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384-well PCR.

Rambler's Top100
Prepared by Anna Guerasimova

    Beforehand.

  1. choose empirically the annealing temperature of primers;
  2. make sure you have enough PCR-plates, Q-covers and sealing tape;
  3. prepare the stocks: PCR-buffer, 5M Betaine - with some excess, dNTPs, primers, Taq:Pfu mix (100:1 calculated by activity units) - with small excess;
  4. PCR-reaction.

  5. thaw the plates with bacterial culture;
  6. sign the 384-plates;
  7. prepare PCR-mix;
  8. dispense PCR mix by multichannel pipet or by "Multidrop 384" machine;
  9. centrifuge Q-covered (or sealed) plates at ~800 rpm, 3' NT;
  10. transfer the bacteria twice with the sterile replicators;
  11. seal the plate and run PCR reaction;
  12. After PCR.

  13. take the plates out with the help of screwdriver (or forceps);
  14. move the plates to +4oC and then to -20oC;
  15. centrifuge at ~800 rpm, 3' NT;
  16. control PCR by agarose gel electrophoresis: 0.5 - 1µl from 5 - 15 wells;
  17. seal the plates again;
  18. move the plates to +4oC and then to -20oC;
  19. for long term storage - -70oC (keep track in your lab book!).

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    Solutions.

    PCR buffer 10x

    (store at +4oC):

    Conc.Stock500ml
    Tris Cl, pH 8.6*0.5M1M250ml
    KCl0.5M2M125ml
    MgCl215mM1M7.5ml
    Tween 201%100%
    p=1.108
    5.0ml
    5.54g

    H2O mQ112.5ml
    Conc.Stock500ml
    Tris Cl, pH 8.6*0.5M1M250ml
    KCl0.5M2M125ml
    MgCl215mM1M7.5ml
    Tween 201%10%50ml
    H2O mQ67.5ml

    p (10x Buf.) = 1.018 g/ml
    * - another possibility: 175ml (1M Trise-base) + 75ml(1M Trise-HCl).

    PCR buffer 2.5x

    (store at +4oC)

    Conc.Stock100ml300ml
    Buffer (15mM MgCl2)2.5x10x25ml75ml
    Betaine3.75M5M74.75ml224.25ml
    Cresol red (Na)125 µM50mM250 µl0.75ml

    p (2.5x buffer) = 1.06g/ml

    PCR mix

    Store - working quantity at +4oC; large stock at -20oC. It is possible to keep PCR mixture with enzymes at at +4oC for about 15h without any decrease of efficiency of PCR reaction.

    Conc.Stock72.5ml**
    PCR buffer1x2.5x29ml
    dNTP’s0.2mM25mM580µl
    Primer#1 & #2200pmol/ml?? µl 
    H2O mQ?ml 
    Taq/Pfu pol***50-250u/ml?u/ µl?µl 

    ** - 72.5ml is enough for 9 plates [20µl in one well] (110ml for 30µl; 145ml for 40µl);
    *** - Taq(u):Pfu(u)=100:1.


    Comments.

    Particular steps.

    #1.

  • To start, one can use the Tmelting value given by the program "Oligo". Take into account probable decrease in annealing temperature when betaine is added (no such effect for sucrose). For example, for the primer pair M-13/23 and M-13/30 maximum annealing temperature decreased from 71oC to 67oC when 1.5M betaine was added.
  • #3.

  • It is convenient to have:
    * all four dNTP's mix (100mM or 25mM stocks);
    * primers mix.
  • #4.

  • The frozen bacteria plates have to be put on a table in one layer one by one, separately. This prevents condensation of liquid on the inner side of the cover and transfer of liquid between wells. The condensation takes place when the temperature of the cover becomes lower than temperature of the liquid in the plate. It is convenient to use air fan to accelerate thawing.
  • #5.

  • Better, if two times - on the narrow side (column "24") and on the wide -corresponds to the raw "P".
  • #6.

