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The Biggest Piece Of DNA Ever Made 70

Posted by Zonk
from the how-long-is-it dept.
An anonymous reader writes "Forbes has a story on 'the biggest piece of artificial DNA ever made'. The real story is that companies are racing to produce longer and longer DNA fragments to serve the growing science of synthetic biology." From the article: "On a piece of DNA as long as the one made for Microbia, ten or more genes may be present. By studying more than one gene at once, researchers hope to get a better picture of how they work in concert to produce an organism. Another advantage: These stretches can also be made to contain all the DNA letters that occur between genes. Scientists once thought of that stuff as junk, but many now believe it may regulate how the genes work or provide some other function."
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The Biggest Piece Of DNA Ever Made

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  • by yams69 (986130)
    How about "bases" or "base pairs"? Are they creating a string, or DNA? Granted, Forbes ain't a science rag, but still...let's show our readers we took some high school biology.
  • by Rob T Firefly (844560) on Friday July 14, 2006 @11:02AM (#15719462) Homepage Journal
    These stretches can also be made to contain all the DNA letters that occur between genes.
    Such gene patterns have also been found in the quick brown foxes which jump over lazy dogs.
  • "junk" DNA (Score:5, Insightful)

    by Scrameustache (459504) * on Friday July 14, 2006 @11:10AM (#15719523) Homepage Journal
    Ah, "junk" in biology.
    There was a piece of the brain that was once thought of as "junk", or "filler", until it was removed by a zealous neurosurgeon during an operation in that region of the brain of his patient. The patient unexpectedly lost the ability to learn new things (as in Memento)... Now we know.
    The pancreas was once though to serve simply as a support structure for the more obvious organs...
    Beware the tendency of the very litterate to dismiss that which they do not understand, it's simple hubris.

    My not-supported-by-resasearch-of-any-kind take on "junk" DNA?
    I think it's stored evolution.
    DNA that isn't expressed, but stored in a way that it can mutate for generations and generations before being randomly reactivated, cueing natural selection. That would result in a simple mutation (only the reactivation of a chunk of stored DNA) with not-so-simple results from generations of stored changes.
    • by timster (32400) on Friday July 14, 2006 @11:15AM (#15719570)
      Yes, and 25 years from now we will all rue the day when surgeons thought they could extract the Zombification Prevention Organ with impunity, as if it were a mere "appendix".
      • Yes, and 25 years from now we will all rue the day when surgeons thought they could extract the Zombification Prevention Organ with impunity, as if it were a mere "appendix".

        Phbtbtbt!!! If that were true, we would have noticed a statistically-valid elevation in the number of people who have had their appendix removed becoming zombies by now.

        So far, the number of zombies with and without their appendix seems to be about equal. Shows what you know!!!

        =)

        Cheers

      • by csoto (220540)
        All the more reason to enact my Protection Against Zombies Act. PAZA will require the removal of teeth and/or dental fixtures prior to the burial of the deceased. After all, zombies aren't much of a threat if the worst they could do is gum you...
      • Point timster.
    • So, the "non-junk" DNA that gives me my male nipples (and an office mate 2 additional superfluous nipples, which is truly a must see freak show), is actually just stored evolution so that one day my children's children's children's children's children can be breast fed by their fathers? Somehow I think not.

      To me a more logical explanation of the filler DNA is to act as a buffer against flaws. If .1% of all your DNA is clobbered by the radiation from a full-body X-ray or a vacation to Hawai'i or from your

      • Re:"junk" DNA (Score:3, Informative)

        by DarthStrydre (685032)
        In soviet Russia, your children can be breast fed by you.

        However odd it may be, human males have the ability to breastfeed, though since pregnancy is impossible, most people do not realize it. Granted, I am not sure the feasability or usefulness, but it is physiologically possible in certain cases.

        http://en.wikipedia.org/wiki/Male_lactation [wikipedia.org] for a start to your research, and the end of mine.
      • Re:"junk" DNA (Score:2, Interesting)

        Isn't that kinda what he's saying? The extra DNS means that a mutation results in an altered species that may or may not be viable. If it weren't for the extra DNA the result would be dead offspring, which doesn't help evolution any. Mutations are random, which means they can be good (opposable thumb), bad (various genetic problems) or ugly (superfluous nipples). What makes a mutation ugly is subjective. What makes a mutation good or bad is decided by natural selection. Most mutations will fall into the bad
      • adding junk data does not protect against %damage because the quantity of damage goes up proportionally to the amount of junk

        it is much more likely that junk dna is really just "compressed" or "encrypted" DNA. not in a deliberate sense so much as some processes rather than reading straight off a segment of DNA use one part to decide what parts of what other strands to read and produce RNA from.
      • If .1% of all your DNA is clobbered by the radiation from a full-body X-ray or a vacation to Hawai'i or from your CRT monitor while reading slashdot, wouldn't you rather it be the .1% that doesn't matter?

