3g ampicillin sodium salt (Fisher BP1760-25)
Add sterile water to raise volume to 30 ml. Filter sterilize through 0.22um syringe filter. Then aliquot into 1 ml and store at 20C.
24.6g ammonium acetate anhydrous (FW 82.03). Dissolve in about 60 ml 3M acetic acid. Stir. Warm. Stir.
When cooled to room temperature, adjust pH to 5.2.
Autoclave
For 100ml 24.6g
200ml 49.2
300ml 73.8
1. Make up protein standard dilutions as follows:
A) 2 ul of BSA stock + 98 ul H20
B) 4 ul of BSA stock + 96 ul H20
C) 6 ul of BSA stock + 94 ul H20
D) 8 ul of BSA stock + 90 ul H20
BSA stock is 2.0 mg/ml H20
2. Make up protein sample dilutions as follows:
For crude lysate and diluted supernantant:
A) 2 ul protein + 98 ul H20
B) 5 ul protein + 95 ul H20
C) 10 ul protein + 90 ul H20
For protein fractions and pools
A)
B) Same as above
C)
D) 15 ul protein + 85 ul H20
3. Add 0.9 ml of Bradford Reagent to each eppie tube, votex each tube for a few seconds.
4. Take 2 readings of each tube at 595 nm
5. Then do the calculations.
1. Protein Standard
Tube mg. Protein OD at 595 nm
A 0.004
B 0.008
C 0.012
D 0.016
E 0.020
2. Plot the standard curve ,OD at 595 nm vs mg of protein standard. Attach graph to back of prep record
3. Next do calculations that determine the protein concentration of your samples:
Sample A: OD at 595 nm = X
Match X up the correct mg of protein that was found from the standardization curve. Divide this amount by the amount of protein which was assayed.
Buffer SP-A (HIV-1 NC Prep) (RD)
Stock Add
50 mM Tris-HCL pH 8.0 FW 121.1 6.06 g
10% glycerol Liq. 100 ml
0.1 M NaCl FW 58.44 5.8 g
0.1 mM ZnCl2 0.2 M 0.5 ml
10 mM BME 14.4 M 0.694 ml
Stock Add for 1 L
20mM NaPO4 pH 6.1 1 M 20 ml
1 M NaCl FW 58.44 58.44 g
10 mM BME 14.4 M 0.714 ml
80% Formamide 8 ml
Xylene Cyanol FF 10mg
Bromophenol Blue 10mg
10 mM EDTA (stock 0.5 M
pH 8.0) 200 ul
fill with water to: 10 ml
Coomassie Stain: Light box computer room 125 22
Et. Br. Gels: Light box in dark room 4.5 max 1 sec
Fisher Stock store at room temperature
EtOH solution store at 20C
1.02 g chloramp.
To 30 ml with EtOH
100
ml
CaCl2 Anhydrous FW 110.99 11.10 g
OR
CaCl2·2H2O FW 147.02 14.70 g
No need to sterilize. Divide into 10 ml aliquots. Store in 20 C
(From Bio-Rad for Tris-Glycine gels)
500
ml
40 % MeOH 200 ml
10 % Acetic Acid 50 ml
Coomassie Blue R-250 0.5 g
Fill to 500ml with water.
Competent Cells
(protocol for one strain)
Day one:
100 ml LB
Small beaker for TSS solution
(extra flasks if preparing more than one strain
Small centrifuge tubes
Day two:
10 % Polyethylene glycol 3350 2.0 g
5 % Dimethyl Sulfoxide (DMSO) 1 ml
20 mM MgCl2 (1 M stock) 4 ml
Add LB to 18 ml
Filter sterilize through 0.22 um syringe filter
Chill until needed
(Everything must be kept cold from this point on. Chill pipets, tips, centrifuge tubes, final storage eppi tubes..)
