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Biotech Science

New Letters Added To the Genetic Alphabet 74

An anonymous reader writes with this excerpt from Quanta Magazine: [A]fter decades of work, [organic chemist Steven] Benner's team has synthesized artificially enhanced DNA that functions much like ordinary DNA, if not better. In two papers published in the Journal of the American Chemical Society last month, the researchers have shown that two synthetic nucleotides called P and Z fit seamlessly into DNA's helical structure, maintaining the natural shape of DNA. Moreover, DNA sequences incorporating these letters can evolve just like traditional DNA, a first for an expanded genetic alphabet. In fact, the article continues, these new nucleotides can actually outperform their natural counterparts: "When challenged to evolve a segment that selectively binds to cancer cells, DNA sequences using P and Z did better than those without."
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New Letters Added To the Genetic Alphabet

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  • by Demonoid-Penguin ( 1669014 ) on Saturday July 11, 2015 @07:08AM (#50087711) Homepage

    That's all I've got to say on the subject - even if I knew much about it the likely outcomes are speculative. Though not the predictable protests.

    • Re: (Score:3, Funny)

      by Anonymous Coward

      Meet my mutant daughter, Gattaca Zappa.

    • Yep, Zombies I bet.

      • Yep, Zombies I bet.

        Of course. How obvious - the Z gene, how's that for intuitive wisdom -and the last zombie movie I watched had Charlton Heston in it (now he is a zombie). I was so stunned that I finished reading the referenced article and found I'd written the first post that I failed to notice the obvious clue. This is going to really drive the preppers batshit.

        I wonder what the P gene does? On second thoughts I'd rather find out second-hand.

    • I wouldn't protest this, but I will say that I expect mostly subtle--with occasional fabulous--disasters.
      It's all fun and games until the Trolloc army comes through, spreading the sort of affection that would make a locust swarm seem a mere inconvenience.
      • I wouldn't protest this, but I will say that I expect mostly subtle--with occasional fabulous--disasters.

        O-K. Sounds like conception as normal.

        It's all fun and games until the Trolloc army comes through, spreading the sort of affection that would make a locust swarm seem a mere inconvenience.

        Or worse - so cute that just a passing glimpse turns the viewers brain to mush. Like cabbage patch dolls and cute kittens times 10000. Everyone will want one, but having got one, do nothing but stand oohing until they die of self-neglect in a pool of their own waste.

    • Of course there will be protests. So many people are using software at home to manipulate their genes as 2-bit values. This is basically DRM, or at least until people go back and fix all their code, which might even be technically illegal for them to do. Fuck that! We need to take to the streets, now!
    • by KGIII ( 973947 )

      Given that we are showing how little is known about DNA should we really be doing genetic modifications to things that might be important - like humans or food?

      • Given that we are showing how little is known about DNA should we really be doing genetic modifications to things that might be important - like humans or food?

        I don't know. Yet.

        • by KGIII ( 973947 )

          You're no fun. ;) You're supposed to throw a wild uneducated opinion out there.

          Meh... I was wondering what effects this *could* have as well - like with immunizations. Obviously viruses would just adapt but the flavors of the day could be stopped maybe.

          • You're no fun. ;) You're supposed to throw a wild uneducated opinion out there.

            Well obviously it will mean people will develop super powers.

            Meh... I was wondering what effects this *could* have as well - like with immunizations. Obviously viruses would just adapt but the flavors of the day could be stopped maybe.

            The most informed opinions seems to be - none. It'll help us understand evolution [ducks rocks thrown by troglodytes], may be useful in gene therapy, and also organic information systems.

            • by KGIII ( 973947 )

              Much thanks. DNA is, as far as I can tell, like coding. I am not a geneticist so I have a very limited understanding. I eagerly await my superhuman strength though! I am going to tell everyone that it is now possible and that science proves it. I do my best to help...

              • Much thanks. DNA is, as far as I can tell, like coding. I am not a geneticist so I have a very limited understanding. I eagerly await my superhuman strength though! I am going to tell everyone that it is now possible and that science proves it. I do my best to help...

                Great news! I am also not a geneticist, but I am pleased to discover that it's another field of so-called knowledge that is intuitive and requires not study or critical thinking to master. At first I doubted the existence of super powers based on what is now obviously a lack of understanding the power of negative thinking. Since reading the summary and checking a mirror I've discovered that I have less hair, and looser skin - clearly evidence of major changes. This can only be good.. I eagerly await the arr

                • by KGIII ( 973947 )

                  Those symptoms indicate that you will probably be getting stretchy skin and bones as your super power. I also intend to tell people that the only reason they do not have access to this technology is because it is being suppressed and that it should really only cost about five dollars for a DNA test and then another five for modifications. It is because of the wealthy and China... I have already emailed the link to my brother. Now I need to reel him in... Victory can be mine!

