Slashdot Mirror

← Back to Stories (view on slashdot.org)

Scientists Create Synthesized DNA Bases

Posted by ScuttleMonkey on from the and-mother-nature-is-pissed dept.

Iddo Genuth writes to tell us that researchers at the Scripps Research Institute in San Diego have created two artificial DNA bases in an effort to "expand biology's potential." "In the future, [chemist Floyd] Romesberg envisions manipulating the genetic code of bacteria in order to assemble better drugs or even man-made proteins. Until now, the bases only work in bacteria, so human augmentation is currently not possible. Another option is to use alpha and beta to help construct nanomachines to be used for drug delivery. 'This is like jumping from the Stone Age to the Bronze Age,' Romesberg says. 'It takes time to figure out how best to use metal.'" Update 18:10 GMT by SM: Roger writes to share the NewScientist link with a bit more information. There is also the original release text for consideration.

31 of 125 comments (clear)

  1. I want my Vitamin C! by snowgirl · · Score: 3, Interesting

    Can we get back our Vitamin C gene again? I would love being able to eat less fruit... Scurvy sucks.

    --
    WARNING! This girl exceeds the MAXIMUM SAFE standards established by the FDA for BRATTINESS
    1. Re:I want my Vitamin C! by twatter · · Score: 3, Insightful

      This has implications beyond the delivery of drugs. Drugs act at the protein level, but imagine a delivery mechanism that does not require a protein receptor, but instead acts at the DNA filament level.

      This is HUGE news.

    2. Re:I want my Vitamin C! by Sir_Real · · Score: 2, Funny

      Can we get back our Vitamin C gene again? I would love being able to eat less fruit... Scurvy sucks.

      Apparently a war has already been delcared on Scurvy, and it appears to almost be won

    3. Re:I want my Vitamin C! by jollyreaper · · Score: 3, Funny

      Can we get back our Vitamin C gene again? I would love being able to eat less fruit... Scurvy sucks.

      Have you ever tried coconut rum and fresh OJ? You'll never bitch about drinking your fruits again.

      --
      Kwisatz Haderach
      Sell the spice to CHOAM
      This Mahdi took Shaddam's Throne
    4. Re:I want my Vitamin C! by snowgirl · · Score: 2, Interesting

      Hahahah, it's so funny, because reading about the history of Scurvy, people actually thought this way for awhile.

      Personally, I really think it'd be awesome if we could just repair our Vitamin C gene, and generate Vitamin C ourselves again... but then we also need to fix the gene that processes uric acid, so that we don't fill up on stuff doing the job of Vitamin C... since high uric acid levels have been associated with Type II diabetes, it might just effect a reduction in diabetes in humans.

      --
      WARNING! This girl exceeds the MAXIMUM SAFE standards established by the FDA for BRATTINESS
    5. Re:I want my Vitamin C! by ShieldW0lf · · Score: 3, Funny

      If it hasn't been sprayed through a pile of burning rotten vegetation from Scotland, it's shite.

      --
      -1 Uncomfortable Truth
    6. Re:I want my Vitamin C! by 93,000 · · Score: 2, Funny

      Pretty reckless with your precious fluilds, there, buddy.

      I only drink grain alcohol and rain water.

      --
      Sweet informative mod.
    7. Re:I want my Vitamin C! by snowgirl · · Score: 2, Interesting

      Have you ever tried coconut rum and fresh OJ? You'll never bitch about drinking your fruits again.

      Just wait until he starts bitching about his liver. :P

      Why does no one look at my name? Is it just standard presumption that everyone on slashdot is a guy, even when their login is "snowgirl"?

      --
      WARNING! This girl exceeds the MAXIMUM SAFE standards established by the FDA for BRATTINESS
    8. Re:I want my Vitamin C! by spazdor · · Score: 2, Funny

      Nicknames are meaningless. The big giveaway that you're a girl was that you drink Rieslings.

      That shit's for ladies and, uh, whoever plays one on the Internet.

      --
      DRM: Terminator crops for your mind!
    9. Re:I want my Vitamin C! by snowgirl · · Score: 2, Informative

      I don't hate the fruit! I just hate that every other animal in the world can synthesize their own Vitamin C, but we can't!

      It's about EQUALITY, not wanting to get rid of fruit. I do like fruit; I have some cherries right now, and they're absolutely divine.

      So, in all, I love fruit, I don't want to get rid of it... I just want to get rid of Scurvy...

      --
      WARNING! This girl exceeds the MAXIMUM SAFE standards established by the FDA for BRATTINESS
  2. Follow the link at the end of the article by Sir_Real · · Score: 3, Informative

    There is a more technical explanation in the link at the end of the article.

  3. These are bases not amino acids by NFN_NLN · · Score: 5, Interesting

    He's adding new bases which have no coding to amino acids. I don't see the purpose of this. Is it just for adding a trace or marker in DNA?

    All the bases do are code for amino acids and it's the amino acid sequence which accounts for a protein's shape. In the end it's the protein's shape that matters for chemical interactions.

