TL;DR: Harvard Medical School and Wyss Institute researchers reported Aug. 26 in Nature a cell-free tool called AGENTEX that builds proteins with up to 34 amino acids instead of 20.

A new way to build proteins without rewriting genomes

Scientists spent more than 20 years trying to instruct biological systems, such as E. coli cells, to produce proteins they do not naturally make, according to Harvard Medical School Communications reporting carried on the Wyss Institute site.

That long effort was motivated by the prospect of faster, cheaper and innovative solutions for medicine, agriculture, materials science, environmental remediation and other industries, as described in that same Harvard Medical School Communications report.

The work so far was arduous because the leading approach appeared to require reprogramming an organism's DNA, according to that report.

Reprogramming DNA proved fiendishly difficult and time-consuming and produced feeble results, according to Harvard Medical School Communications.

The laboratory of geneticist George Church, Ph.D., at Harvard Medical School and the Wyss Institute for Biologically Inspired Engineering at Harvard University has now devised a simpler, faster, safer and larger-scale method to make new proteins without requiring genome recoding or even any organisms, according to that report.

The tool is called AGENTEX and was reported Aug. 26 in Nature, according to Harvard Medical School Communications and the Nature article titled "Automated prototyping of genetic codes."

AGENTEX stands for automated genetic tRNA expansion, according to the Nature abstract.

The Nature article lists authors Felix Radford, Nayan Sapers, Hana M. Burgess, Lucy Ort, Bogdan Budnik and George M. Church.

First author Felix Radford, Ph.D., HMS research fellow in genetics in the Church Lab, spearheaded the study at HMS and the Wyss Institute, according to Harvard Medical School Communications.

Senior author Church is the Robert Winthrop Professor of Genetics in the Blavatnik Institute at HMS and founding core faculty and lead of synthetic biology at the Wyss Institute, according to the EurekAlert! release from Harvard Medical School.

The news was written by Stephanie Dutchen for Harvard Medical School Communications and posted Aug. 26, 2026.

What AGENTEX does in test tubes

AGENTEX allows researchers to design proteins using up to 34 amino acids rather than the naturally occurring 20, according to Harvard Medical School Communications.

The system calls for custom engineering two types of building blocks necessary to make those proteins, transfer RNAs and ribosomes, according to that report.

Researchers then insert those building blocks into a standard lab concoction that contains cell components but no actual cells, according to that report.

There, the components churn out the new proteins without interfering with natural protein-making machinery, according to that report.

"AGENTEX enables researchers to generate entirely new genetic codes on demand in test tubes and use them at scale to build proteins far beyond what nature has evolved," said first author Felix Radford, as quoted by Harvard Medical School Communications.

Radford added that the approach is more rapid and safe than existing methods because it does not rely on handling living cells or altering their genomes, according to that report.

Along the way, the team discovered something unexpected about how DNA gets translated into proteins, one of the most fundamental processes of life on Earth, according to that report.

"It's been really amazing to be working in this environment because not only are we developing new, innovative technologies but we're also discovering new science at the same time," Radford said, as quoted by Harvard Medical School Communications.

Why 34 amino acids matters

All natural life is made of proteins, and proteins are built from combinations of just 20 amino acids, according to Harvard Medical School Communications.

Each amino acid is coded by a triplet of DNA or RNA bases called a codon, according to that report.

The standard genetic code uses 64 codons to encode 20 canonical amino acids across domains of life, according to the Nature abstract.

There are about three times as many codons as amino acids, according to Harvard Medical School Communications.

For instance, UCU, UCC, UCA and UCG all code for serine, according to that report.

This redundancy suggests that many codons could be reprogrammed to make something else, according to that report.

After nine years of effort, the Church Lab demonstrated in 2013 that this could be done, freeing up one codon in E. coli bacteria so the microbes could make whatever new amino acid scientists wanted, according to that report.

It took the lab another 10 years to free up a second codon for E. coli to make other new amino acids, according to that report.

Scientists could then engineer cells to make proteins containing up to 22 different amino acids, according to that report.

