Combinatorial codon scrambling enables scalable gene synthesis and amplification of repetitive proteins.

ABSTRACT: Most genes are synthesized using seamless assembly methods that rely on the polymerase chain reaction (PCR). However, PCR of genes encoding repetitive proteins either fails or generates nonspecific products. Motivated by the need to efficiently generate new protein polymers through high-throughput gene synthesis, here we report a codon-scrambling algorithm that enables the PCR-based gene synthesis of repetitive proteins by exploiting the codon redundancy of amino acids and finding the least-repetitive synonymous gene sequence. We also show that the codon-scrambling problem is analogous to the well-known travelling salesman problem, and obtain an exact solution to it by using De Bruijn graphs and a modern mixed integer linear programme solver. As experimental proof of the utility of this ap

SUBMITTER: Tang NC 

PROVIDER: S-EPMC4809025 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature