A codon pun?
March 9, 2014 1:33 PM Subscribe
I saw a license plate that said CCA TGG, and I was wondering if this is a clever pun by a geneticist.
From looking online, I can see the codons correspond to P W, so one guess is those might be the initials of the car's owner. Does anyone else have an idea what the intended meaning is?
From looking online, I can see the codons correspond to P W, so one guess is those might be the initials of the car's owner. Does anyone else have an idea what the intended meaning is?
I saw that and thought hairpin because it's a palindromic sequence (the second codon is complementary to the first). Maybe two scientists with names P and W who are saying they are "perfectly complimentary" to each other? :P There are several codon choices for each amino acid, so the joke would lie in choosing those particular codons.
If not codons, some phrase starting with "Two seas"?
posted by variella at 2:19 PM on March 9, 2014
If not codons, some phrase starting with "Two seas"?
posted by variella at 2:19 PM on March 9, 2014
Response by poster: This was in Northern California, close to the city of Berkeley. I don't remember the car unfortunately.
posted by Mayhembob at 2:33 PM on March 9, 2014
posted by Mayhembob at 2:33 PM on March 9, 2014
Unless I've read the chart wrong, CCA == glycine and TGG == threonine. What significance that may have is beyond me.
posted by Chocolate Pickle at 3:20 PM on March 9, 2014
posted by Chocolate Pickle at 3:20 PM on March 9, 2014
Best answer: CCA TGG doesn't look like it would for a stable hairpin in ssDNA or ssRNA.
This may or may not be it but I recognize that sequence, its the cut site for NcoI - a commercially available restriction endonuclease.
Restriction endonucleases are a type of enzyme that cut DNA at specific palindromic sequences and are incredibly useful for molecular biology. In nature they are part of a type of cellular immune system where bacteria use a second paired enzyme to modify their DNA with chemical groups that make the DNA invulnerable to the restriction endonucleases they also encode, allowing them to cut up any foreign DNA that might enter the cell without endangering their own genomes as a protection against hostile viruses or plasmids. In the lab we typically use them to cut up pieces of DNA in such a way as the cut sites leave sticky ends that we can then use to paste the DNA back together in ways that are useful - but there are all sorts of clever ways to take advantage of them. Here is a cool video of one working, its the first enzyme that binds to the DNA double helix, processes across it, finds its palindromic recognition site, and then makes its cut - the rest of the video shows another piece of DNA with compatible sticky ends being added to the solution and then being ligated with another enzyme.
This specific restriction endonuclease is named in the traditional way for being the first of this type of enzyme discovered in the critter Nocardia corallina and can be found in the freezers of most labs that do molecular biology, and especially cloning. Strands of DNA that are developed in such a way as to be easy to work with generally have sequences like CCA TGG added into them in convenient places so as to make cutting them up with the 600 or so enzymes that each have their unique recognition sites like NcoI easy.
It is remarkable to me for different reasons though, NcoI is especially sensitive to the kinds of modifications to DNA that the twin enzymes of restriction endonucleases make as well as more exotic kinds of nucleotide chemistry. This made it useful for the work I did for my masters degree developing an assay using a battery of these kinds of enzymes to detect modifications to, or substitutions for, the four canonical nucleotides with the 50+ others that are also sometimes used in DNA. Maybe it is remarkable to someone near Berkley for another reason?
posted by Blasdelb at 3:24 PM on March 9, 2014 [10 favorites]
This may or may not be it but I recognize that sequence, its the cut site for NcoI - a commercially available restriction endonuclease.
Restriction endonucleases are a type of enzyme that cut DNA at specific palindromic sequences and are incredibly useful for molecular biology. In nature they are part of a type of cellular immune system where bacteria use a second paired enzyme to modify their DNA with chemical groups that make the DNA invulnerable to the restriction endonucleases they also encode, allowing them to cut up any foreign DNA that might enter the cell without endangering their own genomes as a protection against hostile viruses or plasmids. In the lab we typically use them to cut up pieces of DNA in such a way as the cut sites leave sticky ends that we can then use to paste the DNA back together in ways that are useful - but there are all sorts of clever ways to take advantage of them. Here is a cool video of one working, its the first enzyme that binds to the DNA double helix, processes across it, finds its palindromic recognition site, and then makes its cut - the rest of the video shows another piece of DNA with compatible sticky ends being added to the solution and then being ligated with another enzyme.
This specific restriction endonuclease is named in the traditional way for being the first of this type of enzyme discovered in the critter Nocardia corallina and can be found in the freezers of most labs that do molecular biology, and especially cloning. Strands of DNA that are developed in such a way as to be easy to work with generally have sequences like CCA TGG added into them in convenient places so as to make cutting them up with the 600 or so enzymes that each have their unique recognition sites like NcoI easy.
It is remarkable to me for different reasons though, NcoI is especially sensitive to the kinds of modifications to DNA that the twin enzymes of restriction endonucleases make as well as more exotic kinds of nucleotide chemistry. This made it useful for the work I did for my masters degree developing an assay using a battery of these kinds of enzymes to detect modifications to, or substitutions for, the four canonical nucleotides with the 50+ others that are also sometimes used in DNA. Maybe it is remarkable to someone near Berkley for another reason?
posted by Blasdelb at 3:24 PM on March 9, 2014 [10 favorites]
A six base pair palindromic sequence is likely to be a site of restriction enzyme cleavage. This one seems to be cut by NcoI. Perhaps the owner's initials are NCO?
Alternatively, CCATGG is part of the Kozak sequence, which helps the ribosome bind mRNA to initiate translation. Perhaps their research resolves around that area, or, my preference, perhaps they're a punny Cossack.
posted by FiveSecondRule at 3:31 PM on March 9, 2014
Alternatively, CCATGG is part of the Kozak sequence, which helps the ribosome bind mRNA to initiate translation. Perhaps their research resolves around that area, or, my preference, perhaps they're a punny Cossack.
posted by FiveSecondRule at 3:31 PM on March 9, 2014
Like Blasdelb, my brain also went straight to restriction enzyme. Maybe the person is a biologist who happens to have the initials NCO and thought it would be cool to encode them in some clever way?
posted by juliapangolin at 3:31 PM on March 9, 2014
posted by juliapangolin at 3:31 PM on March 9, 2014
The codon CCA will generally encode for the amino acid Proline, abbreviated as either Pro or P depending on space considerations, context and dickishness to translation noobs, while TGG typically encodes for Tryptophan, abbreviated as wither Trp or W. I doubt that this is an example of just straight translation though, as much fun as you can have with that*, its probably either related to NcoI or a regulatory sequence specific to whatever model system the driver works on.
*There is a possibly apocryphal story of a post-doc working on Craig Venter's yacht, which travels around the world doing metagenomics on the oceans, synthesizing a DNA oligo that when translated spells out CRAIGVENTERISG*D and dumping it out at the bow of the ship during sampling for the sheer hilarity of pissing off that asshole.
posted by Blasdelb at 3:43 PM on March 9, 2014 [2 favorites]
*There is a possibly apocryphal story of a post-doc working on Craig Venter's yacht, which travels around the world doing metagenomics on the oceans, synthesizing a DNA oligo that when translated spells out CRAIGVENTERISG*D and dumping it out at the bow of the ship during sampling for the sheer hilarity of pissing off that asshole.
posted by Blasdelb at 3:43 PM on March 9, 2014 [2 favorites]
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posted by Conrad Cornelius o'Donald o'Dell at 1:41 PM on March 9, 2014