Quantitation of human Fab in periplasmic extracts was performed by Surface Plasmon Resonance (SPR) on a PARP signaling Biacore A4000 or Biacore 2000 instrument (GE Healthcare, NJ). A standard curve was generated by diluting human Fab (Jackson Immunoresearch) in two-fold serial dilutions into assay running buffer and used for the estimation of Fab concentrations (Supplementary methods, tables and figures). Fab standard and unknowns were injected

over a goat-anti-human IgG [specific for F(ab′)2] surface (Jackson Immunoresearch) immobilized at a high density on a Biacore CM5 Sensor chip (GE Healthcare). Data analysis was performed using the BIAevaluation software (GE Healthcare). For the first round of phage panning using a naïve scFv library (Schwimmer et al., 2013), 4.7 × 1013 cfu of phage particles from a scFv kappa library or 1.6 × 1013 cfu of phage particles from a Fab lambda library combined with 2.2 × 1013 cfu of phage particles from a Fab kappa library were blocked for 1 h at RT in

5% non-fat dry milk (Marvel Premier Foods, UK) in PBS buffer with gentle rotation. Blocked phage was twice deselected for 45 min against streptavidin-coated magnetic Dynabeads® M-280 (Invitrogen Dynal AS, Oslo, Norway). The kinase antigen (R&D Systems, MN) that GSK126 mouse was used for the scFv panning, and Tie-2 antigen (R&D Systems) that was used for the Fab panning, were biotinylated with Sulfo-NHS-LC-Biotin (Pierce) using the manufacturer’s protocol in 20-fold molar excess of biotin reagent and confirmed by ELISA. The biotinylated products were then incubated with blocked streptavidin-coated magnetic Dynabeads® M-280 for 1 h with gentle Glycogen branching enzyme rotation in order to immobilize biotinylated antigen and remove unbiotinylated material. Antigen-captured beads were then washed twice with PBS. For the first, second and third rounds of selection, 100, 50 and 10 pmol of biotinylated kinase or Tie-2 were used, respectively. For the first round, the deselected phage was divided into two aliquots: one was used to infect TG1 cells, and the other was used to infect TG1 cells harboring pAR3-cytFkpA. The rescued, deselected phage was used to perform parallel first round pannings by incubation with

biotinylated kinase streptavidin beads for 90 min at room temperature. The input phage for rounds two and three was generated with separate rescues from either the round one TG1 infection or the round one TG1 with pAR3-cytFkpA. For the first round of panning, beads were washed quickly (i.e., beads were pulled out of solution using a magnet and resuspended in 1 ml wash buffer) three times with PBS—0.05% TWEEN®-20, followed by three times with PBS. For the second round of panning, beads were washed for five times with PBS—0.05% Tween followed by one 5-minute wash. Similar washes were performed with PBS. For the third round of panning, beads were washed quickly for 4 times with PBS—0.05% TWEEN®-20 followed by four 5-minute washes with PBS—0.05% TWEEN®-20.