Expanding the genetic code

From San Diego, at a meeting of the American Chemical Society

DNA is normally made up of four chemical bases, which go by the letters A, T, C, and G and code for all the proteins in a cell. But what if DNA carried a fifth base? In an effort to explore the mechanisms of evolution, researchers have designed an unnatural base and inserted it into synthetic DNA in a test tube.

The four natural bases pair up to form the rungs on DNA’s ladderlike structure. A (adenine) pairs with T (thymine), and C (cytosine) pairs with G (guanine). Floyd Romesberg and his colleagues of the Scripps Research Institute in La Jolla, Calif., designed a fifth base, called 3-fluorobenzene (3FB), that pairs with itself. The trick was figuring out how to incorporate the new base into a DNA molecule, he says.

In nature, an enzyme called DNA polymerase replicates the genetic material by moving along one of the molecule’s two strands, all the while adding complementary bases to form a new DNA molecule. However, the enzyme recognizes only the standard four bases. So, the Scripps researchers engineered a new polymerase enzyme to recognize 3FB, latch on to it, and incorporate it appropriately into a replicating strand of DNA.

The enzyme that the Scripps group created replicates DNA containing the fifth base with relatively high fidelity—only one mistake for every 1,000 base pairs. Natural polymerases, on the other hand, make one mistake every 10 million bases. Still, it’s a start, says Romesberg.

His goal is to incorporate five-letter DNA into bacteria and let the organisms evolve in the lab to see how they adapt to the new coding system. He’ll look to see whether the five letters give bacteria any advantage, perhaps enabling them to make different proteins than natural bacteria do.

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