                  • Those symptoms indicate that you will probably be getting stretchy skin and bones as your super power.

                    My eyebrows are also getting shaggier, I have hair growing on my neck, and my ears do seem to be getting larger.

                    I will become Mambo - the Woolly Mammoth man!

                    I also intend to tell people that the only reason they do not have access to this technology is because it is being suppressed and that it should really only cost about five dollars for a DNA test and then another five for modifications. It is because of the wealthy and China... I have already emailed the link to my brother. Now I need to reel him in... Victory can be mine!

                    There are other things he needs to know.

                    The holes in the ozone layer are being caused by fluorocarbons - every fluorescent light bulb that breaks causes skin cancer. Stop using fluorescent light bulbs now.

                    Vanity (that is why he has moisturiser in his bedside table, right?) causes the extinction of (cute) wild animals. Every year thousands of the now rar

                    • by KGIII ( 973947 )

                      Those will be fluffed out and emailed. Thank you. I should screenshot for "epic lulz" except I would never do that to my brother. Hopefully he does not Google. He knows my screen name.

                      If your fingernails are growing then you just might be turning into Wolverine... That has some benefits.

  • Not news (Score:5, Informative)

    by Improv ( 2467 ) <pgunn01@gmail.com> on Saturday July 11, 2015 @07:10AM (#50087715) Homepage Journal

    This is at least a bit over a year old.

    Nature had a good publication on this a bit (same research group) over a year ago.
    http://www.nature.com/news/fir... [nature.com]

  • it's alive.
  • by Chikungunya ( 2998457 ) on Saturday July 11, 2015 @07:37AM (#50087769)

    It is not clear how the new nucleotides act when transcribing proteins but assuming its at least as efficient as the 4 letter code it could be a very interesting option for artificial viruses. A virus engineered to be totally dependent on the new nucleotides could be used much more safely even inside humans where there is no supply of them, they could infect the cells, produce proteins and a huge immune response but not a single copy of their genetic material could be produced. Also in a controlled environment they would thrive (cheap production?) but without P-Z no danger of new virus production so safety would not need to be as strict.

    Applications on real organisms probably will take much longer time, but the simplicity of virus would make it a natural first step.

    • by Anonymous Coward on Saturday July 11, 2015 @08:52AM (#50087935)

      That's far, far away at this point. In cells, DNA is first "transcribed" to an RNA copy of the same information, then "translated" by building a protein based on that information. Neither of those steps will work correctly here. Transcription enzymes won't handle the new DNA letters, and there's no defined meaning for them in the standard translation code: at best they'll be misinterpreted as a different letter, and it's more likely that translation will simply fail. And unless you can make at least a handful of proteins, you can't make a virus.

      • by Anonymous Coward

        Some viruses in nature already contain RNA, and there are already viruses and bacteria in nature that contain additional nucleotides not of the traditional five seen in human DNA & RNA. They still work fine because the transcription process will confuse or treat some of the different bases with one of the ones normally in the host organism. There is a lot more variation in the nucleotide bases that people would think from looking at a grade school biology textbook, something that should be easy to fin

  • by nut ( 19435 )
    They've changed the genome from a 2 bit computer to a 3 bit computer. In theory they should be faster than us. But only over generations.
  • by crow ( 16139 ) on Saturday July 11, 2015 @07:55AM (#50087797) Homepage Journal

    They say the new DNA outperforms the standard DNA in evolving to meet the researcher's criteria. That means it changes more easily. In other words, it's less stable.

    In most situations, what we want is stability. Nature needs some ability to mutate and evolve, but considering that the wrong mutations result in cancer and death, too high of a mutation rate leads to failure. I suspect this is particularly true in long-lived larger organisms.

    • by Megane ( 129182 ) on Saturday July 11, 2015 @09:14AM (#50088027) Homepage

      The article I read also said "IT HAS 216 COMBINATIONS!!1!!@@!! REGULAR DNA ONLY HAS 20!!!@!". Which is stupid because they're counting two different ways. 6^3 is indeed 216, but 4^3 is 64, and 20 is 31% utilization of 64 possibilities.

      The reason is that some combinations are reserved for start and stop codons, and most amino acids have 2 or 4 redundant codings. This both reduces the effect of random mutations, and also makes multi-frame coding work better by being less strict. The bits that match the codes to amino acids when building proteins probably use some kind of wildcards, reducing the number of them needed when you have to basically have a unique small chemical around to match each valid combination. It would be more realistic to say that the new base pairs would allow 45-50 or so new protein codings, still more than tripling the potential number of amino acids.

