Week 27th June - 3rd July

Week 4th - 10th July

Week 11th - 17th July

NEB Ph.D.™-7 Phage Display Peptide Library Kit solutions preparation

NEB protocol recommends to prepare a mixed solution of ITPG and X-gal. Because I already have IPTG stock, I prefer to do 2 separate solution for IPTG and X-gal (also avoids throwing both IPTG and X-gal if anything were to happen to the tubes).

IPTG

M.W.= 238.31g/mol
NEB protocol recommends to put 1.25g in 25mL DMF, which is [IPTG]=50mg/mL
[IPTG]mass=[IPTG]/MW=0.05/238.31=0.21mol/L=210mM.
They recommend diluting 1000-fold to prepare plates. So [IPTG]working_concentration=50µg/mL which is 210µM.
In order to simplify things, I'll use [IPTG]working_concentration=200µM.
IPTG stocks are at 1M and 0.1M (100mM).
If preparing 1M stock, add 2.383g of IPTG to 10mL of milli-Q water. For 0.1M, add 238.3mg of IPTG to 10mL of milli-Q water.
2µL IPTG / mL medium should be added if using the 0.1M solution (0.2µL / mL of using the 1M solution).

X-gal

M.W.= 408.63g/mol
NEB protocol recommends to put 1g in 25mL DMF, which is [X-gal]=40mg/mL.
Sigma-Aldrich recommends having stock solution at 20mg/mL.
I decided to do a stock at 20mg/mL.
2 µL X-gal / mL of medium should be added.

Tetracycline

NEB protocol recommends doing a 20mg/mL stock solution in 50% EtOH. Most of the protocol found online recommend 70% EtOH, so that's what I did (it probably does not matter much).
300mg were dissolved in 15mL 70% EtOH.

TBS

NEB protocol recommends 50mM Tris-HCl (pH7.5), 150mM NaCl.

Tris-HCl 1M, pH 7.5:
M.W. Tris-Base=121.14g/mol
12.11g of Tris-Base were dissolved in 60mL of H2O.
pH was adjusted to 7.5 using HCl 5M.
Volume was adjusted to 100mL.

25 mL of Tris-HCl 1M, pH 7.5 were diluted in 500mL H2O.
M.W. NaCl=58.44g/mol
mNaCl=(58.44/1000)*150=8.766g for 1L
So 8.766/2=4.383g were added to the solution of Tris-HCl 50mM.
pH was measured after completion of the solution and was around 7.7.

Blocking Buffer

M.W. NaHCO3=84.007g/mol
2.1g of NaHCO3 were put in 225mL osmosed H2O.
pH was adjusted to 8.6 with 5M HCl.
Volume was adjusted to 250mL.
1.25 BSA was added to final concentration 5mg/mL.
Solution was kept 6 days at 4°C.
On 21/07/16, 0.05g NaN3 (0.02%) were added to the solution to avoid growth of microorganisms.
Solution was filter sterilized and aliquoted by ~75mL.

Week 18th -24th July

M13KE Phage Titering

In order to train ourselves with the phage titration that we will need to perform when doing the phage display from the NEB kit, we decided to do a phage titration using M13KE. The following protocol is the one given by NEB with their M13KE phages.

The number of plaques will increase linearly with added phage only when the multiplicity of infection (MOI) is much less than 1 (i.e., cells are in considerable excess).

Note: We used MGZ1 F+ to perform this titration

1. Inoculate 10 ml of LB with both MGZ1 F+ from a plate and incubate with shak­ing 4–6 hrs (mid-log phase, OD600 ~ 0.5).
   Media was inoculated at 8h56.
2. While cells are growing, melt Top Agar in microwave and dispense 3 ml into sterile culture tubes, one per expected phage dilution. Maintain tubes at 45°C.
3. Pre-warm, for at least one hour, one LB/IPTG/Xgal plate per expected dilu­tion at 37°C until ready for use.
4. Prepare 10 to 1000-fold serial dilutions of phage in LB; 1 ml final volumes are convenient. Suggested dilution ranges: for amplified phage culture super­natants, 10^8 –10^11 ; for unamplified panning eluates, 10^1–10^4. Use aerosol-resistant pipette tips to prevent cross-contamination, and use a fresh pipette tip for each dilution.
   As I expect to have 10^11 pfu/mL after amplification and that they recommend 10^8 to 10^11 dilutions from that, beginning from M13KE tube (10^13 pfu/mL), I used the following dilutions: 10^10, 10^11, 10^12 and 10^13 (shift of 2 order of magnitude).
5. When the culture in Step 1 reaches mid-log phase, dispense 200 μl into microfuge tubes, one for each phage dilution.
6. To carry out infection, add 10 μl of each phage dilution to each tube, vortex quickly, and incubate at room temperature for 1–5 minutes. Here cells were incubated with the phages 3 to 4 minutes.
7. Transfer the infected cells one infection at a time to culture tubes containing 45°C Top Agar. Vortex briefly and IMMEDIATELY pour culture onto a pre-warmed LB/IPTG/Xgal plate. Gently tilt and rotate plate to spread top agar evenly.
8. Allow the plates to cool for 5 minutes, invert, and incubate overnight at 37°C.
9. Count plaques on plates that have approximately 100 plaques. Multiply each number by the dilution factor for that plate to get phage titer in plaque form­ing units (pfu) per 10 μl.

M13KE phage amplification

This phage amplification protocol is the one given by NEB.

1. Inoculate a 20 ml culture in a 250 ml Erlenmyer flask with 200 µL overnight E. coli culture. Add 1 µL phage suspension. Shake flask at 37°C, 150 rpm for 4 -5 hrs.
2. Remove cells by centrifugation at 4500 g for 10 min. Transfer supernatant to a fresh tube. Repeat centrifugation.
3. Transfer top 16 ml of supernatant to a new tube and add 4 mL of 2.5 M NaCl/20 % PEG-8000 (w/v). Briefly mix. Precipitate phage for 1 hr or overnight at 4°C.
4. Pellet phage by centrifugation at 12000 g for 15 min. 55 min at 4000 rpm (Rotor radius: 195 mm, 4000 rpm -> ~3400 g, 12000/~3400=3.5, 3.5*15 min=52.5 min) used was done instead due to problems with centrifuge. Decant supernatant. Resuspend pellet in 1 mL TBS. Transfer to an eppendorf tube. Spin briefly to remove any cell debris.
5. Transfer supernatant to a fresh tube. Add 200 µL of 2.5 M NaCl/20% PEG-8000. Incubate on ice for 60 min. Spin 14000 rpm in a benchtop centrifuge for 10 min. Discard supernatant. Spin again briefly and remove remaining supernatant with pipette. Resuspend pellet in 200 µL TBS.

Week 25th -31th July