Caltech's DNA 'Page Numbers' Breakthrough Could Revolutionize Bioeconomy

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Caltech researchers have invented a groundbreaking method called Sidewinder that could finally break through the decades-long bottleneck in DNA synthesis, potentially unleashing a new era of AI-designed biological applications.

The power of artificial intelligence has already transformed our ability to design genetic sequences for applications ranging from proteins that form materials stronger than steel to personalized cancer treatments. Yet a critical bottleneck has persisted: the inability to construct DNA sequences long enough to realize these designs.

The DNA Construction Problem

For decades, chemical DNA synthesis has been limited to creating short pieces of genetic material called synthetic oligonucleotides, or "oligos." These fragments, typically 10 to 100 base pairs long, have enabled significant biotech advances like mRNA vaccines. However, genes and genomes that encode useful proteins are often thousands of times longer than current synthesis capabilities allow.

This limitation has meant that AI-powered biological designs cannot be verified or improved in practice. The blueprints for futuristic technologies remain theoretical because we cannot build the DNA sequences needed to bring them to life.

The Sidewinder Solution

Caltech's innovation, developed in the laboratory of Kaihang Wang, an assistant professor of biology and biological engineering, introduces a method that utilizes the conceptual equivalent of page numbers for DNA. This approach enables researchers to stitch together any arbitrary number of short oligos in the correct order to create much larger pieces of DNA—up to the scale of a gene or potentially an entire genome.

"DNA is the source code of all earthly life and biological functions," Wang explains. "As such, biomedical applications and the future bioeconomy depend on the ability to write DNA. Sidewinder provides a new path to the ancient and persisting desire of humankind to rewrite the very source code of life."

How It Works

The Sidewinder process attaches DNA "page numbers" to each oligo, enabling each piece to match up with the right neighbors in the sequence. The method uses a technique called a 3 Way Junction (3WJ), which causes the page number pieces to stick out of the side of the assembled DNA construct like little tags.

This separation of construction information from the encoded DNA sequence is crucial. After assembly, these little tags extending from the 3WJ are smoothly removed, resulting in a perfectly assembled, uninterrupted DNA double helix ready for any desired applications.

The ability to remove the third helices from the 3WJs in a single, seamless step after using them as "page numbers" to guide DNA construction represents a critical part of the Sidewinder invention.

Unprecedented Accuracy

Guided by these removable DNA page numbers, Sidewinder achieves an incredibly high fidelity in DNA construction with a measured misconnection rate of just one in one million. This represents a four to five magnitude improvement over all prior techniques, whose misconnection rates range from 1-in-10 to 1-in-30.

"Sidewinder is wonderfully creative, and a powerful step toward the goal of writing DNA of any complexity," says Caltech's Frances Arnold, the Linus Pauling Professor of Chemical Engineering, Bioengineering and Biochemistry, and winner of the 2018 Nobel Prize in Chemistry. "Sidewinder addresses a key bottleneck in translating computational design into reality, with applications across health and sustainability."

Historical Context and Future Implications

To explain Sidewinder's significance, Kaihang Wang draws an analogy to the history of book printing. "In 1441, Johannes Gutenberg invented the printing press, enabling the creation of individual printed pages," he says. "But Gutenberg's bibles never contained any page numbers. These books were painstakingly assembled by aligning the contexts at the beginning and end of each page, for hundreds of pages. Thus, the eventual invention of page numbers, which took about 50 years, was revolutionary."

The seemingly simple concept of page numbers was actually non-trivial, and Wang sees a parallel in today's DNA construction challenge. "We are facing a surprisingly identical challenge: how to guide the construction of long sequences from individually synthesized pieces. In this case, they are DNA oligos instead of printed pages. It has been 40 years since the invention of oligo synthesis, the equivalent of a Gutenberg press for DNA, and now it is high time that we invent the equivalent of 'DNA page numbers' to guide the assembly of these short oligos to construct long and functional DNA."

Applications and Impact

With Sidewinder, synthetic biologists can write new genes and entire genomes within just a few days, if not hours. This breakthrough could have vast applications across multiple sectors:

• Agriculture: Engineering crops with enhanced traits or resistance to climate challenges
• Therapeutics: Creating personalized cancer vaccines and other targeted treatments
• Materials Science: Designing proteins that form advanced materials stronger than steel
• Industrial Biotechnology: Developing new enzymes and biological processes for manufacturing

The technology clears a major bottleneck for bioengineering new compounds and materials, potentially accelerating the bioeconomy significantly.

The AI Connection

Kaihang emphasizes the importance of interfacing Sidewinder with artificial intelligence. "Interfacing with AI will give us the freedom both to design and to construct," he says. "Whatever can be designed by AI as a biological function can be constructed through Sidewinder."

This convergence of AI design and advanced DNA construction may enable an alternative to how life can come about, in addition to evolution. "Now maybe it can be designed and made," Wang suggests.

Commercial Development

Genyro, a biotechnology company co-founded by Kaihang Wang, has entered into an exclusive licensing agreement for Sidewinder to advance next-generation DNA construction. This move suggests strong commercial interest in translating the academic breakthrough into practical applications.

The Research Team

The paper describing the technique, titled "Construction of complex and diverse DNA sequences using DNA 3-Way Junctions," appears in the journal Nature on January 21. In addition to study first author Noah Robinson (PhD '25) and Kaihang Wang, Caltech co-authors include graduate students Weilin Zhang, Bryan Gerber, Hanqiao Zhang, and Sixiang Wang; and research scientist Charles Sanfiorenzo (PhD '24). Additional co-authors are Rajesh Ghosh and Dino Di Carlo of UCLA.

Funding was provided by the National Science Foundation, the Shurl and Kay Curci Foundation, the National Institutes of Health, and Caltech's Center for Environmental Microbial Interactions.

Technical Deep Dive

DNA is written with an "alphabet" of nucleotides: adenine (A), thymine (T), cytosine (C), and guanine (G). A and T bind together, as do C and G. These nucleotides form a long chain, which twines together in the characteristic double-helix shape. The structure and function of a gene is determined by the unique order of the nucleotides.

Nature has evolved through iterative copying and editing of pre-existing templates over millions of years. Humans have taken advantage of this evolutionary process for millennia; for example, over the course of about 9,000 years, humanity domesticated and selectively bred maize. With the advent of modern biology, researchers began to explore the possibility of synthesizing new DNA sequences from scratch for the first time in human history.

In the 1970s, researchers developed the ability to synthesize short pieces of DNA—the aforementioned oligos. However, attempts to accurately synthesize oligos longer than a few hundred nucleotides were not successful. Genes that encode for many useful proteins are on the order of thousands to tens of thousands of nucleotides, far too long for current synthesizing methods.

The Sidewinder team now plans to address additional bottlenecks in scaling up construction of sequences, suggesting this breakthrough is just the beginning of a new era in synthetic biology.

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