Affinity Selection of Peptide Binders with Magnetic Beads via Organic Phase Separation (MOPS)

We describe a new method for affinity selection of peptide binders for soluble protein targets using magnetic beads via organic phase separation (MOPS) from a phage display library. As a model target molecule, a mouse monoclonal antibody against human integrin α9β1 (Y9A2) immobilized onto protein G magnetic beads was incubated with a 15-mer or 20-mer random peptide phage-display library. The suspensions containing the phage-magnetic beads conjugates were then transferred onto the organic phase and centrifuged in order to recover the Y9A2 bound phage immobilized on the protein G magnetic beads in the lower organic phase. After three rounds of biopanning, we were able to isolate specific phage clones that could not be obtained by the conventional approach. Furthermore, this new approach was found to be highly effective for isolating phage-binders for Fc-fusion constructs; indeed, enrichment of specific phage-binders was observed after only the first panning cycle. Thus, MOPS can improve the selection of specific phage-binders for soluble protein targets mainly due to the removal of non-specific binders.