Comments on: “Codon” is now a four letter word http://bytesizebio.net/index.php/2010/02/17/codon-is-now-a-four-lettered-word/ The musings and ravings of a computational biologist about science, computers, music and, you know, stuff Wed, 01 Feb 2012 18:43:57 +0000 hourly 1 http://wordpress.org/?v=3.3.1 By: Iddo http://bytesizebio.net/index.php/2010/02/17/codon-is-now-a-four-lettered-word/comment-page-1/#comment-696 Iddo Mon, 22 Feb 2010 03:29:03 +0000 http://bytesizebio.net/?p=3277#comment-696 <a href="#comment-695" rel="nofollow">@Andrew Perry </a> That is exactly what they did with the calmodulin. One tetracodon was read in-frame to add the p-azido-l-phenylalanine to the calmodulin. the rest of the protein was translated from tricodons. @Andrew Perry
That is exactly what they did with the calmodulin. One tetracodon was read in-frame to add the p-azido-l-phenylalanine to the calmodulin. the rest of the protein was translated from tricodons.

]]> By: Andrew Perry http://bytesizebio.net/index.php/2010/02/17/codon-is-now-a-four-lettered-word/comment-page-1/#comment-695 Andrew Perry Mon, 22 Feb 2010 03:07:51 +0000 http://bytesizebio.net/?p=3277#comment-695 Very cool. Now for a new challenge ... design a DNA sequence that uses overlapping 3-base and 4-base codons, where the 3-codon phase AND the 4-codon phase both produce folded protein products. This would better fit the analogy of program source code being read by two different compilers, each producing a different (but functional) program. Very cool. Now for a new challenge … design a DNA sequence that uses overlapping 3-base and 4-base codons, where the 3-codon phase AND the 4-codon phase both produce folded protein products. This would better fit the analogy of program source code being read by two different compilers, each producing a different (but functional) program.

]]> By: Dr. Shyamala Pillai Shah http://bytesizebio.net/index.php/2010/02/17/codon-is-now-a-four-lettered-word/comment-page-1/#comment-690 Dr. Shyamala Pillai Shah Thu, 18 Feb 2010 12:41:09 +0000 http://bytesizebio.net/?p=3277#comment-690 That is really something. I am quite new to the field of synthetic biology and am trying to catch up. But even to me the implications of a four letter codon are evident! This is going to vastly enhance the repertoire of what we can do in the lab! Great post! That is really something. I am quite new to the field of synthetic biology and am trying to catch up. But even to me the implications of a four letter codon are evident! This is going to vastly enhance the repertoire of what we can do in the lab! Great post!

]]> By: Iddo http://bytesizebio.net/index.php/2010/02/17/codon-is-now-a-four-lettered-word/comment-page-1/#comment-688 Iddo Wed, 17 Feb 2010 15:05:58 +0000 http://bytesizebio.net/?p=3277#comment-688 Well, the idea of orthogonal translation is that the cell (a bacterium in this case) already encodes for the o-ribosome. Or did I miss something here? Regarding the wobble: I am not sure what the thermodynamic aspects are. They do provide a structure of the o-ribosome in the paper. But they did not look at the thermodynamics of the 4 base codon, as far as I can tell. If anything, I am thinking there will be more wobble, as a 4-mer has more degrees of freedom than a 3-mer. Also, they only generated one working quadruple codon so far. Much more to explore. Well, the idea of orthogonal translation is that the cell (a bacterium in this case) already encodes for the o-ribosome. Or did I miss something here?

Regarding the wobble: I am not sure what the thermodynamic aspects are. They do provide a structure of the o-ribosome in the paper. But they did not look at the thermodynamics of the 4 base codon, as far as I can tell. If anything, I am thinking there will be more wobble, as a 4-mer has more degrees of freedom than a 3-mer. Also, they only generated one working quadruple codon so far. Much more to explore.

]]> By: Lab Rat http://bytesizebio.net/index.php/2010/02/17/codon-is-now-a-four-lettered-word/comment-page-1/#comment-687 Lab Rat Wed, 17 Feb 2010 13:13:03 +0000 http://bytesizebio.net/?p=3277#comment-687 Wow...that is amazing. Could have a huge potential for synthetic biology; if you can make a 'cell' structure that contains synthetic DNA that codes for this synthetic ribosome, you could make all sorts of things! I'm guessing their O-ribosomes didn't have any 'wobble' usually associated with the third position of normal ribosomes. Wow…that is amazing. Could have a huge potential for synthetic biology; if you can make a ‘cell’ structure that contains synthetic DNA that codes for this synthetic ribosome, you could make all sorts of things!

I’m guessing their O-ribosomes didn’t have any ‘wobble’ usually associated with the third position of normal ribosomes.

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