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Gene Knockout with Conventional Mutagens

Gene Knockout with Conventional Mutagens

Leon Avery

 ENG (enriched nematode growth medium):  1.  in a 6 L flask add: 	3800 ml DH2O 	20 g. bactopeptone 	4 g yeast extract 	12 g. NaCl 	4 ml 5mg/ml cholesterol in EtOH stir with a large stir bar until dissolved.  2. Add 120 g. agar and stir well.  3. Cover w/ Al foil, autoclave liq. cycle 30'    (turn on the 70C water bath before the agar is autoclaved)  4. Equilibrate temp. in water bath.  5. Just before pouring the plates add (sterile solutions) with    stirring: 	4 ml 1M CaCl2 	4 ml 1M MgSO4 	100 ml 1M KHPO4 (pH6)         4 ml 200 mg/ml streptomycin 	1 ml 40 mg/ml nystatin in DMF (add dropwise)  AENG (agarose ENG): Same recipe as ENG, except replace 3% agar with 2% agarose, and you probably won't want to make so much.  Making a grid:  1. Inoculate one or more 10 cm ENG plates with 10 N2 L4    hermaphrodites.  Four or five days later, when there are many    gravid adults, prepare eggs by the alkaline hypochlorite method.    Leave the eggs in M9 after the final wash.  2. Put the tube of eggs in M9 on a rocker (or something else that will    aerate them) overnight.  3. Count the healthy L1s in a 10 ul aliquot of the suspension.  (I use    a 10 ul microcap to spread them on an unseeded 6 cm plate.)  Based    on the count, put 5000 healthy L1s on each of 10 10 cm ENG plates.    These will be your P0s.  4. When the P0s have reached L4, harvest them in 3 ml M9.  (You'll    probably have to spin them down and transfer them to new M9 to get    the volume that low.)  5. Dissolve 20 ul EMS in 1 ml M9.  Add this solution to your P0s.  6. Aerate for 4 hours.  7. Spin down, transfer to 4 ml fresh M9.  8. Put 5000 P0s on each of 10 10 cm ENG plates.  Allow them to become    gravid adults with lots of eggs.  (I do this at 15C, since the L4s    will become gravid adults inconveniently soon at 20C.)  9. Harvest all the plates and prepare eggs by alkaline    hypochlorite.  Aerate overnight.  10. Count the healthy F1 L1s in a 10 ul aliquot.  There will be a lot    of sick or dead ones (their parents were mutagenized) -- don't    count these.    Determining numbers of F1s  11. Put 1250 F1 L1s on each of 110 6 cm AENG plates.    F1s per plate  12. After 3 days at 20C most of the F1s should be gravid adults.    Count the gravid adults on one or two of your plates.  There should    be about 1000 (less than 1250, because many of the F1s didn't grow    up or were sterile).    F1s per plate  13. After another 2 days (5 days total) the plates have starved, and    almost all the worms on them are L1s.  Harvest 96 of the plates    with 5 ml M9 each.  Discard any extra plates -- they're just in    case some of your plates got moldy, or otherwise didn't work.    Harvesting the plates  14. Count a 10 ul aliquot from a few of the tubes.  You should have    recovered between 100,000 and 200,000 F2 L1s from each plate.    F2s per plate  15. Let the tubes sit on your bench until the worms have settled to    the bottom.  with a Pasteur pipet attached to vacuum, suck off    liquid so that you have about 1.5 ml left in each tube.  (This is    the step I worry about -- I'm afraid if the worms sit at the bottom    of the tube too long they may go anaerobic and die.  I do plates in    batches, so that they don't have to sit too long, and mix the tubes    from the earlier batches occasionally while working on the later    ones.)  16. For this step, I use sterile 1.2 ml tubes in an 8x12    microtiter-spaced rack.  You want three racks of 96, two for worms    to be recovered later, and one for DNA preps.  Put 0.5 ml of 2x    freezing solution in each of the tubes of the two worm racks.    Then, for the first of your 96 tubes, put 0.5 ml into the A1    position of each of the three racks.  For the second, put 0.5 ml    into the A2 position, etc.  17. Put the two worm racks into a styrofoam box in a -80C freezer and    leave overnight.  You can freeze the worms for the DNA preps now,    or go ahead and do the DNA preps immediately.  18. Let the worms settle to the bottoms of the tubes, and suck off all    the liquid you can.    DNA preps  19. Add 250 ul fresh lysis solution (200 mM NaCl, 100 mM Tris-HCl pH    8.5, 50 mM EDTA, 0.5% SDS, 100 ug/ml proteinase K) to each tube.  20. 50C, 1h.  (This is shorter and cooler than the typical incubations    used for DNA preps.  It works fine, and long incubations at high T    are mutagenic.)  21. Prepare DNA from each tube by phenol:sevag extraction, sevag    extraction, and EtOH precipitation.  Redissolve in 150 ul TER (10    mM Tris-HCl pH 8, 1 mM EDTA, 1 ug/ml RNAase A.  