B
M2D5
prior to laboratory:
- dilute 200 μM chymotrypsin (prepared in 1 mM HCl containing 2 mM CaCl2) to 2 μM chymotrypsin in H2O
per team:
- 18 μL 1 mg/mL FKBP12
- buffer reagents
- 0.8 mL 1 M Tris-HCl, pH=8 containing
- 40 μL 2 μM chymotrypsin
- X μL DMSO (?), prepare such that 1 μL needed per reaction (final concentration = 0.2% in 200 μL)
- Y μL B μM rapamycin (?), prepare such that 1 μL needed per reaction (final concentration = 10 μM in 200 μL)
- Chembridge ligands (most at 100 mM), prepare such that 1 μL needed per reaction (final concentration = 40 μM in 200 μL)
aliquot amounts calculated for each team only using Abcam protein and 15 reactions, if in-house protein used aliquots should be increased and/or if ligands not used values should be reduced
during the laboratory:
- prepare 5 mM suc-AAFP-pNA in TFE containing 460 mM LiCl
M2D6
prior to laboratory:
- prepare serial dilutions of all reagents
- dye: 1000x → 100x (2 μL dye + 18 μL 1X PBS); 100x → 5x (10 μL of 100x dye + 190 μL 1X PBS)
- DMSO: 100% → 10% (1 μL DMSO + 9 μL 1X PBS); 10% → 1% (1 μL of 10% DMSO + 9 μL 1X PBS)
- rapamycin: prepare 5 mM in DMSO; 5 mM → 500 μM (5 μL of 5 mM rapamycin + 45 μL 1X PBS); 500 μM → 50 μM (5 μL of 500 μM rapamycin + 45 μL 1X PBS)
- ligands:
Dilute 500uM → 50uM in PBS 50uM will be the stock conc used in the reaction C. ChemBridge compounds (most are at 100mM) -conc in well will be 20uM 100mM→10mM in DMSO (1uL compound +9uL DMSO) 10mM→ 1mM into PBS (5uL of 10mM stock +45uL PBS) MIX WELL 1mM→ 0.1mM (100uM) in PBS 100uM is the stock concentration used in the reaction
per team:
- 18 μL 1 mg/mL FKBP12
- X μL 5x dye solution in 1X PBS
- Y μL 1% DMSO in 1X PBS
- Z μL 50 μM rapamycin in 1X PBS
- A μL 100 μM ligand in 1X PBS
M2D7
per team:
- none