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Four new DNA letters double life’s alphabet

Synthetic DNA seems to behave like the natural variety, suggesting that chemicals beyond nature’s four familiar bases could support life on Earth.

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An X-ray diffraction image of part of a molecule of DNA.

An X-ray diffraction image of part of a molecule of DNA. The new, 8-letter version, is similarly stable. Credit: Science Source/Science Photo Library

The DNA of life on Earth naturally stores its information in just four key chemicals — guanine, cytosine, adenine and thymine, commonly referred to as G, C, A and T, respectively.

Now scientists have doubled this number of life’s building blocks, creating for the first time a synthetic, eight-letter genetic language that seems to store and transcribe information just like natural DNA.

In a study published on 22 February in Science1, a consortium of researchers led by Steven Benner, founder of the Foundation for Applied Molecular Evolution in Alachua, Florida, suggests that an expanded genetic alphabet could, in theory, also support life.

“It’s a real landmark,” says Floyd Romesberg, a chemical biologist at the Scripps Research Institute in La Jolla, California. The study implies that there is nothing particularly “magic” or special about those four chemicals that evolved on Earth, says Romesberg. “That’s a conceptual breakthrough,” he adds.

Normally, as a pair of DNA strands twist around each other in a double helix, the chemicals on each strand pair up: A bonds to T, and C bonds with G.

For a long time, scientists have tried to add more pairs of these chemicals, also known as bases, to this genetic code. For example, Benner first created ‘unnatural’ bases in the 1980s. Other groups have followed, with Romesberg’s lab making headlines in 2014 after inserting a pair of unnatural bases into a living cell.

But the latest study is the first to systematically demonstrate that the complementary unnatural bases recognise and bind to each other, and that the double helix that they form holds its structure.

Benner’s team, which includes researchers from various US companies and institutions, created the synthetic letters by tweaking the molecular structure of the regular bases. The letters of DNA pair up because they form hydrogen bonds: each contains hydrogen atoms, which are attracted to nitrogen or oxygen atoms in their partner. Benner explains that it’s a bit like Lego bricks that snap together when the holes and prongs line up.

By adjusting these holes and prongs, the team has come up with several new pairs of bases, including a pair named S and B, and another called P and Z2. In the latest paper, they describe how they combine these four synthetic bases with the natural ones. The researchers call the resulting eight-letter language ‘hachimoji’ after the Japanese words for ‘eight’ and ‘letter’. The additional bases are each similar in shape to one of the natural four, but have variations in their bonding patterns.

The researchers then conducted a series of experiments that showed that their synthetic sequences shares properties with natural DNA that are essential for supporting life.

Data retrieval

To work as an information storage system, DNA has to follow predictable rules, so the team first demonstrated that, in a similar way to regular bases, the synthetic bases reliably formed pairs. They created hundreds of molecules of the synthetic DNA and found that the letters bound to their partners predictably.

They then showed that the structure of the double helices remained stable no matter what order the synthetic bases were in. This is important because for life to evolve, DNA sequences need to be able to vary without the whole structure falling apart. Using X-ray diffraction, the team showed that three different sequences of the synthetic DNA retained the same structure when crystallised.

This is a substantial advance, says Philipp Holliger, a synthetic biologist at the MRC Laboratory of Molecular Biology in Cambridge, UK, because other methods of expanding the genetic alphabet are not as structurally sound. Instead of chemicals that use hydrogen bonds to pair up, these other approaches use water-repelling molecules as their bases. These can be placed at intervals in-between the natural letters, but the structure of DNA breaks down if they are placed in a row.

Finally, the team showed that the synthetic DNA could be faithfully transcribed into RNA. “The ability to store information is not very interesting for evolution,” says Benner. “You have to be able to transfer that information into a molecule that does something.”

Converting DNA into RNA is a key step for translating genetic information into proteins, the workhorses of life. But some RNA sequences, known as aptamers, can themselves bind to specific molecules.

Benner’s team created synthetic DNA that codes for a certain aptamer and then confirmed that the transcription had occurred and the RNA sequence functioned correctly.

Holliger says that the work is an exciting starting point, but there is still a substantial distance to go before reaching a true eight-letter synthetic genetic system. One key question, for example, will be whether the synthetic DNA can be replicated by polymerases, the enzymes responsible for synthesizing DNA inside organisms during cell division. This has been demonstrated for other methods such as Romesberg’s, which uses water-repelling bases.

Variety of life

Still, Benner says that the work shows that life could potentially be supported by DNA bases with different structures from the four that we know, which could be relevant in the search for signatures of life elsewhere in the Universe.

Adding letters to DNA could also have more down-to-earth applications.

With more diversity in the genetic building blocks, scientists could potentially create RNA or DNA sequences that can do things better than the standard four letters, including functions beyond genetic storage.

For example, Benner’s group previously showed that strands of DNA that included Z and P were better at binding to cancer cells than sequences with just the standard four bases3. And Benner has set up a company which commercialises synthetic DNA for use in medical diagnostics.

The researchers could potentially use their synthetic DNA to create novel proteins as well as RNA. Benner’s team has also developed further pairs of new bases, opening up the possibility of creating DNA structures that contain 10 or even 12 letters. But the fact that the researchers have already expanded the genetic alphabet to eight is in itself remarkable, says Romesberg. “It’s already doubling what nature has.”

Nature 566, 436 (2019)

doi: 10.1038/d41586-019-00650-8

References

  1. 1.

    Hoshika, S. et al. Science 363, 884-887 (2019).

  2. 2.

    Georgiadis, M. M. et al. J. Am. Chem. Soc. 137, 6947–6955 (2015).

  3. 3.

    Zhang, L. et al. J. Am. Chem. Soc. 137, 6734–6737 (2015).

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