The thing I like most about the idea of DNA encoding is the idea that using this method, all human knowledge could survive catastrophic world events. Inject a few million roaches or termites and even if we all perish and the human race is wiped from the face of the planet, our progress will have been recorded and live on.
The thing I like most about the idea of DNA encoding is the idea that using this method, all human knowledge could survive catastrophic world events. Inject a few million roaches or termites and even if we all perish and the human race is wiped from the face of the planet
Synthesize bases with various combinations of stable nitrogen, carbon, and oxygen isotopes. There are two stable isotopes of nitrogen, two of carbon, and three of oxygen. I'm too lazy to do the math, but that gives you a huge number of subtypes for each base—different masses, but more or less identical chemical behavior.
You'll need a Mass Spec for data retrieval, and writing will be a nightmare, but the potential information density would exceed that of natural DNA by many orders of magnitude.
4 years worth, he posts his collection every December 26th: *NSFW* *NSFL*.
You're talking angstrom level differences while the wavelength of visible light is on the order of hundreds of nanometers, you'd need to be making gamma rays before you got precise enough, which would have their own issues.
Eric Kool, a chemist now at Stanford University in California, wondered whether his team could develop unnatural bases with fixed hydrogen-bonding arrangements. He and his colleagues made a base similar to the natural base T, but with fluorine in place of the oxygen atoms (see'Designer DNA'), among other differences5. The structure of the new base, called difluorotoluene (designated F), mimicked T's shape almost exactly but discouraged hydrogen from jumping.
The team soon discovered that F was actually terrible at hydrogen bonding5, but polymerases still treated it like a T: during DNA copying, they faithfully inserted A opposite F (ref. 6) and vice versa7. The work suggested that as long as the base had the right shape, a polymerase could slot it in correctly. “If the key fits, it works,” says Kool.
Floyd Romesberg, a chemical biologist at the Scripps Research Institute, has expanded the repertoire of hydrophobic bases. Starting with molecules such as benzene and naphthalene, his team built “every imaginable derivative”, he says. “It drove us very much away from anything that looked like a natural base pair at all.” But while testing steps in the replication process, the researchers found two contradictory requirements. A crucial position in the base had to be hydrophobic for enzymes to insert the base into DNA, yet it also had to accept hydrogen bonds if enzymes were to continue with copying the strand.
Romesberg's team screened 3,600 combinations of 60 bases for the pair that was copied the most efficiently and accurately8. The two that won, MMO2 and SICS, “walk a thin line” between being hydrophobic and hydrophilic at the key position, Romesberg says.
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