DNA2.0 is developing ProteinGPS for systematic engineering of protein functionality, and Codon Optimization for increased expression of recombinant proteins. The technologies take advantage of efficient gene synthesis and advancements in linear and nonlinear systems optimization to map and navigate in sequence space.

The ProteinGPS method calculates the specific location of a protein variant in multidimensional space and places unique information rich variants at important crossroads within the space assessed. The resulting datasets are synthesized and used to map the functional protein hyper space and calculate new protein variant sequences that fulfill the functional constraints needed. Examples of of ProteinGPS based protein engineering are to be presented.

Codon Optimizaion: DNA2.0 has actively studied the relationship of gene design to heterologous expression yield. DNA2.0 has created large systematically varied gene sets for multiple gene types and analyzed expression in several commonly utilized host systems. Striking differences are observed for the dependence of expression on synonymous codon usage in different hosts. In E. coli, protein expression levels varied over two orders of magnitude for each of two gene sets tested. Our data show that codon bias is a strong determinant of expression levels in E. coli; however, the preferred codon bias is distinctly different from that of genes naturally highly expressed in the bacterium and no correlation is seen between expression and the codon adaptiveness index. The correlation between codon bias and protein expression in multiple systems is compared.