500ml PPCO 13,700 X g
250ml PPCO 27,500 X g
50ml PPCO 50,000 X g
16ml PPCO 50,000 X g
1 M Dithiothreitol
(DTT)
Stock 32.4ml
DTT FW 154.25 5 g
Filter Sterilize with 0.22um syringe filter.
Aliquot into 1 ml. Store at 20 C
Fisher BP172-5
1
L
10 % HOAc 100ml
40 % MeOH 400ml
ddH2O 500ml
1
L
5 % MeOH 50ml
7 % HOAc 70ml
dd H2O 880 ml
Stock 2 L
25 mM NaPO4 1M 50 ml
25 mM NaCl FW 58.44 2.92g
10 mM BME 14.4 M 0.714ml x 2
De-gas by vacuum filtration.
Ethidium Bromide
1000 X (0.5 ug/ml)
Dissolve 5 mg Et. Br in 10 ml ddH2O
Or 50 mg Et. Br. In 100 ml dd H2O
Use amber bottle
Keep at room temperature
Working solution : 0.5 ug/ml
e.g. for 100ml gel, use 100.0 ul Et. Br soln.
1L
40 % EtOH 400 ml
5 % Glycerol 5 ml
100
ml (~ 6 plates)
Tryptone 1 g
Yeast Extract 0.5 g
NaCl 1 g
Agar 1.5g
Fill to 100 ml final volume with ddH2O.
Solutes will dissolve when autoclaved
25ml
100ml 500ml 1L
Tryptone 2.5 g 1 g 5 g 10 g
Yeast Extract 1.25g 0.5 g 2.5 g 5 g
NaCl 2.5 g 1 g 5 g 10 g
NaOH (1 M) 0.25 ml 0.1 ml 0.5 ml 1 ml
Agarose Gel
Electrophoesis
% Agarose Size
DNA Separated
0.3 5 60 kb
0.5 1 30
0.7 0.8 12
1.0 0.5 10
1.2 0.4 7
1.5 0.2 3
2.0 0.05 2
Small Gel:
40 ml TAE
40 ul Et Bromide (0.5 mg/ml)
250 ml Buffer
250 ul Et Bromide
Votage: 1 5 V/cm (cm between electrode) ~ 55V
Detection limit: ng scale
1. Inoculate a single colony into 50 ml media w/ amp in a 250 ml flask.
2. Incubate with vigorous shaking at 37 C until OD 600 = 0.6 to 0.8.
3. 0.9 ml cells
0.1 ml 80% glycerol
4. Mix well, store at 70 C
120 ml H2O
129 ml of Conc. HCL , 11.6 M (from under hood)
40% Glucose (2.2 M
Glucose)
Glucose 40 g
ddH2O fill to 100 ml
Dissolve in about 50 ml warm H2O with stirring
Then add the remaining H2O
Also called Dextrose, FW 180.16
Warm gently to dissolve. Filter sterilize through 0.22 um
Flame top with each use
0.1M HCl
Used in wash bottle for RNA work.
Volume of wash bottle 750 ml.
Add 6.5 ml of conc. HCl, then fill to volume with ddH2O
IPTG 2.38 g
Fill to 10 ml with ddH2O
Or
IPTG 3 g
Fill to 12.6 ml final volume
Filter sterilize with 0.22 um syringe filter.
Aliquot in 1 ml, store at 20 C.
Three things to do to avoid formation of inclusion bodies
1. Change Temperature. Grow at 30 C instead of the usual 37 C
2. Change cell line
Try BL21(DE3)
HMS174(DE3)
3. Lower level of expression.
Kanamycin 1000x
Kanamycin 0.9 g
Fill to 30 ml final volume with ddH2O
Filter sterilize, aliquot to 1 ml
Makes a 30 g/L stock
keep at 20 C
use at 1000-fold dilution 30 ug/L
KCl 7.46 g
Fill to 100 ml final volume with ddH2O
No need to sterilize.
Stock 5 ml
20 % Ficoll 400 (w/v) 1 gm
0.1 M Na2EDTA pH 8.0 0.5 M 1 ml
1.0 % SDS 10 % 0.5 ml
0.25 % (w/v) BPB 12 mg
Lysis Buffer (for
NC p7 prep)
50 mM Tris-HCl pH 8.0
10% Glycerol
0.1 M NaCl
0.1 mM ZnCl2
Add
DTT to 5 mM (for 200 ml add 1 ml of 1M DTT)
EDTA to 2 mM ( 0.8 ml of 1 M EDTA)
n To estimate ε280 of proteins based on sequence.
No. of Tyr x 1280
No. of Trp x 5690
No. of Cys x 120
Add three
numbers = ε m-1cm-1
Ref: S.C.
Gill & P.H. von Hippel
Anal. Biochem.
182, 319-326, 1989
MW= A
x 312.2
G x 328.2
C x 288.2
+T x 303.2
Then
subtract 61.0
yields
concentration in g/mol
M9 Minimal Media (Maniatis)
Na2HPO4·7H2O 12.8 g
KH2PO4 3 g
NaCl 0.5 g
NH4Cl 1.0 g
1M MgSO4 2 ml
Glucose 4 g
1 M CaCl2 0.1 ml
100X Vitamin mix 10 ml (Gibco Cat # 11120-052)
1000X Trace metal 1.0 ml (Recipe below)
MgCl2·6H2O
40.66 g
Fill to
final vol. of 100ml
Autoclave
to sterilize, flame top each use
TB 1
L
H2O 900 ml
Tryptone 12 g
Yeast
Extract 24 g
Glycerol 4 ml
Autoclave
M9ZB Media
1
L
Tryptone 10
g
NaCl 5
g
Autoclave,
cool. Then add:
10X M9
salt (see below) 100 ml
IM MgSO4·7H2O 1 ml
40 %
glucose* 10
ml*
*Dont add
for overnight cultures.
1 L
NH4Cl 10 g
KH2PO4 30 g
Na2HPO4·7H2O 60 g
Autoclave.
Use in
making M9ZB Media.
Non-Denaturing Gel Buffers
Separating Gel Buffer:
90.85 g Tris-Base
Fill with DI H2O to 500 ml
Stacking Buffer:
15.43 g Tris-Base
Fill with DI H2O to 500 ml
Potassium Phosphate & M9
100 ml
KH2PO4 2.31
g + 3 g
K2HPO4 12.54
g
NH4Cl 1.00
g
Na2HPO4·7H2O 6.00 g
Autoclave.
Wash
bottle volume 750 ml
Add 5.3 g
NaOH, fill bottle to volume
Stock 30 ml 40 ml
25 mM d3-acetate FW 85.06 0.06457 g 0.086 g
25 mM NaCl 2 M 0.375 ml 0.50
ml
0.1 mM
ZnCl2 0.2 M 0.015 ml 0.20 ml
0.1 mM BME 14.4 M 2 ul 0.003
ml
Use 50 ml
Falcon Tube.
Degass by Argon,
15 min
Filter
Sterilize using 0.22 um filter
Exchange
in Amicon 4 5 times.
A x
15.4 ml/umol
G x
11.7 ml/umol
C x
7.3 ml/umol
T x
8.8 ml/umol
Add up all
values = ε
Concentration
= OD 269 = umol
ε ml
Pepstatin A (1 mg/ml) or 1000 x
ICN cat
no. 195368, 10 mg
Dissolve
10 mg in 10 ml freezer cold EtOH
Store at
20 C.
Use at 1
ug per ml cell lysate
Ex. 30 ml Lysis buffer = Add 30 ul Pepstatin A solution
100 ml Lysis buffer = Add 100 ul
10 % PEI
20 ml 50 %
(w/v) stock J. T. Baker PEI and H2O
Add conc.
