Discussion

Protein microarrays, defined as large numbers of proteins immobilized on a two-dimensional surface, represent a major opportunity for the interrogation of biological samples and systems. Unfortunately, they also represent a number of challenges, including complexity and cost. Affimers are combinatorial engineered proteins, alternatives to antibodies, that are uniquely stable when immobilized on a range of inorganic materials.
Here, we describe the establishment of a new, robust, high throughput protein expression, purification and quality control pipeline that is currently producing 4,608 Affimer proteins a week. The process includes automated colony picking into 96 well plates, overnight growth with built-in temperature ramping and auto-induction, a manual freeze/thaw step and automated, magnetic-bead-based Affimer purification. Greater than 85% of the purifications have yields that meet or exceed the levels and purity required for microarray printing.