The Affimer library was prepared by the BioScreening Technology Group in the School of Molecular and Cellular Biology.122
Screening
For the selection against Biotin-58 to Biotin-63, four panning rounds were performed, described as follows:
First panning round
A colony of ER2738 E. coli cells was picked into 5 ml of 2TY media with 12 μg/mL tetracycline and incubated overnight at 37°C, 230 rpm. Streptavidin Coated (High Binding Capacity, Thermo Scientific) 8-well strips (4 wells per target) were pre-blocked with 300 μL 2x Blocking Buffer (BB) and incubated overnight at 37°C. The wells were washed 3 times with 300 μL phosphate buffered saline with 0.1% tween (PBST) and 100 μL 2x BB per well was added. 5 μL of phage library (1012colony-forming units/mL) were pre-panned three times, and each time incubated at
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room temperature for 40 minutes on a platform shaker (Heidolph VIBRAMAX 100, speed 3). 5 μL of the biotinylated target (1 mM in DMSO) was added to the panning well and incubated for 1 hour on the platform shaker. The phage was added to the target and incubated for 2 hours at room temperature on the platform shaker, while the overnight ER2738 culture was diluted 15 times with 2TY media with 12 μg/mL tetracycline and incubated for 1 hour at 37°C, 230 rpm. The panning wells were washed 6 times with 300 μL of PBST and eluted with 100 μL of glycine (0.2 mM, pH 2.2) for 10 min, neutralised with 15 μL of Tris-HCl (1M, pH 9.1), further eluted with 100 μL of triethylamine (100 mM in PBS) for 6 minutes at room temperature, and neutralised with 50 μL of Tris–HCl (1 M, pH 7). The eluted phage were incubated with ER2738 for 1 hour at 37°C and 90 rpm and plated onto LB agar plates with 100 μg/mL carbenicillin (carb) and grown overnight. Colonies were scraped with 2TY media containing 100 μg/mL carbenicillin (2TYcarb) (5 mL then 2 mL), diluted to get a 8 mL solution with an absorbance at 600 nm of 0.2, and incubated for 1 hour at 37°C, 230 rpm. 0.32 μL of M13K07 helper phage (1014/mL) was added and the cells were incubated for 30 minutes at 37°C, 90 rpm. 16 μL of kanamycin (25 mg/mL) was added and the cells were incubated overnight at 25°C, 170 rpm. The phage were precipitated with 2 mL of polyethylene glycol (20% (w/v) PEG 8000, 2.5 M NaCl), incubated overnight at 4°C, and re-suspended with 320 l of TE buffer (10 mM Tris, pH 8.0, 1 mM EDTA).
Second panning round
A colony of ER2738 E. coli cells was picked into 5 mL of 2TY media with 12 μg/mL tetracycline and incubated overnight at 37°C, 230 rpm. 20 μL of streptavidin beads (Dynabeads® MyOne™ Streptavidin T1, 10 mg/mL) were pre-blocked in 100 μL of 2x BB and incubated overnight at room temperature and 20 rpm.
KingFisher Flex (Thermo Scientific) plate were pre-blocked:
1 panning deep well 96 plate: 1 mL per well of 2x BB
2 elution well 96 plates: 300 μL per well of 2x BB 4 washing deep well 96 plates: 950 μL per well of 2x BB
After 2 hours at 37°C, the buffer was removed from the panning and the elution plates. 100 μL per well of glycine (0.2 M, pH 2.2) was added to one elution plate and 100 μL per well of triethylamine (100 mM in PBS) was added to the other. The Streptavidin beads were centrifuged for 1 min at 800 xg, the buffer was removed, and the beads were re-suspended in 100 μL of fresh 2x BB. 5 μL of the phage from the first panning round were pre-panned with 245 μL of 2x BB and 25 μL of pre-blocked Streptavidin beads. After incubating for 1 hour at room temperature at 20 rpm, the phage were centrifuged at 800 xg for 1 minute and the supernatant was collected and pre-panned as previously. 15 μL of the biotinylated target (1 mM in DMSO) was bound to 50 μL of pre-blocked Streptavidin beads in 200 μL of 2x BB and incubated for 1 hour at room
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temperature on the rotator (20 rpm). The biotinylated target was centrifuged for 1 minute at 800 xg, and washed 3 times with 500 μL of 2x BB. The pre-panned phage were centrifuged for 1 minute at 800 xg and the supernatant was transferred to the biotinylated targets, re-suspended, and transferred to the pre-blocked deep well plate. The beads were washed 4 times with 950 μL of PBST and eluted as previously on an automated KingFisher robotic platform (ThermoFisher). The eluted phage were neutralised, amplified and precipitated following the same procedure as for the first panning round.
