Four-Nucleotide Codon System Expands Protein Engineering Possibilities

Scripps Research scientists have developed a novel method for incorporating non-canonical amino acids (ncAAs) into proteins, potentially accelerating advances in bioengineering and drug discovery. The innovative approach, detailed in Nature Biotechnology, uses four-nucleotide codons instead of the traditional three, allowing for easier integration of new amino acids without disrupting cellular biology or requiring extensive genome editing.

Led by Ahmed Badran, the team discovered that surrounding a four-nucleotide codon with frequently used three-letter codons enhanced the cell's ability to read and incorporate ncAAs. This method proved successful with 12 different four-nucleotide codons and was used to design over 100 new cyclic peptides containing up to three ncAAs each.

"Our goal is to develop proteins with tailored functions for applications in fields spanning bioengineering to drug discovery," says Badran. The new technique offers significant advantages over previous approaches, as it only requires altering a single gene rather than an entire genome.

The researchers demonstrated that by maintaining sufficient levels of the four-nucleotide tRNA, cells could incorporate any new amino acid attached to the corresponding four-letter tRNA. This breakthrough opens up possibilities for creating "new-to-nature small molecules" with exciting applications in drug discovery and beyond.

Badran emphasizes the technique's potential for re-engineering existing proteins or creating entirely new ones with applications in medicine, manufacturing, and chemical sensing. The method's simplicity and effectiveness make it accessible to the broader scientific community, potentially accelerating advancements in protein engineering and synthetic biology as well.