Ampicillin Stock  100g/L

 

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.

 

 

3M Ammonium Acetate, pH 5.2, 100ml

 

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

 

 

Bradford Assay

 

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.

 

 

Bradford Assay Calculation Sheet

 

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

 

 

Buffer SB

 

                                                            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

 

 

Blue/ Green Dye

 

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

 

 

Camera DS34

 

Coomassie Stain:        Light box computer room  125 22

Et. Br. Gels:                Light box in dark room 4.5 max 1 sec

 

 

Chloramphenicol    34g/L

 

Fisher Stock store at room temperature

EtOH solution store at –20C

 

1.02 g chloramp. 

To 30 ml with EtOH

 

 

1 M  Calcium Chloride

 

                                                            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

 

 

Coomassie Blue R-250 Staining solution

 

(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:

  1. Prepare 100 ml LB with agar for 2 plates.
  2. Autoclave:

100 ml LB

Small beaker for TSS solution

(extra flasks if preparing more than one strain

Small centrifuge tubes

  1. Pour 2 plates LB agar with NO antibiotic (except for strains containg pLys, both S and E, plasmid-then add 34 g/L chloramphenicoll)
  2. Remove stock cells from –70 C freezer and place on ice to thaw
  3. Streak two plates, label, place in 37 C incubator overnight.

Day two:

  1. Make and autoclave 150 ml LB without antibiotic again except for pLys.
  2. Make TSS (18 ml Is more than enough for 100 ml prep)

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

  1. Inoculate room temperature LB with cells from a single colony.  Grow cells until OD (600) reaches approx 0.4-0.5.  (This time varies greatly with the cell strain.) 
  2. After OD reaches 0.4, take cells out and put them on ice IMMEDIATELY

(Everything must be kept cold from this point on.  Chill pipets, tips, centrifuge tubes, final storage eppi tubes..) 

  1. Put cells in the chilled centrifuge tubes and spin down,  use big rotor at 6000 g, 4 C for 10 min.
  2. Decant off liquid from cell pellet. (pellet will be small). Place pellet back on ice.
  3. Resuspend in 10 % initial volume of TSS.  (i.e. 100 ml cell culture, resuspend pellet in 10 ml TSS)
  4. Aliquot cells into pre-labeled, pre-chilled eppi tubes with pre-chilled pipets.  Make aliquots from 30 ul to 100 ul.

 

 

Centrifuge Bottle Limits

 

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

 

 

Destain I

 

                                    1 L

10 %  HOAc               100ml

40 % MeOH                400ml

ddH2O                        500ml

 

 

Destain II

 

                                    1 L

5 %  MeOH                 50ml

7 %  HOAc                 70ml

dd H2O                       880 ml

 

 

Dialysis Buffer 195

 

                                                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.

 

 

Gel Drying Solution/ Gel drying directions

 

                                                1L

40 % EtOH                              400 ml

5 %  Glycerol                          5 ml

 

  1. Soak gels in soln. above for approx. 30 min
  2. Soak Cellophane in soln. until completely wet.
  3. Place gels between two sheets of cellophane and push out bubbles.

 

 

LB Agar Plates

 

                                    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

 

 

LB Miller

 

                                    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

 

 

Glycerol Stocks

 

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

 

 

6 M HCl

 

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

 

 

1M IPTG

 

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.

 

 

Inclusion Bodies

 

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

 

 

1M KCl

 

KCl     7.46 g

Fill to 100 ml final volume with ddH2O

 

No need to sterilize.

 

 

10 X Loading Buffer:  For Agarose Gel

 

                                                            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)

 

 

Molar Extinction Coefficient (ε)

 

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

 

 

Calculate Molecular Weight of Oligos

 

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)

 

M9 Salts                                  1L

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

For some proteins (e.g. Zinc finger Proteins)

1 M ZnCl2                               0.1 ml

100X Vitamin mix                     10 ml (Gibco Cat # 11120-052)

1000X Trace metal                   1.0 ml (Recipe below)

 

 

2M MgCl2

 

MgCl2·6H2O                40.66 g

Fill to final vol. of 100ml

 

Autoclave to sterilize, flame top each use

 

 

M9TB & 0.4 % Glucose

 

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*

 

*Don’t add for overnight cultures.

 

 

10X M9 Salt

 

                                    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.

 

 

NaOH 0.1 M for Wash Bottle used in RNA work

 

Wash bottle volume 750 ml

 

Add 5.3 g NaOH, fill bottle to volume

 

 

NMR Buffer for NC 55

 

                                    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.

 

 

Extinction Coefficient for DNA (ε)

 

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

 

 

PMSF

 

10 mM             Use at             Cell Lysis

                        575 λ               100 ml

 

Make stock in Isopropanol

 

 

Phenol/Chloroform Extract

 

  1. Add 1 Vol phenol/chloroform/isoamyl alc.   Vortex 10 sec.
  2. Spin, Room temp, 2 min.  Transfer top layer to another tube.
  3. Add 1/10 vol 3 M Sodium Acetate, pH 5.2
  4. Add 2.5 vol ice cold 100 % EtOH.  Vortex.
  5. Spin down, 5 min, 4 C, Decant, Let stand.

 

(more?…)

 

 

Protease Inhibitors

 

                                    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

 

 

RNA Gel Running Protocol

 

 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. 

 

 

RNase A

 

5 mg RNase A (BMC),

5 ml TE, pH 8.0

 

Boil 15 min

 

Aliquot into 0.5ml.

Store at –20 C

 

 

2X SDS Gel Loading Buffer

 

                                                            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

 

 

SDS Loading Dye

 

                                    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

 

 

SDS-PAGE (2x) Sample Buffer

 

                                    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) 

 

  1. Wash Gel in H2O 15 min
  2. Pretreatment of solution 10 min
  3. Silver Stain Solution 25 min
  4. Wash 3x with H2O,  2 min
  5. Develop
  6. Pour off developer
  7. Stop in 3x H2O wash

 

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  (Sigma E9379)

 

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/SOC Media

 

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

 

---(?)----

 

 

Trace Metals

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

 

Tris-Glycine Electrophoresis Buffer (10X Laemmli Buffer)

 

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.

 

 

Tris-Tricine Gel Stain

 

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

 

 

TB

 

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

 

 

TSS (for Competent Cells)

 

                                                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

 

 

TE , pH 7.4, pH 7.5, pH 8.0

 

                                                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.

 

 

TAE Electrophoresis Buffer 10X stock

                       

                                                            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

 

 

Tetracyline Stock

 

                                    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  

 

           

Vit Mix

                                    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.     

 

 

ZB Top Agar

 

                                    1 L

Tryptone                      10 g

NaCl                            5 g

Agar                            7 g

 

Amp

 

Use 2.5 ml melted top agar for plating.

 

 

ZB Plate

 

                                    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

 

  1. Mix in H2O.
  2. Autroclave 15 min.
  3. When warm to touch (approx. 50 C) add antibiotics if needed
  4. Pour plates. 

 

Note: 100 ml is enough for about 6 plates