Progress around the world has remained slow and fraught with challenges, according to that report.

Those challenges included that codon reprogramming hampers other normal cell functions and that genetically engineered organisms need to be kept safely walled off from natural life, according to that report.

AGENTEX takes a leap forward by making 34 codons customizable, allowing researchers to make proteins with up to 34 different amino acids, according to that report.

It does so in test tubes without touching an organism's natural DNA, according to that report.

"It took us a decade per new amino acid added to the code, so this remarkably opens the door to 34 at once and with almost none of the usual collateral damage to the genome," said senior author Church, as quoted by the Harvard Medical School release on EurekAlert!.

From years of genome rewriting to parallel testing

"The breakthrough turns protein engineering into something closer to a molecular design and discovery platform," Radford said, as quoted by Harvard Medical School Communications.

Radford explained that thousands of unique molecules can be built, tested and evolved in parallel, without the years of genome rewriting in living cells that was previously required to add each new amino acid, according to that report.

The Nature abstract describes AGENTEX as multiplexed robotic prototyping of genetic codes in cell-free translation systems.

The work was presented as a fully automated workflow to design and test new genetic codes that can accelerate genome engineering and allow unprecedented control over sequence-defined polymer synthesis, according to the Nature article.

By combining custom lysate-based translation systems with synthetic pools of tRNAs carrying engineered anticodons, researchers can rapidly prototype alternative genetic codes and evaluate their performance in polypeptide synthesis, according to that article.

The abstract says the team developed multiplexed and automated methods to read aminoacylation in libraries of synthetic tRNAs.

Each genetic code is synthesized as a pool of otRNAs that are robotically produced and introduced into the lysate, according to the Nature figure description.

Similarly, mRNA templates for polypeptide translation are automatically synthesized and purified, and all reaction steps are automated, according to that description.

The otRNAs are continuously aminoacylated by aminoacyl tRNA synthetases in the lysate and specifically interact with the engineered ribosome while avoiding crosstalk with the natural translation system, according to that description.

The effect of each genetic code, specified in the composition of an otRNA pool, can be analysed and used for rapid generation of the next genetic code experiments, according to that description.

The tRNA tail that was not as fixed as thought

Transfer RNAs add amino acids one by one into a chain to build a protein, making them crucial for both natural and engineered protein synthesis, according to Harvard Medical School Communications.

There are tRNAs that correspond to each codon in the genome, according to that report.

For example, one matches with UCU and attaches a serine to the chain, according to that report.

Every tRNA has the genetic sequence CCA on its tail end, according to that report.

Dogma has held that any other sequence in that spot will flag the tRNA as defective, according to that report.

Under that longstanding view, enzymes will not give the tRNA its amino acid cargo, and ribosomes — the factories in which proteins are made — will not allow the tRNA in to deliver it, according to that report.

To their surprise, and contrary to previous evidence, Radford and colleagues discovered that the first part is not true, according to that report.

The enzymes do allow some tRNAs with alternative tail-end sequences to receive amino acids, according to that report.

A tool the team built as part of AGENTEX, dubbed tSCAN, identified nonstandard sequences that work best, including CGA, according to Harvard Medical School Communications.

"We've shown that we can alter one of the most fundamental portions of one of the most fundamental systems found in nature, the protein-synthesis system that has existed pretty much unchanged for billions of years across all organisms, and it's functional," Radford said, as quoted in that report.

Radford added that the CCA end is much more flexible than people assumed, according to that report.

The Nature abstract states the same core finding in technical terms: the tRNA 3' end shows remarkable flexibility to mutation, allowing aminoacylation of most otRNAs by all Escherichia coli aminoacyl tRNA synthetases.

The paper calls tRNAs with alternative 3' sequences non-CCA-3' tRNAs, abbreviated otRNAs, according to that abstract.

The team investigated the extent to which those otRNAs would be aminoacylated by natural aminoacyl tRNA synthetases, allowing pools of otRNAs to specify unique genetic codes using ribosomes with altered large subunits, according to that abstract.