HCl to adjust pH to 7.9 or 8.0.
Filter
through 0.45 um filter
Store at 4
C
10 mM Use at Cell Lysis
575 λ 100 ml
Make stock
in Isopropanol
(more?
)
Use At Stock
Leupeptin 1 2 ug/ml 10 mg/ml, H2O
Pepstatin
A 1 ug/ml 1 mg/ml, EtOH
PMSF 100 ug/ml 1.74 mg/ml, 10 mM IPA
EDTA 1 mM 0.5 M, H2O
RNA Analytical (Denaturing)
Gels
1. Wipe off inside of small plates, small spacers and comb with ethanol.
2. Grease the square plate, approx Ό in from edge on three sides. Do not get grease in the middle of plate. Place spacers on grease on plate.
3. Mix 20 % denaturing gel solution according to the recipe for 45 ml (below)
4. Slowly pour gel onto bottom plate while sliding up top plate with outher hand. Be careful not to cause bubbles while pouring.
5. Be sure comb is in position so that top of wells are visible above top of notched plate.
6. Clamp around all sides, including around comb.
7. Allow gel to polymerize for 1 hr. (some suggest 1.5 hr is best)
8. Make 1 L 1X degassed TBE buffer.
9. Secure gel with clamps onto electrophoresis apparatus. (Do not remove comb yet)
10. Add 1+/- L of TBE buffer so that bottom of gel is covered and fill top so that top of wells are covered.
11. Remove comb carefully, trying not to lose any wells. Try running a razor blade along each side of comb before removing.
12. Add 2 ul blue-green dye and begin 1 hr- 1.5 hr prerun. Most RNA settings are 900 Volts, 300 mA, 3-7 Watts.
13. Load samples, which are all in 25% glycerol.
14. Add another 2 ul of blue-green dye.
20 % RNA,
Denaturing, Purification Gels
Big
Gels Analytical Gels
Sequa-gel Concentrate 400 ml 24 ml
Sequa-gel Diluent 50 ml 3 ml
Sequa-gel Buffer 50 ml 3 ml
10% APS 3.5 ml 210 ul
TEMED 170
ul 12
ul
Total Vol 500 ml 30 ml
12% RNA, Denaturing, Purification
gels
Beginner Expert
Sequa-gel
Concentrate 240 ml 216
ml
Sequa-gel
Diluent 210 ml 189 ml
Sequa-gel
Buffer 50 ml 45 ml
10% APS 3.5 ml 3.15 ml
TEMED 170 ul 153 ul
1. Wear
gloves and face shield at all times.
2. Wipe off inside of clean gel plates
with ethanol.
3. Grease sides and bottom of the
bottom plate (the plate that is rectangular) with vacuum grease. Approx. 1/4 inch in from edge. Avoid getting grease elsewhere on plate.
4. Wipe off spacers (two long, one
short) and comb with ethanol and place spacers on the grease on bottom
plate. (Set comb aside)
5. Mix gel solution following recipe
for desired percentage of acrylamide.
6. Slowly pour gel onto bottom plate
while sliding up top plate with other hand.
Be extra cautious not to cause bubbles while pouring. (bubbles, however, can be removed by using a
clean analytical gel spacer).
7. Be sure both plates are squarely
together and the spacers seal together the corners to avoid leaks.
8. Clamp around all sides and at the
comb.
9. Allow to polymerize for 1 hr.
10. Make about 1.5 L 1X degassed TBE
buffer per gel.
11. Once gel has solidified, wipe off
outside notched plate. This is very
important as not to ruin the electrophoresis equipment. Wipe off gold plate on apparatus as well.
12. Secure gel, notched side to gold
plate, into apparatus.
13. Tighten opposing knobs
simultaneously using an equal amount of torque on each knob. (This will help avoid breaking plates and
plastic knobs.)
14. Be sure drain in back of apparatus
is closed and fill top and bottom of apparatus with 1 X TBE buffer.
