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@iGEM_Paris

Week 27th June - 3rd 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

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.

Time after inoculation	OD 600nm
3h14	0.0584
4h11	0.2717
4h28	0.4022
4h28	0.5644

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.
Pre-warm, for at least one hour, one LB/IPTG/Xgal plate per expected dilution at 37°C until ready for use.
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).
When the culture in Step 1 reaches mid-log phase, dispense 200 μl into microfuge tubes, one for each phage dilution.
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.
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.
Allow the plates to cool for 5 minutes, invert, and incubate overnight at 37°C.
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.

Results:

Dilution	Number of plaques
10^10	25
10^11	16
10^12	26
10^13	16

M13KE phage amplification

This phage amplification protocol is the one given by NEB.

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.
Remove cells by centrifugation at 4500 g for 10 min. Transfer supernatant to a fresh tube. Repeat centrifugation.
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.
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.
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

NEB Phage Display protocol on cotton - DAY 1

Cotton used: Khadi (from Khadi and Co - Bess Nielsen, given by Teja) - Hand Woven - 100% cotton.
A square of 1cm x 1cm was used (total surface: 2 cm² counting both sides).

Inoculate 10 ml of LB+Tet medium with ER2738. This culture will be used for titering in Step 8 and can be used in ~4 hours. Incubate at 37°C with vigorous shaking. Incubate the titering culture until needed.
Incubate for at least 1 hour at 4°C a piece of fabric with blocking buffer.
Remove the piece of fabric from the blocking solution. Wash the fabric rapidly 10 times with TBST (TBS + 0.1% [v/v] Tween-20) by dipping the fabric in a beacker filled with TBST and going back and forth through the washing solution.
Dilute a 25-fold representation of the library (e.g., 2 x 10 11 phage for a library with 2 x 10 9 clones) with 250µl of TBST (therefore add 10µL of phage library). Pipette onto piece of fabric in Eppendorf tube and rock gently for 60 minutes at room temperature.
Rem: The square shape of the piece of fabric does not seem best suited for the incubaction with the phages as the sides seem not to be immersed in the phage library solution. It is probably better to use a rectangle shape thereafter so that the piece of fabric fits nicely into the tube and is fully immersed.
Remove piece of fabric from the Eppendorf tube.
Wash fabric 20 times with TBST as in step 3.
Elute bound phage with 1 ml of an appropriate elution buffer for the interaction being studied. A general buffer for nonspecific disruption of binding interactions is 0.2 M Glycine-HCl (pH 2.2), 1 mg/ml BSA. Rock gently for 15 minutes. Discard the piece of fabric (save it in TBST). Neutralize supernatant with 150 μl of 1 M Tris-HCl, pH 9.1.
Inoculate 20 mL of LB medium in a 250-ml Erlenmeyer flask with ER2738. Incubate culture at 37°C with vigorous shaking. Carefully, monitor the 20-ml culture so that it does not grow beyond early-log phase (OD600 0.01–0.05), for use in Step 10.
Titer a small amount (~2 μl) of the eluate as described in General M13 titration protocol. Plaques from the first or second round eluate titering can be sequenced if desired.
Rem: As this eluate is not amplified, dilutions used for titration are as follow: 10, 100, 1000, 10000.
Amplify the rest of the eluate by adding the eluate to the 20-ml ER2738 culture from Step 1 (should be early-log at this point) and incubating with vigorous shaking for 4.5 hours at 37°C.
Transfer the culture to a centrifuge tube and spin for 10 minutes at 12,000 g at 4°C. Transfer the supernatant to a fresh tube and re-spin (discard the pellet).
Transfer the upper 80% (here 12.8mL) of the supernatant to a fresh tube and add to it 1/6 volume of 20% PEG/2.5 M NaCl (here ~2.1mL). Allow the phage to precipitate at 4°C for at least 2 hours, preferably overnight.

Time after inoculation - Titration culture	OD 600nm - Titration culture	Time after inoculation - Amplification culture	OD 600nm - 20mL Amplification culture
0	0	0	0
3h30	0.3811	0h40	0.008/0.006/0.009
3h40	0.5101	1h50	0.0116
		2h25	0.0193

NEB Phage Display protocol on cotton - DAY 2

Results titration unamplified phage eluate 1st round:

Dilution	Number of plaques
10	>1000
100	230
1000	17
10000	3

Therefore, we have a phage concentration of 230x(10^2)x(10^2) = 2.3 x 10^6 pfu/mL.

Inoculate 10mL of LB+Tet medium with ER2738 for titration.
Spin the PEG precipitation at 12,000 g for 15 minutes at 4°C. Decant and discard the supernatant, re-spin the tube briefly, and remove residual supernatant with a pipette. The phage pellet should be a white finger print sized smear on the side of the tube.
Suspend the pellet in 1 ml of TBS. Transfer the suspension to a microcentrifuge tube and spin at maximum (14,000 rpm) for 5 minutes at 4°C to pellet residual cells.
Transfer the supernatant to a fresh microcentrifuge tube and reprecipitate by adding 1/6 volume of 20% PEG/2.5 M NaCl (here 166µL). Incubate on ice for 15–60 minutes. Microcentrifuge at 14,000 rpm for 10 minutes at 4°C, discard the supernatant, re-spin briefly, and remove residual supernatant with a micropipet.
Suspend the pellet in 200 μl of TBS. Microcentrifuge for 1 minute to pellet any remaining insoluble material. Transfer the supernatant to a fresh tube. This is the amplified eluate.