Store at -80C.  22. Use 2 ul of 1:5 diluted DNA in each detection reaction.  Mutation detection protocols:  I have used three different protocols for detecting mutations.  The first is for detecting point mutations in a restriction site.  I won't describe this, since I don't currently think it's the best way to knock out a gene.  The second method is that commonly used for detecting deletion of a Tc1 by relying on the much greater efficiency of standard PCR in amplifying shorter fragments.  I call this method "primer approximation", since it relies on the deletion approximating (bringing close together) the primers.  The third method asks for the deletion of a cluster of restriction enzyme sites.  It has the theoretical advantage that it may detect small deletions that don't much change the efficiency of amplification.  Whether this is a practical advantage is not clear.  I do not use nested primers.  I think this reduces the false positive rate, but it does mean the primers have to be pretty good, since you need to be able to amplify from as little as 10 molecules to a good strong band.  Therefore, before screening with any primer pair, I first run a series of reactions inoculated with 0, 10, 1000, and 100,000 wild-type genomes, and run under long PCR conditions (basically the conditions for site deletion below).  I make 25-mer primers with 40-60% GC, using the Whitehead Institute primer program to help find them and avoid primer-dimers, etc.  Most of the pairs work.  Mutation detection by primer approximation:  Solution A:     0.4 ul 5 U/ul Taq polymerase     5   ul 10x PCR buffer (100 mM Tris pH 8.3, 500 mM KCl, 20 mM MgCl2)     0.5 ul 10 mg/ml acetylated BSA (NEB)     1   ul 10 uM left primer     1   ul 10 uM right primer     1   ul 10 mM dNTPs (10 mM each of dATP, dCTP, dGTP, dTTP)    39.1 ul water    -------    48   ul  Put 48 ul A in each of 96 thin-wall 200 ul tubes.  Add 2 ul 1:5 diluted DNA to each tube.  Run PCR program (MJR PTC-200):      Control method: CALCULATED     1: 92 degrees forever, beep.     2: 92 degrees, 55 sec.     3: 92 degrees, 5 sec.     4: 65 degrees, 30 sec (adjust for the Tm of your primers).     5: 68 degrees, 1 min.     6: go to step 3 for 39 more cycles.     7: 68 degrees, 4 min.     8: 4 degrees forever, beep.  Start the PCR machine and wait for the block to heat up.  Now put the tubes (kept on ice) in the block.  The solution in thin-wall tubes will heat up very fast when placed in a preheated block: this is almost as good as a hot start.  Push the proceed button on the PCR machine once all the tubes are loaded.  Add 10 ul 6X gel loading buffer and run 12 ul on 1% gel.   Mutation detection by site deletion:  In this example, the enzyme BstBI is used.  You need to use a thermophilic enzyme, since cooling the reaction down to 37C for the second digestion has disastrous effects on PCR.  You also want an enzyme that will work pretty well in PCR buffer, and that is pretty cheap.  There are a whole series of enzymes from Bacillus stereothermophilus that meet these criteria.  Solution A:     0.25 ul 20 U/ul BstBI, NEB     1 ul 10x NEBuffer 4     0.1 ul 10 mg/ml acetylated BSA, NEB     6.65 ul water     ------     8.0 ul  Solution B:     0.01 ul 5 U/ul Pwo polymerase     0.09 ul 5 U/ul Taq polymerase     3.5 ul 10x PCR-NEB4 (75 mM tris pH 8.6, 500 mM KCl)     0.35 ul 10 mg/ml AcBSA     1 ul 10 uM primer 1     1 ul 10 uM primer 2     1 ul 10 mM dNTPs     28.05 ul water     --------     35.0 ul  Solution C:     0.3 ul 5 U/ul Taq polymerase     0.5 ul 20 U/ul BstBI     0.5 ul 10x PCR-NEB4     0.05 ul 10 mg/ml AcBSA     3.65 ul water     -------     5.0 ul  LAMD45 PCR program (CALC mode, MJR PTC-200):     1 92C forever, beep     2 92C, 1 min     3 65C, 30 sec (annealing temp)     4 68C, 5 min     5 65C forever, beep (T in steps 5 & 6 is digestion T for enzyme)     6 65C, 30 min     7 92C, 5 sec     8 65C, 30 sec     9 68C, 2 min     10 go to step 7 for 8 more cycles     11 92C, 5 sec     12 65C, 30 sec (annealing temp)     13 68C, 2 min + 10 sec/cycle     14 go to step 11 for 34 more cycles     15 72C, 10 min     16 4C forever, beep  1.  Mix 2 ul DNA solution (intended to be about 100,000 genomes) with     8 ul A.  Incubate 65C, 10 min.  2.  Add 35 ul B to each tube.  Keep everything on ice while you do     this.  3.  Start the PCR machine.  When it reaches 92C (step 1), transfer the     tubes from the ice to the block.  Once all the tubes are in the     block, tell the machine to proceed.  4.  At step 5, the machine will halt again at 65C.  Leaving the tubes     in the block, add 5 ul C to each.  When finished, tell the machine     to proceed.  6.  Run on 1% agarose gel. 

Leon Avery (Leon@eatworms.swmed.edu)
Last modified: Sat Nov 29 15:51:47 1997