Difference between revisions of "20.109(S18): Prep notes for M1"
From Course Wiki
Noreen Lyell (Talk | contribs) |
Noreen Lyell (Talk | contribs) (→M1D5) |
||
Line 73: | Line 73: | ||
**1.6 mL 1 M Tris-HCl, pH = 8 | **1.6 mL 1 M Tris-HCl, pH = 8 | ||
**80 μL 2 μM chymotrypsin | **80 μL 2 μM chymotrypsin | ||
− | *20 μL 40% DMSO | + | *20 μL 40% DMSO; prepared such that 1 μL needed per reaction (final concentration = 0.2% in 200 μL) |
− | *10 μL 2 mM rapamycin | + | *10 μL 2 mM rapamycin; prepared such that 1 μL needed per reaction (final concentration = 10 μM in 200 μL) |
− | *10 μL 8 mM Chembridge ligands (most stocks at 100 mM) | + | *10 μL 8 mM Chembridge ligands (most stocks at 100 mM); prepared such that 1 μL needed per reaction (final concentration = 40 μM in 200 μL) |
<font color = red>aliquot amounts calculated for each team using in-house and Abcam protein, 30 reactions total with each protein</font color> | <font color = red>aliquot amounts calculated for each team using in-house and Abcam protein, 30 reactions total with each protein</font color> |
Revision as of 15:11, 9 February 2018
M1D1
per team:
- 100 μL nuclease-free H2O
during the laboratory:
- 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
M1D3
prior to laboratory:
- prepare dialysis buffer (1X PBS), 1 L 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
M1D4
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
M1D5
prior to laboratory:
- dilute 200 μM chymotrypsin (prepared in 1 mM HCl containing 2 mM CaCl2) to 2 μM chymotrypsin in H2O
- prepare serial dilutions of reagents
- DMSO:
- rapamycin:
- ligands:
per team:
- 18 μL 1 mg/mL FKBP12
- buffer reagents
- 1.6 mL 1 M Tris-HCl, pH = 8
- 80 μL 2 μM chymotrypsin
- 20 μL 40% DMSO; prepared such that 1 μL needed per reaction (final concentration = 0.2% in 200 μL)
- 10 μL 2 mM rapamycin; prepared such that 1 μL needed per reaction (final concentration = 10 μM in 200 μL)
- 10 μL 8 mM Chembridge ligands (most stocks at 100 mM); prepared such that 1 μL needed per reaction (final concentration = 40 μM in 200 μL)
aliquot amounts calculated for each team using in-house and Abcam protein, 30 reactions total with each protein
during the laboratory:
- prepare 5 mM suc-AAFP-pNA in TFE containing 460 mM LiCl
M1D6
prior to laboratory:
- prepare serial dilutions of reagents (MIX WELL BETWEEN DILUTIONS)
- 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: 100 mM → 10 mM (1 μL ligand in 9 μL DMSO); 10 mM → 1 mM (5 μL of 10 mM ligand + 45 μL 1X PBS); 1 mM → 100 μM (5 μL of 1 mM ligand + 45 μL 1X PBS)
per team:
- 18 μL 1 mg/mL FKBP12
- 60 μL 5x dye solution in 1X PBS
- 20 μL 1% DMSO in 1X PBS
- 10 μL 50 μM rapamycin in 1X PBS
- 20 μL 100 μM ligand in 1X PBS
- 30 μL 1X PBS
during the laboratory:
- control protein
- control ligand
- sterile H2O
- filtered pipet tips
M1D7
per team:
- none