Titer the amplified eluate on LB/IPTG/Xgal plates following the general M13 titration protocol. The eluate can be stored for up to 3 weeks at 4°C. For long-term storage, add an equal volume of sterile glycerol and store at –20° C.
OD measurements:

Time after inoculation	OD 600nm
0	0
3h08	0.3167
3h21	0.4415
3h25	0.4955

Incubate overnight at 4°C a new piece of fabric (both a 1 cm x 1cm square and 0.5 cm x 2 cm were incubated) in 1 mL of Blocking Buffer for the 2 nd round of panning.

Week 01st - 07 August

NEB Phage Display protocol on cotton - DAY 3:

Results titration amplified phage eluate 1st round:

Count blue plaques from the titering plates in Step 17 and determine the phage titer, which should be on the order of 1013–14 pfu/ml. Use this value to calculate an input volume corresponding to the input titer in Step 7. If the phage titer of the amplified eluate is too low, succeeding rounds of panning can be carried out with as little as 109 pfu of input phage.

Dilution	Number of plaques
10^8	>1000
10^9	92
10^10	8
10^11	1

Therefore, we have a phage concentration of 92x(10^9)x(10^2) = 9.2 x 10^12 pfu/mL.

Inoculate 10 ml of LB+Tet medium with ER2738. This culture will be used for titering in Step 9 and can be used in ~4 hours. Incubate at 37°C with vigorous shaking. Incubate the titering culture until needed.
Remove the piece of fabric from the blocking solution. Wash the fabric rapidly 10 times with TBST (TBS + 0.5% [v/v] Tween-20) by dipping the fabric in a beacker filled with TBST and going back and forth through the washing solution.
Dilute a 11.5-fold representation of the library (e.g., 2 x 10 11 phage for a library with 2 x 10 9 clones) with 250µl of TBST (therefore add 10µL of phage library). Pipette onto piece of fabric in Eppendorf tube and rock gently for 60 minutes at room temperature.
Rem: The square shape of the piece of fabric does not seem best suited for the incubaction with the phages as the sides seem not to be immersed in the phage library solution. It is probably better to use a rectangle shape thereafter so that the piece of fabric fits nicely into the tube and is fully immersed.
Remove piece of fabric from the Eppendorf tube.
Wash fabric 20 times with TBST as in step 3.
Elute bound phage with 1 ml of an appropriate elution buffer for the interaction being studied. A general buffer for nonspecific disruption of binding interactions is 0.2 M Glycine-HCl (pH 2.2), 1 mg/ml BSA. Rock gently for 15 minutes. Discard the piece of fabric (save it in TBST). Neutralize supernatant with 150 μl of 1 M Tris-HCl, pH 9.1.
Inoculate 20 mL of LB medium in a 250-ml Erlenmeyer flask with ER2738. Incubate culture at 37°C with vigorous shaking. Carefully, monitor the 20-ml culture so that it does not grow beyond early-log phase (OD600 0.01–0.05), for use in Step 10.

Titer a small amount (~2 μl) of the eluate on LB/IPTG/Xgal following general M13 titration protocol. Plaques from the first or second round eluate titering can be sequenced if desired.
OD measuerments:

Time after inoculation	OD 600nm
0	0
3h33	0.1130
4h03	0.2107
4h35	0.3251
4h50	0.5356

Amplify the rest of the eluate by adding the eluate to the 20-ml ER2738 culture from Step 1 (should be early-log at this point) and incubating with vigorous shaking for 4.5 hours at 37°C.
OD measuerments:

Time after inoculation	OD 600nm
0	0
1h01	0
1h33	0.006
2h06	0.0388

Transfer the culture to a centrifuge tube and spin for 10 minutes at 12,000 g at 4°C. Transfer the supernatant to a fresh tube and re-spin (discard the pellet).
Transfer the upper 80% (here 14.4mL) of the supernatant to a fresh tube and add to it 1/6 volume of 20% PEG/2.5 M NaCl (here 2.4mL). Allow the phage to precipitate at 4°C for at least 2 hours, preferably overnight.

NEB Phage Display protocol on cotton - DAY 4

Results titration unamplified phage eluate 2nd round:

Dilution	Number of plaques
10	>1000
100	788
1000	38
10000	10

Therefore, we have a phage concentration of 38x(10^3)x(10^2) = 3.8 x 10^6 pfu/mL

Inoculate 10mL of LB+Tet medium with ER2738 for titration.
Spin the PEG precipitation at 12,000 g for 15 minutes at 4°C. Decant and discard the supernatant, re-spin the tube briefly, and remove residual supernatant with a pipette. The phage pellet should be a white finger print sized smear on the side of the tube.
Suspend the pellet in 1 ml of TBS. Transfer the suspension to a microcentrifuge tube and spin at maximum (14,000 rpm) for 5 minutes at 4°C to pellet residual cells.
Transfer the supernatant to a fresh microcentrifuge tube and reprecipitate by adding 1/6 volume of 20% PEG/2.5 M NaCl (here 166µL). Incubate on ice for 15–60 minutes. Microcentrifuge at 14,000 rpm for 10 minutes at 4°C, discard the supernatant, re-spin briefly, and remove residual supernatant with a micropipet.
Suspend the pellet in 200 μl of TBS. Microcentrifuge for 1 minute to pellet any remaining insoluble material. Transfer the supernatant to a fresh tube. This is the amplified eluate.