    1. Re:These are bases not amino acids by olyar · · Score: 5, Funny

      Mostly they just want to be able to write a technical paper called "All your base (pairs) are belong to us".

      --
      Custom, hands-free Linux installs. Instalinux
    2. Re:These are bases not amino acids by Robert1 · · Score: 4, Interesting

      You're totally right. This is such a non-story and frankly mildly offensive in how full of himself the scientist is with sweeping comments like that.

      As it stands currently, the amount of genetic degenerecy in amino acid coding means that they would easily have those double and tripled coded amino acids switched to something else. They could potentially add another 20-30 new amino acids with absolutely no change in the number or form of the base pairs used.

      Its like finding a solution to a problem that doesn't exist, will never exist, and serves no purpose even if it was found. But apparently its equivalent from going to the iron age from the bronze age. Ha!

    3. Re:These are bases not amino acids by Eponymous+Bastard · · Score: 2, Informative

      TFA's TFA mentions information storage in DNA, which makes sense as this basically moves from base-4 to base-5 (The base pairs up with itself, so it's only one new base) thereby improving storage density. They also did some work to evolve a polymerase that replicates the DNA with the new base.

      DNA (single strands) and RNA also fold into themselves, and there is some evidence that the folding affects some mechanisms in the cell. Modifying them with these self-binding pairs could probably be hacked up to change the folding patterns. Also, DNA has activation sites and a whole bunch of things other than just the protein coding.

      Even without DNA computers, I could see modifying a ribosome to encode a new set of amino acids with the extra base. Also consider, retroviral genetic-therapy style techniques where one of these are inserted into genes to disable them, putting these into introns/extrons to allow for better experiments on DNA transcription, etc.

      Interestingly, neither article mentions transcription of this base into RNA, so your concern about amino acids is a little premature.

    4. Re:These are bases not amino acids by Edward+Kmett · · Score: 2, Informative

      Grossly simplifying, you read off codons (via mRNA, etc.) generating peptides so that you can build up proteins, etc. Some of those codons turn on or off transcription to amino acids.

      As noted in the article the fidelity of transcription of these is lower than conventional DNA. So perhaps they could make perfectly suitable markers for areas you want to provoke a mutation at a higher rate, perhaps dropping them into large introns to encourage mutation in those areas.

      The 3FB self-pair also expands the vocabulary of base pairs, potentially opening more options for possible nucleases, yielding more ways to cut up the resulting sequences.

      The 3FB-3FB pair is symmetric. I'm not sure of any applications of that at this point, but there are people who actually do this stuff for a living who I'm sure can come up with some sort of use for that feature. ;)

      Finally the code used need not remain fixed, (i.e. the various mitochondrial DNA codes) so the fact that they don't yield codons in any code we have now, doesn't mean that will always hold. Combined with the fact that transcription error rates are different for them leads to some interesting possibilities.

      --
      Sanity is a sandbox. I prefer the swings.
    5. Re:These are bases not amino acids by Gat0r30y · · Score: 2, Interesting

      ahh, come on - this is exactly like the transition from the stone age to the bronze age. If bronze had no additional useful function other than to help keep track of who made a stone.
      I'm pretty sure the only use for this is going to be marking genes, probably just to keep track of who owns the patents.
      The first genetic DRM?

      --
      Prediction: The real iPhone killer is going to be sex robots from Japan. Think about it.
    6. Re:These are bases not amino acids by ZackZero · · Score: 2, Informative

      Actually, if you read the second article (or the first link in the updated story), you'll see that the first base would pair up with itself instead of the second synthetic base - its intended pair. They "tweaked" it and it now pairs correctly... supposedly.

      However, this makes it base-6 instead of base-5 or the current base-4. If you recall your high-school biology class, the base pairs only exist in two combinations, but in a total of four permutations. There's adenine-thymine, thymine-adenine, cytosine-guanine and guanine-cytosine. Each permutation codes something slightly different. The new bases would add two more permutations, thus making it base-6.

    7. Re:These are bases not amino acids by tempest69 · · Score: 2, Insightful
      aarrgggg.... intergenic regions of bacteria are reasonably important.. regulation of the production of proteins is a really important process. being able to add an artificial control mechanism to genes that are guaranteed not to exist in nature is a powerful tool.. While temperature sensitive promoters are impressive, they still have some problems. But having a fully artificial promoter sequence should allow for some really impressive experiments once a bit more technology is added to the system. Plus it can make some really big changes in RNA folding..

      Storm

    8. Re:These are bases not amino acids by ViperOrel · · Score: 2, Interesting

      Actually, even though you have redundancies in the current set, with this new pair you could code for new amino acids (or anything else you wanted to stick in there) without having to worry about disrupting other things those redundancies were already coding for.

      My 2c.

    9. Re:These are bases not amino acids by Anonymous Coward · · Score: 3, Insightful

      Yeah, while the science here is kind of neat, it's not the biggest news in the world. The article title does not at all reflect what's newsworthy here, anyway. Scientists have been creating synthetic and/or modified nucleotides for decades and successfully incorporating them in to DNA and RNA. The news is that they found a synthetic base that can be copied by DNA polymerase. This is the enzyme that copies your DNA, putting an A next to a T on the opposite strand, a C opposite a G, a T opposite an A, and a G opposite a C. DNA polymerase will now put their new base, 3FB, opposite another 3FB on the opposite strand, and they set up some directed evolution to screen for mutant polymerases that will do a better job of it.

