20.109(F15): TA notes for module 2

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Long overdue for a revision

General notes

Key preparation:

  • Lots of wild-type inverse pericam plasmid (in the pRSET vector) must be available.
  • Mutant IPC plasmid (M124S, E67K, and T79P) should also be prepared in advance.
  • Need to streak out DE3 and DE3/IPC(wild-type) from frozen stocks in advance of liquid culture setup.
    • To be most careful, may want to freshly transform DE3 with pRSET-IPC miniprep.
    • DE3 in collection is NB301/AB2
    • DE3 w/IPC is NB303/AB4

Scheme: each pair of students will make two protein mutants, and test two candidate colonies per mutant. Specifically, students will choose only one mutation of their own, and run a 'positive control' mutation in parallel.

Daily notes

Day 1

Materials required:

  1. None: all work today is computer work.

Day of lab:

  • No quiz.
  • Primers for mutagenesis must be ordered right away, rush delivery!
  • Enzymes for diagnostics may need to be ordered as well, check designs.

How it went:

  • Two odd issues cropped up:
    • In fact, compared to most CaM sequences, two base pairs are missing in the IPC CaM. The Met is easily understandable, the other throws students off more.
    • Watcut link should be strictly checked and instructions should be included for each pair to name their primer something unique. Sometimes old primers or incomplete enzyme lists were automatically used.
  • Also, instructions to re-check primer Tm should probably be in bold or even emphasized during pre-lab. I think many folks skipped that step.

OLD Day 2

Materials required:

  1. RT water for primer resuspension
  2. Quick-Change SDM kit. 1 reaction per student, plus 1 control reaction, plus spare reagents (ideally).
    • cat # 200519

Day of Lab (T/W):

  • Quiz (prepared by TA)
  • Prepare PCR tubes on racks obtained from the freezer
  • Get primers (forward and reverse) ready just before lab lecture ends
  • Prepare a few aliquots of Master Mix for students, plus a control reaction:
    • Each mutagenesis reaction should have 5 μL of buffer, 1 μL of dNTPs, and 37 μL of water, for a total of 43 μL.
    • See googledoc for total calculations
    • Control rxn. is: 43 μL Master Mix, 2 μL DNA, 1.25 μL each primer, and thus 2.5 μL extra water.
  • Guide journal article discussion (assign figures at beginning of class).
  • At end of day: freeze SDM DNA

OLD Day 3

Materials required:

  1. Agarose gel electrophoresis
    • 1% agarose gels, all groups can fit on one gel
    • TAE buffer
    • 1 Kb ladder
    • Post sample table at gel bench, put out nitrile gloves
  2. Bacterial transformation
    • LB+Amp plates - > 1.5 l of LB requires 45 min of autoclave and is hard to pour, should separate into 2 flasks for 30 min of autoclave
    • autoclaved glass tubes
    • super-competent XL1-Blue cells (come with SDM kit, plus buy extra for negative controls)

Day of Lab (R/F)

  • Pre-warm water bath to 42 C, tube racks, etc.
  • Teaching faculty should prepare one positive control plate (in addition to the ones made by the students).

Days after Lab:

  • Check student plates for colonies next day.
  • During spring break, check a few colonies. Then, pluck two colonies per mutant plate day before next lab, and grow liquid O/N cultures. (Amp only, no Cam yet!)
  • Students with no colonies will be given their choice of any student candidate. (Some check on repeatability this way.)

How it went:

  • About half the groups got lots of colonies, three more groups got just a few colonies, and several groups got no colonies.

Day 4

Materials required:

  1. Sub-culture DE3 in the morning.
    • Need 1x5mL tubes per pair, plus two extra to be safe.
    • Typical sub-culture: about 1.5 hours from 0.15 OD to early/mid-log.
    • Last time starting batches at 12:10, 12:30 pm worked well (w/ lecture going till 1:45 pm), but test current crop of cells to double-check growth rate.
  2. Put calcium chloride (prep ~8 mL aliquots) on ice.
  3. LB+Amp/Cam plates
  4. LB broth, Amp, Cam
  5. Miniprep solution aliquots
  6. Sequencing primer thawed and diluted 1:100 TK CHECK/UPDATE
  7. Sterile DI water (200μL aliquots)
  8. Thaw NEB buffers and keep on ice, have enzymes at the ready.
  9. For digests: 12 μL parent IPC and 8 μL M124S miniprep for each group. TK UPDATE, FIGURE OUT AMOUNTS
    • For sense of miniprep stock concentrations, see S10 Day 5 Talk W/F Yellow (E67K), S10 lane 3 in all gels, my notebook (T79P), Fahim's notebook (WT)

Day of Lab (T/W):

  • Quiz (prepared by TA).
  • Keep an eye on DE3 densities before and during lab.
  • Prepare an aliquot each of M124S, T79P, and E67K to be sequenced at Genewiz, so we only need one set of alignment instructions for the students.