Engineered ribosomes that accept only engineered tRNAs

Two Watson-Crick interactions in the ribosomal large subunit mediate recognition of the 3' CCA end of tRNAs, preventing tRNAs with alternative 3' sequences from being accommodated during translation, according to the Nature abstract.

Building on these interactions, the researchers used ribosomes with altered large subunits to accommodate otRNAs, according to that abstract.

Ribosomes containing G2251C and G2553C mutations in the large subunit, called CGA ribosomes, specifically accommodate tRNAs with 3' CGA ends and do not accept natural tRNAs for translation, according to the Nature figure description.

Natural aminoacyl tRNA synthetases can aminoacylate all otRNAs in a one-pot reaction, allowing their use in translation, according to that description.

A cell-free translation system, called lysate, is generated by lysing cells containing CGA ribosomes and used for subsequent translation tests in an automated workflow, according to that description.

Revealing that scientists can make functional tRNAs that do not end with CCA is important because the non-CCA tRNAs will not be allowed into natural ribosomes when added to cells or cell-component soup, according to Harvard Medical School Communications.

Instead, scientists can engineer ribosomes that only work with the new tRNAs, according to the extended Harvard Medical School Communications account.

That separation lets the engineered translation operate alongside the standard system while avoiding crosstalk with the natural translation system, according to the Nature figure description.

Compressed codes and biocontainment

The Nature team developed cell-free translation systems enabling compressed genetic codes of 34 aminoacyl tRNA synthetases for 34 codons, according to the abstract.

Compressing the 64-codon near-universal genetic code to only 20 sense codons, one start codon and one stop codon liberates 14 codons for non-standard building blocks, according to the Nature article.

Given 64 otRNA triplet codons and normal wobble rules, 20 canonical amino acids can each be decoded by a single tRNA and 14 codons become available for reassignment, according to the Nature figure description.

Alternatively, all 34 codons could be used for making peptides analogous to non-ribosomal peptide synthase using a mixture of canonical and other amino acids, according to that description.

Using AGENTEX, the researchers evaluated two genetic codes alongside the standard genetic code, with non-standard amino acid incorporation and reassignment of up to three codons, according to the abstract.

Synthetic genetic codes have previously enabled construction of organisms with new properties such as increased virus resistance and reduced horizontal gene transfer, as well as production of genetically encoded materials, therapeutics and biocatalysts, according to the Nature introduction.

Using engineered ribosomes, tRNAs and aminoacyl tRNA synthetases, genetic code expansion has enabled the introduction of more than 400 non-standard amino acids into proteins in living cells and synthesis of sequence-defined polymers, according to that introduction.

However, reassigning more than a handful of sense codons across an entire genome remains challenging, as does incorporation of multiple non-standard amino acids into polypeptides with high purity, according to that introduction.

The authors state that much more radical redesign of translation systems is required to achieve complete control, from genetic sequence space to sequence-defined chemistry, according to that introduction.

The makeup of the AGENTEX system ensures biocontainment, because the components of AGENTEX are not functional if transferred to living organisms in the environment, according to the Nature figure description.

Cell-free translation platforms are divided into lysate-derived systems and PURExpress systems, according to the Nature article.

Lysate is produced from crude cell extracts and retains both translational machinery and enzymes for RNA and post-translational modifications, according to that article.

PURE uses individually purified components, including ribosomes, aminoacyl tRNA synthetases, tRNAs and translation factors, according to that article.

The findings have implications for the design of radically new translation systems, the synthesis of biopolymers with several instances of non-standard monomers, and understanding of possible past and future genetic codes, according to the Nature abstract.

The Harvard Medical School Communications summary lists the same practical direction: the work promises to expand the development of novel protein-based medicines and other materials.

Its at-a-glance summary also states that the new tool allows researchers to design and produce synthetic proteins faster, more safely and at larger scale than previously possible.

The summary adds that each protein can contain up to 34 custom amino acids rather than the naturally occurring 20, and that the technology arises from a discovery that overturns decades of understanding of how transfer RNAs help turn the genetic code into proteins.

Sources referenced