15. Use bent needle to remove air
bubbles from bottom of gel, between plates.
16. Prerun gels for approx. 2 hrs at
(usually) 60-80 watts, 300 mA, 900 Volts.
17. Add 2 ul of blue-green dye when pre-running, as a marker, into
each of the two small wells on the far sides of the gel.
16. During this time, clean up any spilled gel as it contains
acrylamide which is very toxic (and messy).
18. Load sample. No more than 2 ml should be loaded in each
well. The optimum amount depends on the
depth of each particular well and the experience of the loader.
19. Load another 2 ul of blue-green
dye.
20. Run sample on gel at a rate and
time pre-determined on the size of the molecule being purified and time
availability.
5 mg RNase
A (BMC),
5 ml TE,
pH 8.0
Boil 15
min
Aliquot
into 0.5ml.
Store at
20 C
Stock 50ml
100 mM
Tris HCl, pH 6.8 1 M 5 ml
200 mM BME 14.4 M 700 ul
4 % SDS 10
% 20 ml
0.2 %
Bromophenol Blue Solid 0.1 g
20 %
Glycerol 100
% 10 ml
Stock 10 ml
Tris HCl
pH 6.8 1 M 1.3 ml
SDS 10 % 5.3 ml
Bromophenol
Blue Solid ~mg ( a pinch.
Very scientific)
Glycerol 100 % 2.6 ml
Store at
20 C in 1 ml aliquots
Use 1000x
of dye with 18 λ BME
Stock 10 ml
Tris HCl 0.5 M 2.5 ml
Glycerol 100 % 2.0 ml
SDS 10 % 4.0 ml
Bromophenol
Blue 0.1 % 0.5 ml
Use at
least one part sample buffer to one part sample.
Silver Stain (ICN Kit)
Pretreatment soln. Stain
Soln. Developer
45 ml H2O 5 ml (2) 95
ml H2O
40 ml MeOH 5 ml (3) 2.5
ml (5)
10 ml EtOH 5 ml
(4) 2.5 ml (6)
5 ml Soln 1 85 ml H2O
Stains-all 1.5 g
Formamide 600 ml
H2O 400 ml
Keep at 4
C. Can be reused.
Stain gel
20 min.
Rinse gel
with H2O.
Do Not
Stain Ag Stained gel w/ stains-all.
(will destroy stains-all soln.)
SOB: 1 L 500ml 200ml
Tryptone 20 g 10 g 4 g
Yeast
Extract 5 g 2.5 g 1.25 g
NaCl 0.5 g 0.25 g 0.10 g
1 M KCl 2.5 ml 1.25 ml 0.5 ml
1 M NaOH 1 ml 0.5 ml 0.2
ml
(autoclave
above ingredients)
Add Before
use:
2 M MgCl2 5 ml 2.5 ml 1
ml
For SOC
add:
40 %
Glucose 9 ml 4.5 ml 1.8 ml
Siliconizing Solution (RNA Plates)
500
ml
20 % v/v
Dichlorodimethylsilane 100
ml
80 % v/v
Methylene Chloride 400
ml
Sodium Azide (NaN3) (poison!!)
Use 0.01 %
for NMR samples
Use 0.05 %
for G sephadex
---(?)----
1% FeCl3 . 6H2O 2.45 ml
1% NaMoO4 . 2H2O 0.01 ml
1% ZnSO4 . 7H2O 2.0 ml
1% MnSO4 . H2O 0.085 ml
1% H3BO4 0.075 ml
1% CoCl2 . 6H2O 0.25 ml
1% NiCl2 . 6H2O 0.05 ml
H2O 45.08 ml
10 X
stock 500 ml 1
L
1.92 M
Glycine 72.1 g 144.2 g
0.25 M
Tris 15.1 g 30.2 g
1.0% SDS 5.0 g 10.0 g
Dissolve
in warm water.
