Benchmarking cassette-based deep mutagenesis by Golden Gate assembly

Abstract

Protocols for the construction of large, deeply mutagenized protein encoding libraries via Golden Gate assembly of synthetic DNA cassettes employ disparate, system specific methodology. Here we benchmark a broadly applicable Golden Gate method for building user-defined libraries. We demonstrate that a 25 l reaction, using 40 fmol of input DNA, can generate a library on the order of 1x106 members and that reaction volume or input DNA concentration can be scaled up with no losses in transformation efficiency. Such libraries can be constructed from dsDNA cassettes generated either by degenerate oligonucleotides or oligo pools. We demonstrate its real-world effectiveness by building custom, user-defined libraries on the order of 104 to 107 unique protein encoding variants for two orthogonal protein engineering systems. We include a detailed protocol and provide several general-use destination vectors.