MrTypie

All good questions deserving of upvotes.

Briefly, the genome was assembled in four stages: 1kb, 10kb, 100kb, and complete. The entire M. Mycoides genome is about 1.1 Mb long - this means 1,100,000 base pairs of DNA. It was first divided into chunks of roughly 1,000 bases. These 1,078 "1kb" pieces were ordered from a DNA synthesis company. 10, 1kb pieces were assembled using an in-vitro technology to produce the 110, 10kb cassettes. 10, 10kb cassettes were then put together using a technique called yeast homologous recombination to yield the 100kb segments. The final assembly step (of combining 11, 100kb segments) is also done in yeast, taking advantage of their natural ability to stitch together overlapping pieces of DNA.

To answer your 2nd question, the genome is assembled "from scratch" in the sense that the DNA itself is synthesized using a machine, and then put together in a stepwise fashion. The sequence of the DNA, however, is almost identical to the native M. mycoides genome. So the genetic information is indeed borrowed from an already existing species, and the genome transplantation process also requires a recipient cell that is very much pre-existing.

That's an easy one, nope!

The genome contains only As, Ts, Gs, and Cs. In living organisms, three bases in a row are called a "codon" and specify an amino acid. The 64 possible codons encode stop/start instructions and only 20 amino acids. In other words, there is a lot of redundancy. So, I think you could imagine a system where each codon stands for a different letter of the alphabet, plus plenty of extra codons to cover symbols and punctuation. That is how the watermarks were designed. We know these regions are "inert" because they do not contain promoter sequences or ribosomal binding sites and thus won't be transcribed/translated.

ಠ_ಠ

• What's something that is even more amazing than people think?

Forgetting about the transplantation, the synthetic genome itself is the largest man-made molecule of a defined structure ever created.

• How about something that you didn't know if it would work, but it did?

In the beginning, there was never any guarantee that they synthetic genome would ever be able to be "booted up" in a recipient cell. The transplantation step is truly unprecedented in the history of molecular biology.

• What's a limitation of the technology that isn't immediately apparent?

The "recipient cell" (M. capricolum) is a very closely related species to the "donor cell" synthetic genome from M. mycoides. It's not yet clear just how different the donor genome can be for the transplantation step to still work.