  • 12.2ml per plate, if PCR volume is 30µl/well (maximum for old ABT-384 plates #TF-0384) or 16.3ml per plate, if PCR volume is 40µl/well (maximum for new ABT-384 plates #AB-0937).
  • Add the enzyme in the last place. We hear that the Pfu polymerase can destroy the primers if PCR mix stored at room temperature for too long. So just before you add the enzyme, in front of you should be signed 384-plates, the reservoir for multi-channel pipette, bacterial plates and the replicators. In principle, it is possible to keep PCR mixture with enzymes at at +4oC for about 15h without any decrease of efficiency of PCR reaction.
  • After the PCR mix is aliquoted to the plates, transfer the rest volume to the 50ml Falcon tube and keep it at -20oC. You can use this volume for the last series of PCR (with the same primers) - so that for the last plates the volume of set up PCR mix can be smaller.
  • #8.

  • To remove air bubbles from the bottom of the wells. It is optional for accurate multichanel pipet dispensing.
  • #9.

  • You need twice as much of replicators as number of PCR-plates. Insert replicator from the nearer edge, holding it leaned at 5-10o so that the nearer pins are closer to the plate (the row "P" in the PCR plate). The pins should be directed to the center of the wells.
  • Double inoculation is used not to increase amount of transferred material but to decrease the probability of no transfer at all.
  • It is better to mix bacteria in the plate by replicator before transfer. Try to avoid mixing in only one direction, because it can induce sticking partly lysed bacteria to the needles of replicator.
  • The volume of media captured on one needle of the replicator is ca 0.2µl.
  • In principle the plates with inoculated bacteria can be stored at -20oC before PCR up to a few weeks. But! Don't freeze them on dry ice. Either in the freezer or on the towel soaked with the liquid nitrogen. If freezed on dry ice, 100% CO2 atmosphere will shift the pH. If betain- or sucrose-containing PCR mix was used, most likely PCR would succeed anyway, but you don't want be unsure about it, do you?
  • The same precautions should be taken for the PCR/NaOH mixtures for spotting. It is possible to freeze them in dry ice (for about 0.5 - 1h) only if they are sealed by "Tesafilm" or "Adhesive Sealing Sheet".
  • #10.

  • Sealing films: the best is the office tape from TESA (Tesafilm #2826775): (i) easily taped and removable; (ii) reliable; (iii) cheap - about 10DM per roll. Much worse variants:
    • "Adhesive Sealing Sheet" from ABgene: (hardly removable, expensive);
    • Microseal "A" film. Fragile: don't press the PCR machine cover very tightly, it can damage Microseal "A", it shrinks after PCR and unsuitable for freezing. For Microseal "A" film:
      • when PCR is finished - immediately (plate still in the PCR block) take off the upper film;
      • take the plates out of PCR machine;
      • remove the isolating film layer;
      • get rid of the PCR mix which is in between wells with the yellow tip connected to the vacuum pump;
      • use soft blotting paper to remove liquid from the plate surface;
      • cover with the "Genetix" covers;
    • "Bio-stat" film. It has to be sealed tightly, e.g. using the backside of the marker to help. One can put a piece of thin rubber on top, as well. Funny: there were cases when PCR's worked fine with a quite sloppily attached Bio-stat film. In that case considerable volume was evaporated uniformly from each well. Probably there is some sort of equilibrium inside the PCR block so that the content of the well does not dry out completely.
  • For 384-PCR it is better to change the parameter exceed of temperature of the lid "Setup/Lid/Tracking/Lid offset" from the default 15oC to 5oC.
  • PCR-mix: our impression, that in general betaine is slightly worsening PCR reaction. The enzyme speed and activity became lower. But it is impossible to exclude betaine from the buffer for 384 plates. Without it we observed smear, differing from PCR plate to plate (in an 8-strip from the same PCR-mix PCR worked fine). Adding of sucrose has similar effect - the smear partially disappeared, but with betaine - completely.
  • If a sub-cycle PCR is used (see below) the product yield is more stable and a little bit higher (probably it is because of low-melting regions in some sequences). We used the following program:
    Step:T (oC):Time:
    1951:00
    2940:15
    3590:15
    4650:55
    5go to 32 add. times
    6go to 229 add. times
    76810:00
    840
    9END 
  • #11.

  • Lift each four edges carefully and hold the plate with your hand. Avoid the abrupt moves, if not, your PCR ends up on the cover.
  • The plate holder for 384-plates can be treated with "Teflon spray", then the plate can be removed easier.
  • #14.

  • Concentration should be more then 0.15µg/µl.

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Last modification: 10/11/02



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