Codon Compression Algorithms for Saturation Mutagenesis
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Abstract
Saturation mutagenesis is employed
in protein engineering and genome-editing
efforts to generate libraries that span amino acid design space. Traditionally,
this is accomplished by using degenerate/compressed codons such as
NNK (N = A/C/G/T, K = G/T), which covers all amino acids and one stop
codon. These solutions suffer from two types of redundancy: (a) different
codons for the same amino acid lead to bias, and (b) wild type amino
acid is included within the library. These redundancies increase library
size and downstream screening efforts. Here, we present a dynamic
approach to compress codons for any desired list of amino acids, taking
into account codon usage. This results in a unique codon collection
for every amino acid to be mutated, with the desired redundancy level.
Finally, we demonstrate that this approach can be used to design precise
oligo libraries amendable to recombineering and CRISPR-based genome
editing to obtain a diverse population with high efficiency