Unbiased libraries in protein directed evolution

Abstract

Directed evolution is a powerful approach to study the molecular basis of protein evolution and to engineer proteins for a wide range of applications in synthetic organic chemistry and biotechnology. There are many methods based on random or focused mutagenesis to engineer successfully any protein trait. Focused approaches such as site-directed and saturation mutagenesis have become methods of choice for improving protein activity, selectivity, stability and many other traits because the screening step can be practically handled (bottleneck in directed evolution). Although novel mutagenesis methods based on CRISPR or solid-phase gene synthesis can eliminate bias when creating protein libraries, traditional PCR approaches, although imperfect, remain widely used due to their ease and low cost. One of the most common approaches in focused mutagenesis relies on NNK mutagenesis, however, the primer-based 22c-trick and small-intelligent methods have emerged as key tools for constructing less biased and unbiased libraries when all 20 canonical amino acids are needed for various reasons. In this minireview, we assess studies employing such methods for library creation and their areas of application. We also discuss the advantages and disadvantages of both methods and provide a perspective for creating smarter libraries.