Sunday, February 14, 2010

Adding DNAv4 to DNAv3

From New Scientist
Jason Chin at the University of Cambridge and his colleagues have now redesigned the cell's machinery so that it reads the genetic code in quadruplets. …

To achieve this, the team had to redesign three pieces of the cellular machinery that make proteins.

But they didn't stop there. The team went on to prove their new genetic code works by assigning two "unnatural" amino acids to their quadruplet codons, and incorporated them into a protein chain.

"It's the beginning of a parallel genetic code," says Chin.

What's more, they've shown that these amino acids can react with each other to form a different kind of chemical bond to those which usually hold proteins together in their three-dimensional shape.

The normal kind of bonds – disulphide bonds – can be broken by changes in heat and acidity, causing proteins to lose their 3D structure. This, for instance, is why egg whites change colour and texture when cooked: as the albumen in the whites loses its structure, its physical appearance is transformed.

But the bonds created between Chin's new amino acids are stronger – and so could allow proteins to work in a much wider range of environments. This could help make drugs that can be taken orally without being destroyed by the acids in the digestive tract, for instance.

But that's just the beginning. In the longer term it might be possible to create cells that produce entirely new polymers, such as plastic-like materials. Organisms made of these cells could incorporate the stronger polymers and become stronger or more adaptable as a result.
Here's how The puts it.
Scientists have developed a new genetic language using a ribosome that can read instructions that are 4 base pairs long [rather than the three that are found in nature], enabling the construction of designer proteins containing a variety of unnatural elements, according to a study published online today (February 14) in Nature. …

[Using 3 base pairs there is only] one spare codon to work with. [As a result] scientists have largely been restricted to incorporating only one such unit per protein.

To overcome this limitation, synthetic biologist Jason Chin of the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, and his colleagues decided to devise a system that could read codons that are 4 base pairs long. Such a system could "open the door to what will be [the] truly revolutionary possibility [of creating] genetically coded polymers comprised of up to 256 [unique] building blocks."

The problem was that normal ribosomes -- which translate 3-base codons into any of the 22 naturally occurring amino acids -- don't read such quadruplet codons, at least not usually. Furthermore, the team couldn't simply manipulate the existing ribosomes, as they are responsible for producing all of the cell's proteins that are required for its survival; altering this system could quickly cause a cellular collapse. Their solution: make a whole new ribosome.

A few years ago, the researchers created the new ribosome, known as an orthogonal ribosome, by altering the region that recognizes the ribosome-binding sequence of the messenger RNA (mRNA). They then created special mRNAs with complementary binding regions to this new sequence, which the orthogonal ribosome selectively bound to and read, leaving natural mRNAs to be recognized only by the natural ribosomes.

"Now you've got two ribosomes -- one reading a new message and [the] normal ribosome" reading the old messages, Chin explained. "That's the basis of how you would write a parallel genetic code in the cell."

With the two ribosomes systems working independently, the researchers could then manipulate the orthogonal ribosome without disrupting normal cellular function. In the present study, they did just that, inducing mutations in the ribosome where the tRNA and mRNA molecules interact in hopes of creating a ribosome that could read quadruplet codons with comparable efficiency and accuracy to that of natural protein synthesis.

To test their mutated ribosomes, the team put them in bacterial cultures growing on a medium containing antibiotics, and provided the cells with an antibiotic resistance gene that included a 4-base codon. Ribosomes that could read the quadruplet codon successfully produced the antibiotic resistance protein, and survived even in the presence of high concentrations of the antibiotic. Those that couldn't read the quadruplet, couldn't create the protein to protect themselves from the antibiotic and died as a result. "In the end we get cells that are surviving this selection pressure," Chin said, and in those cells are ribosomes that can successfully read quadruplet codons.

The new ribosome can still read triplet codons as well, Chin added, but it preferentially reads the 4-base sequences. In this way, the ribosome can still incorporate natural amino acids as well as modified units attached to the amber codon.

But now with the ability to read the quadruplet codons, scientists can easily create proteins with more than one unnatural unit. Using the amber codon and a quadruplet codon to code for two different unnatural amino acids, the researchers generated a protein, synthesized by the new ribosome, that contained both unnatural units.
In many ways this is similar to the move from IPv4 to IPv6 in Internet addressing. (See here and here). It creates a much collection of potential addresses, which therefore can refer to a much larger space of things. In the Internet case the things are distinct items that can have their own internet address. In the DNA case the things are proteins that DNA can be interpreted as referring to.

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