Third panning round
A colony of ER2738 E. coli cells was picked into 5 ml of 2TY media with 12 μg/mL tetracycline and incubated overnight at 37°C, 230 rpm. Neutravidin Coated (High Binding Capacity, Thermo Scientific) 8-well strips (5 wells per target) were pre-blocked with 300 μL of 2x BB and incubated overnight at 37°C. The wells were washed 3 times with 300 μL of PBST and 100 μl of 2x BB was added. 8 μL of the phage library from the previous round was pre-panned four times, and each time incubated at room temperature for 1 hour on a platform shaker. 10 μL of the biotinylated target (1 mM in DMSO) was added to the panning well, incubated for 1 hour on the platform shaker, and washed three times with PBST. The phage was then incubated with the target for 45 minutes at room temperature on the platform shaker. The panning wells were washed 27 times with 300 μL of PBST and eluted with 100 μL of glycine (0.2 mM, pH 2.2) for 10 min, neutralised with 15 μL of Tris-HCl (1M, pH 9.1), further eluted with 100 μL of triethylamine (100 mM in PBS) for 6 minutes at room temperature, and neutralised with 50 μL Tris–HCl (1 M, pH 7). The phage were eluted, neutralised, amplified and precipitated following the same procedure as for the first panning round.
Fourth panning round
A colony of ER2738 E. coli cells was picked into 5 mL of 2TY media with 12 μg/ml tetracycline and incubated overnight in an orbital incubator at 37°C, 230 rpm. Streptavidin Coated (High Binding Capacity, Thermo Scientific) 8-well strips (6 wells per target) were pre-blocked were filled with 300 μl of 2x BB and incubated overnight at 37°C. The wells were washed 3 times with 300 μL of PBST and 100 μl of 2x BB was added. 8 μL of the phage library from the previous round was pre-panned four times, and each time incubated at room temperature for 1 hour on a platform shaker. 10 μL of the biotinylated target (1 mM in DMSO) was added to the panning well, incubated for 1 hour on the platform shaker, and washed three times with 300 μL of PBST. The last well (blank) was washed with 300 μl of PBST. Half of the phage (100 μL) was transferred to the target and the other half (100 μL) transferred to the control well, and both were incubated for 45 minutes at room temperature on the platform shaker. The panning wells were washed 27 times with 300 μL of PBST and the phage were eluted, neutralised, and amplified following the same procedure as for the first panning round.
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Phage ELISA
50 L of Streptavidin (5 g/ml in PBS) was placed in a F96 Maxisorp Nunc-Immuno Plate (Thermo Scientific) and incubated for 4 hours at room temperature. The plates were blocked with 200 µL of 2x BB, incubated overnight at 37°C, and washed with 300 μL of PBST. 50 μL of the biotinylated targets (1 M in of 2x BB) was placed in the 6 fist columns of the streptavidin-coated wells, and negative control wells were prepared in the 6 last columns with 50 μL of 2x BB. The plate was incubated for 1 hour at room temperature on a platform shaker and washed with 300 μL of PBST.
48 individual colonies from the final panning round of the phage display were picked, inoculated into 96 well V bottom deep filled with 200 L of 2TYcarb, and incubated for six hours at 37°C, 1050 rpm. 25 L of the cultures were transferred into a 96 well V bottom deep well plate with 200 L of 2TY carb and incubated for 1 hour at 37°C, 1050 rpm. 10 L of a 1011/mL solution of M13K07 helper phage in 2TY carb was added to the freshly grown cultures and incubated for 30 minutes at room temperature. 10 L of a kanamycin solution in 2TY carb (1.25 mg/mL) was added to the cultures and incubated overnight at room temperature, 750 rpm. The cultures were centrifuged at 3,500 xg for 10 minutes and 40 μL of the phage-containing supernatant was transferred to the previously prepared streptavidin-coated 96-well plates with 10 μL of 10x BB. The plate was incubated for 1 hour at room temperature on a platform shaker and washed with 300 μL of PBST. 50 μl Anti-Fd-Bacteriophage-HRP (Seramun, diluted 1000 times in 2x BB from the commercial bottle) was added to the wells, the plate was incubated for 1 hour at room temperature on a vibrating platform shaker and washed 10 times with 300 μL of PBST. 50 μL of TMB (SeramunBlau® fast TMB/substrate solution) was added to the wells and allowed to develop for 3 minutes and the absorbance was measured at 620 nm on a Thermo Multiskan Ascent plate reader. The reading of the phage ELISA plates are shown below.
Sequencing
When sequencing was required, the plasmid DNA was extracted from selected hits using a QIAprep Spin Miniprep Kit (QIAGEN), the plasmids were eluted with water (50 L) and an aliquot of DNA (15 L, 100 ng/l) was sent to Beckman Coulter Genomics for sequencing using a T7P primer.