      That being said, a new set of base pairs is really cool. There have been experiments to create alternate DNA codings by re-purposing some of the redundant codings, but there is a backward compatibility kind of problem when doing that. This not only allows a lot of new codes, but the new base pairs themselves have interesting properties. One even has a bond out to the side that you can connect things too. And the twisty folding stuff that RNA likes to do can become a lot more complicated.

      And why does Earth life use only 4 base pairs? Probably because the extra complexity just isn't all that useful. CGAT has been around for a couple of billion years, so it's got more installed base behind it than QWERWTY vs DVORAK could ever have. Except this is more like adding a new row or three to QWERTY for more roman-letter characters, such as a bunch of letters with diacritical marks on them, like how the French went nuts romanizing Vietnamese.

      • by Anonymous Coward

        And why does Earth life use only 4 base pairs?

        Earth doesn't use just 4 base pairs, just most people think of that because human DNA and RNA use four base pairs each (5 total). There are a couple more around in more primitive organisms, eight to a dozen total depending on how you want to count things as variations or different base pairs (many actual functionally the same in the end).

  • by 140Mandak262Jamuna ( 970587 ) on Saturday July 11, 2015 @08:09AM (#50087827) Journal
    The article talks about the potential benefits and drawbacks of the six letter system. If there were advantages nature would have stumbled on it eons ago. Why did it not happen?

    Of course we did not evolve wheels neither. Almost all animals above worms are torii topologically. (The digestive tract is the hole in the ring). There is one bacteria that has a free spinning flagellum. So nature started on that kind of disjoint topology, but could not scale it beyond bacteria. Two symbiotic animals one providing a wheel with shaft and another providing the bearing, together could have formed a wheeled animal. But that never happened, there is no path in the fitness landscape to achieve that configuration. Is it something fundamental like this that prevented six letter DNA

    Or, more prosaically, the drawbacks outweigh the benefits. After all computers use binary not tertiary numbers. The four letter DNA is technically a binary system. Two pairs. So even if this thing escapes the laboratory it won't thrive in the wild and wipe out all the present forms of life Comforting if it is so.

    • by Anonymous Coward

      Because evolution doesn't strive to be perfect it just needs to be good enough to not die.

      A 4 letter system worked so there was no need to evolve into 6.

      If evolution worked that way then humans wouldn't have a blind spot where the optic nerve goes through and I would't keep having to shave my balls.

      • by Anonymous Coward

        Because evolution doesn't strive to be perfect it just needs to be good enough to not die.

        Evolution does not strive, it has no aim or goal or purpose.

        Random mutations happen, some survive (those we call "the fittest" - "survival of the fittest" is a tautology), others die off.

    • by Anonymous Coward

      The only real advantage to 6 instead of 4 would be increasing the seek size of 15-nucleotide strands (the mechanism to find a gene uses 15 base samples). Humans are near the maximum where this works successfully with 4 pairs.

    • If there were advantages nature would have stumbled on it eons ago. Why did it not happen?

      Evolution is not working toward anything. Evolution is always working away from extinction.

  • ...by sequencing cancer.
    • Re: (Score:1, Flamebait)

      by Megane ( 129182 )
      Cancer doesn't work that way, you idiot. Cancer is like randomly changing data in a file. This is like changing a computer from binary into ternary, a computer virus can't do that.
  • by Goldsmith ( 561202 ) on Saturday July 11, 2015 @11:09AM (#50088361)

    This is part of a broader DARPA driven effort to expand what biology is capable of.

    The end goal is to be able to create new materials (better fuels, medicines, building materials, etc) using biology. This requires expanding the "toolkit" biology uses to incorporate biologically incompatible elements, chemicals and processes.

    So, starting from the end: We want a better biofuel. To do that, we want proteins that can better incorporate inorganic catalysts and work at higher energies than existing biology. To do that, we need different amino acids and protein construction machinery. To do that, we want to expand DNA to code for these new amino acids.

    This is a "good" DARPA project in that we're not able to do all of this yet. What this means is that technology is pushed forward significantly, and we're able to clearly identify the real challenges.

  • ... with a copy of Milla Jovovich, I'm OK with this.

  • If we replaced our DNA and RNA with these new letters, and updated all our DNA and RNA related proteins to use those letters instead, we should be immune to any virus. Of course, I don't think we could actually pull off such a change since we'd have to change so many proteins as well.

  • by peter303 ( 12292 ) on Saturday July 11, 2015 @03:42PM (#50089657)
    The 64 three letter codons specify 20 amino acids and punctuation. For some amino acids the third element of the codon doesn't matter or has couple redundancies. This suggest an earlier two element codon with 15 amino acids or less.
  • Look. All I want is that colour changing thing from cuttlefish, and to glow in the dark. Get back in the lab and let me know when it's ready. I'll pay the delivery boy at the door.

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