To make their DNA bases, Kool started with a molecule similar to thymine-called an analog-and made five different sizes by adding increasingly larger atoms. The first analog was smaller than natural thymine, the second about the same size and the last three were increasingly larger. The difference between the smallest and largest analogs was only one angstrom, or a tenth of a nanometer.
Bigger is better
When the researchers offered the analog bases to DNA polymerase I, the enzyme not only recognized the synthetic molecules as it would natural DNA but also copied one of the slightly larger analogs at a rate 22 times more efficiently than the natural-sized analog. In fact, DNA polymerase I incorporated the slightly larger analog almost as efficiently as it did natural thymine, both in the test tube and in live E. coli bacteria. In contrast to this, the smallest and largest analogs in the set were rejected by the enzyme and the bacteria.
According to Kool, these results indicate that size is a strong factor determining enzyme efficiency-and a mechanism for allowing mutations into the DNA molecule.
''It's a way the organism can evolve,'' Kool says. ''If the protein that copies DNA prefers a molecule that's slightly bigger than natural DNA, then it can accept mistakes more readily.'' For example, although T is supposed to match up with A, it might be inclined to pair with G, which has a slightly larger configuration.
The sheer fact that a living system readily used a base-or nucleotide-that was artificially created is itself groundbreaking. ''Here we have, I think, the first example of an efficient, human-designed nucleotide working in a live cell,'' he says.
Kool and the gang are now exploring ''the funny finding that the bugs prefer DNA that's larger than natural DNA'' by making larger nucleotides. ''Size and shape are related issues, so we