Good for 6
months.
Tris-Tricine Running Buffer
10X,
500 ml 10X, 300 ml
Tris Base 60.58 g 36.35 g
Tricine 89.6 g 53.76 g
SDS 5.0 g 3 g
Run at 100
V, 150 min. Blue dye to reach end.
500 ml
: 50 ml HOAc
0.125
g G-250 Coomassie
To Stain:
1. Fix gel 30 min in Destain I
2. Stain 1 hour in Tris-Tricine stain
solution.
3. Destain 3X 15 min, 10% HOAc
4. Keep in Destain II overnight
A) Tryptone 12
g
Yeast Extract 24 g
Glycerol 4
ml
H2O 900 ml
B) KH2PO4 2.3
g
Yeast Extract 12.5 g
H2O 100 ml
Autoclave
Separately.
When at
room temperature, add and mix together.
10 ml B to 90 ml A
Stock Add
LB LB 4.5 ml
10 % PEG
3350 (w/v) Solid 0.5 ml
5 % DMSO Liq. 0.250 ml
20 mM MgCl2
I M 0.100 ml
Use 15 ml
Falcon tube.
No need to
pH, it should be around 6.4-6.8.
Filter
sterilize through 0.22 um filther
Place on
ice until added to cells
If stored
for later, store at 20C
Stock 100
ml (10x) 10 ml
10 mM
Tris-HCl 1 M 1
ml 10 ml 0.100 ml
1 mM EDTA 0.5 M 0.2 ml 2 ml 0.020
ml
Sterilize.
1
L 500 ml
Tris Base 48.4
g 24.2 g
Glacial
Acetic Acid 11.42
ml 5.71 ml
EDTA free
acid, FW 292.2 5.84 g 2.92 g
1X working
Concentration:
40 mM Tris acetate
2 mM EDTA
10X TBE (not for RNA)
1
L 500 ml 250 ml
Tris base 108 g 54 g 27 g
Boric Acid 55 g 27.5 g 13.8 g
EDTA, 0.5
M, pH 8.0 40 ml 20 ml 10 ml
1X working
Concentration:
89 mM Tris
89 mM Boric
Acid
2 mM EDTA
10 ml
(H2O)
Tetracyline 0.2 g
Store at
20 C.
Trace Metals Mix (2000 X)
Use at 0.5
ml per liter prep
FW Metal metal/liter Add per liter 40 ml
FeCl3·6H2O 270.0 55.85 10 ug/L 48.4 x 10-6 0.48
CuSO4·2H2O 170.5 63.5 10 ug/L 26.9 0.27
MnCl2·4H2O 197/9 54.9 10 ug/L 36.1 0.36
ZnCl2 136.28 65.4 4 mg/L 1.67 g
CoCl2·6H2O 237.9 58.9 2 ug/L 8.08 0.081
Na2MoO4·2H2O 241.9 95.9 2
ug/L 5.04 0.050
NiCl2·6H2O 237.7 58.9 2 ug/L 8.07 0.081
Storage 40 ml 1 L prep
working concentration
Thiamine R.T. 0.1 g 3
mg
Choline R.T. 0.1 g 3 mg
Niacinamide R.T. 0.1 g 3
mg
D-Pantothenate 4 C 0.1
g 3 mg
Pyridoxal -20 C 0.1 g 3 mg
Folic Acid R.T. 0.1 g 3
mg
Filter
sterilize 0.22 um filter
Aliqout
into 5 ml. Store at 20C.
Use at 0.5
ml per 1 L prep.
1 L
Tryptone 10 g
NaCl 5 g
Agar 7 g
Amp
Use 2.5 ml
melted top agar for plating.
1 L 200 ml 100
ml
Tryptone 10 g 2 g 1 g
NaCl 5 g 1 g 0.5 g
Agar 15 g 3 g 1.5 g
Note: 100
ml is enough for about 6 plates