Days after Lab (W/R):

  • Store plates in fridge, wrapped in parafilm.
  • On T/W, pick two colonies per mutant to grow O/N in liquid culture (Amp+Cam).
  • Also pick a positive control colony per student plate. (Or just three done by us, known to be correct.)
  • Prepare DE3/WT-IPC in advance for all.
    • Assuming will need to make 1:20 dilutions next time, need at least 2.4 mL of each
    • Prep 3 (3 mL) O/N tubes to be on safe side

How it went:

  • T/R
  • W/F

Day 5

Materials required:

  • Advance prep
    • O/N cultures (see sub-culture notes below)
  • Ice buckets out, per two teams to share.
  • Part 1
    • Put out LB for OD measurements, 10 mL per group plus a couple extra tubes.
    • Sub-cultures
      • Prepare each BL21 mutant candidate, 6 mL per tube.
      • Prepare enough BL21-wild-type and BL21-reference mutants for each pair to have one tube as needed (plus make two extra of WT, and one of each reference mutant).
      • In sum, there should be 4 tubes of BL21 per pair.
      • In the past, ~1:20 dilution initiated between 10:00 and 10:30 am usually worked well. M124S grows somewhat more slowly.
    • Thaw frozen IPTG or prepare fresh (0.1 M stock). IPTG MW = 238.3 g/mol = 0.095 g in 4 mL for 0.1 M. Put out 550 μL per two teams to share.
  • Part 2
    • Thaw digests
    • One-half gel per group and ~ 500 mL TAE buffer per gel available.
      • T/R: Three 1% gels and one 1.3% gel.
      • W/F: Ideal is 2.5 1% gels and 1.5 1.3% gels.
    • Loading dye out at teaching bench, about 4 aliquots (50 μL size) for those groups that did not yet add it on D4 and/or who forgot to prepare uncut samples.
    • Check which groups didn't prepare uncut WT, have miniprep thawed and available in one or a few shared aliquots as needed.
    • 1 Kbp and 100 bp ladders available. Two 100 μL aliquots of the 1 Kbp should suffice for both days.
    • Put out sample sign. at gel bench as reminder.
  • Part 4
    • Colonies out at teaching bench

Day of Lab (R/F):

  • Make sure students turn roller back on!
  • Make sure students measure, then spin down and save at least their -IPTG samples.
  • For recalcitrant +IPTG samples (no color change), continue induction at RT overnight.

Day after Lab (F/Sa):

  • Measure the OD (1:10 dilution), then spin down and freeze any +IPTG samples cultured O/N.
    • Post the OD values to the wiki.

How it went:

  • S13
    • T/R: Lots of samples growing quite slowly compared to previous years. Should start at 10 am instead of 10:30 am for W/F. Possible reasons: chloramphenicol made very fresh -- maybe lower slightly? Ditch antibiotics altogether?
    • W/F:


  • Starting 1:20 sub-culture at 10:30 am (T/R) or even 11:15 am (W/F) gave high log ODs, 1.5 or 1, respectively.
  • More than half the groups had green pellets after 2-2.5 hours of culture.
    • M124S grows more slowly :( Most students had pale yellow pellet, some went with it, some grew O/N. After O/N growth, all pellets were quite green and large.

Day 6

Materials required:

Stuff requiring advance thought/prep: protein purification buffers, BSA standards

  • Part 1: cell lysis, all up at teaching bench
    • BPER (3 mL aliquots, 30 μL 10% BSA and 30 μL protease inhibitors)
      • last-minute prep, as it should be kept at room temp but has enzymes in it
    • Lysis enzyme available on ice up front
  • Part 2: SDS-PAGE advance prep
    • Water (150 μL aliquots)
    • 2X sample buffer available in hood
      • about 100μL group, three 300 μL to share should be fine
      • add 5% β-Me at last minute
  • Part 3A: protein purification (see also googledoc!), in ice buckets at their benches
  • Nu
    • Note: prepare solutions ~15% in excess of needed volume
    • Water, Charge Buffer
    • Binding Buffer, Wash Buffer, and Elution Buffer with protease inhibitors
    • Small BSA aliquots ready.
  • Part 3B: protein purification
  • Part 4: protein concentration, at teaching bench
    • put out closer to end of lab
    • 5X Coomassie stain from Bio-Rad out, three 8 mL aliquots to share (each team needs 2.4 mL)
    • 9.6 mL aliquot of water, one per team (plus an extra)
    • BSA standards --

Day of Lab:

  • Quiz


  • Transfer gels to fresh water at end of lab and/or next day.
  • Collect all purified protein samples from students and store at 4 °C.

Day after Lab:

  • Transfer gels to water and take pictures.
  • Put up sign in BPEC reserving Day 7 platereader use.

How it went:

  • This is another long day that may need a bit more black-boxing/efficiency work.

Day 7

Materials required:

  1. Pipetting reservoirs - 2 per group
  2. Calcium solutions - 0.5 mL/soln/group

Day of Lab:

  1. SDS-PAGE, gel bench
    • Polyacrylamide gels (1 per pair).
    • TGS buffer (1 L per box)
    • Staining boxes, couple of spatulas
    • Coomassie bottle and 50 mL conical tubes for measuring
    • Distilled water in 1 L bottles
  2. SDS-PAGE, in hood
    • Water baths with boiling chips, turn early on in lab
    • Lid locks
    • Waste bottle for stain
  • Quiz (prepared by TA).
  • Post data to wiki.
  • Instructor teaches the first group of students how to do the multichannel pipetting (avoid bubbles, make sure all tips are actually taking up the same volume, etc.); then TA takes over while instructor is in BPEC for plate reading.

How it went:

  • Protein amounts (fluorescence values) were pretty consistently higher this year than in year's past. In part may be due to using Invitrogen instead of Novagen resin, due to a mix-up; in part may be due to the higher cell ODs for many students. Perhaps in future should aim for high-log rather than mid-log growth, in fact.

Day 8

Materials required:

  1. None: all computer work today.

Day of Lab:

  • Quiz (prepared by TA).

How it went:

  • M124S a much better parallel sample than S101L (run in S09). The change in affinity and cooperativity was dramatic and consistent across the class.
  • The only strange issue is that at very low calcium concentrations the data is noisy rather than simply being a high plateau, or even somewhat consistently starts a little low, then has the high plateau, then proceeds as expected.