      This is kind of neat, but the medical applications of this are pretty limited. First of all, it's unclear if RNA polymerase is able to perform the same reaction, or if only DNA polymerase can. If RNA polymerase can't insert a 3FB base opposite a 3FB base, then this news will basically go nowhere. An expanded genetic code is useless if it's confined to DNA only. The information in the DNA has to get into the RNA before protein can be synthesized, and it takes an RNA polymerase that can insert 3FB in order to do that.

      However, even if RNA polymerase or a mutant will perform that addition, there's currently no use for it. There are no natural tRNAs that will pair with a codon containing 3FB, and even if you add some 3FB-containing tRNA genes to an organism, you still have to get an amino-acylation enzyme to strap an amino acid to that tRNA (not a trivial thing), and if you do, it'd have to be a novel amino acid to really mean something. Otherwise, you've just found an extremely difficult way of doing what could have been done with the machinery that's already in place.

      This is kind of cool and all, but if Slashdot posted an article every time some scientist found a non-natural function of a given enzyme, it'd completely drown out all the articles hating on the RIAA, and we can't have that.

    10. Re:These are bases not amino acids by Atmchicago · · Score: 3, Informative

      All the bases do are code for amino acids

      That's actually not true. A lot of DNA bases are important in mediating binding to proteins, such as RNA or DNA polymerase, histones, etc. Other bases are important in RNA-based regulator mechanisms, such as anti-terminators.

      So the truth is that although we can't really say what we can do with these extra bases right now, the possibilities extend way beyond making new proteins and have many implications for regulation. Why is regulation important? Because differential gene expression is the fundamental principle that allows for cell differentiation and mediating responses to external change.

      And for the record, IAAB (I am a biologist).

      --

      You can lead a horse to water, but you can't make it dissolve.

  4. Still missing critical information by Raul654 · · Score: 4, Informative

    For those of you who forgot your biology, 3 DNA consecutive DNA base pairs (called a codon) are translated into a single amino acid. (Khorana, Holley and Nirenberg won the 1968 Noble prize in medicine for figuring this out and determining the mapping from base pairs to amino acids)

    So, after reading the technical article, it says that DNA polymerase can bind to the new base pairs (allowing it to replicate), but it doesn't say what amino acids (if any) these new base pairs code for. That's important information because this alleged breakthrough is useless if it doesn't so something useful where proteins are concerned.

    --


    To make laws that man cannot, and will not obey, serves to bring all law into contempt.
    --E.C. Stanton
  5. Re:I for one... by eviloverlordx · · Score: 4, Funny

    The Island of Dr. Moreau called; they want their genetic manipulation with unintended consequences back. I told the caller to take a number.

    --
    'Loose' is when your pants are three sizes too big. 'Lose' is when you misuse 'loose'.
  6. Re:I might be wrong but by Spy+der+Mann · · Score: 2, Informative

    Has this not already been posted?

    Yes, it has.

    Tagged oldnews.

  7. Article? by Rob+Simpson · · Score: 2, Insightful

    This is a crappy nonsensical blog post about a news story from three years before.

  8. Old News by dwye · · Score: 3, Interesting
    We have seen this before. The new bases just make new STOP codons, until someone creates new types of MRNA and/or TRNA to let the mitochondria process them to add a matching amino acid.

    Where is the whatcanpossiblygowrong tag, like last time? Have the Luddites left, already?

  9. Bronze Age by wcrowe · · Score: 3, Insightful

    'It takes time to figure out how best to use metal.'

    I don't think it took too much time to figure out that the best use of bronze was to make it sharp and run someone through with it.

    --
    Proverbs 21:19
  10. In the brave new world of patented genetics ... by winomonkey · · Score: 2, Funny

    ... all your base are belong to us.

  11. "DNA Origami" by peter303 · · Score: 2, Informative

    Nanotechnology can coerce the DNA sugar (ribose) into exotic chapes like tri-helicies, platonic solids, etc. However there are no known biological applications of these exotic molecules. They mainly demonstrate the increasing skill of nanotechnology.

  12. Re:Maybe good for nanotech, but probably not genet by ChromaticDragon · · Score: 2, Insightful

    I would suggest your logic here is flawed or at the very least belies a bit of a gap in understanding how evolution works.

    All the other folk who have commented that this is like giving artists new colors nobody can see are perhaps a bit closer.

    Once we got started with anything even close to DNA, I would imagine we were more or less locked into that pattern. Evolution branches more so than tries all permutations and possibilities. It seems far more likely that once life got going with all the support systems (RNA, tRNA, etc.) and current coding mechanisms that it would have been very difficult to "back up" and try something new. Evolutionary history is full of examples like this where for what a lifeform is doing at the moment something else would be a bit better (human eye and blind spot?) but there is no going back, per se.