        This is more or less akin to leasing every apartment in your building so that if you get .1% broken windows, the likelihood of the broken window being in the apartment you live in is reduced. It doesn't work that way. Most mutations seem to be caused by cosmic radiation and the like. If you have more DNA, y
      • To me a more logical explanation of the filler DNA is to act as a buffer against flaws.

        Nothing in biology has a "purpose". It isn't like a car where every part serves a well thought out function. You can find some organs with single well-defined functions, like the heart, but most serve a range of ill-defined roles. Bones, for example, are making white blood cells. The liver does all sorts of stuff. Everything happens because it happened before in a way that it can happen again. Everything is needlessly com
      • No, your male nipples are for breastfeeding, just like those of the fairer of the species. Most guys can do it, it just takes more coaxing, because we (obviously) don't have the "pregnant" hormone changes to kick it off.
    • As I understand it, "junk" DNA still serves useful known purposes. In particular, just about everything in the genetic world seems to have regulatory function in terms of the transcription process. Also I suspect there are some structural benefits to having this extra DNA in there.
      • Yes, it provides room for an activly coding region to be unzipped and transcoded without neighboring active coding regions being activated or ever touched.
      • I've heard the argument made that one of its purposes is an evolved defense against viruses. The real genetic data (the exons) are scattered amongst garbage data (the introns), and when it's needed the exons are extracted and spliced together, with the introns just being thrown away.

        The use of splicing is a defence against viral attack because the virus would need to be sure to insert its DNA into an exon. If it inserts its DNA into an intron, it will just get thrown away. If it inserts it half into an e
    • Re:"junk" DNA (Score:5, Interesting)

      by ultramk (470198) <ultramk@noSPAM.pacbell.net> on Friday July 14, 2006 @11:50AM (#15719902)
      The argument you're making isn't a new one, but the main piece of evidence against it is pretty compelling. "Genetic drift" is a phenomena where over time, random mutations add up to change areas of DNA. The thing is, if the DNA in an area is used for something that is important to keep the organism alive (or gives some sort of reproductive advantage), it can't take too many changes or the organism will die (or not be able to reproduce, very much the same thing from an evolutionary standpoint). So you get some areas where there are lots of changes, and areas where there are essentially no changes.

      Picture it this way, you have a fleet of 500 Geo Metros starting out in Kuwait City, with direction to drive north to Turkey through Iraq. The whole time, guys with AK47's are taking pot shots at them (random mutations). For the ones who get all the way to Turkey, you'll find that none of them have sustained major damage to their engines/coolant systems/drivetrain/tires (because if they had, they wouldn't have made it this far). This is one way of identifying what's important to the functioning of the organism. You can drive without windows or an air conditioner, but without a transmission you're screwed.

      Beware the tendency of the uneducated to assume that people who devote their lives to a subject haven't considered the most basic of possibilities. It's simple hubris.

      m-
      • Good that at least someone made this point. What's more interesting is of course that for structural regulatory purposes, the effects of single point mutations can be quite minimal. If we need to put exactly one histone package between a binding site and the gene itself for the regulation to work properly, then it might be totally irrelevant what that sequence contains, but it's still not possible to just remove it and get no change in function.
      • Car analogy, fascinating.
        Now, exlain how the hell that relates to what I said.
        Though you might have to -read- what I said, this time.

        P.S. Ooooh, a condescending tone followed by an assumption that I'm uneducated. Someone has issues he feels will be helped with some anonymous passive-afressive behaviour!
    • I've read studys suggesting that a lot of the "junk" DNA is actually more on the line of a biological CRC checksum. If that is the case, it'll have pretty solid ramifications for any sort of genetic manipulation...Wouldn't want your spliced DNA "correcting" itself in the next generation.
      • True in a sense, the long, supposedly identical, sequences, might help chromosomes align during meiosis (creating of sex cells), but that's the case anyway, one will keep lines and do repeated inbreeding until we've a homozygothic line for the new trait. (Germ line modification of humans without IVF would of course also introduce this, but that's far away.)
    • "Junk DNA" is a significant misnomer among lay people. Genetists have a reasonably good idea about what much of it actually is. Some of it pretty much what you said, redundant copies of genes which, modified over time, may become activiated again and serve some useful function (although it may in fact do nothing at this point) Large portions of it are retroviral remanants, DNA inserted into genomes by retroviruses in the distant past, that have since mutated and become more or less non-functional (the d
    • awesome job, misspelling "literate". that's hilarious.

      no, no: it's hilareus.
  • by DavidV (167283) on Friday July 14, 2006 @11:14AM (#15719560)
    A friend once got told size doesn't matter, it's what you do with your DNA. Yeah..it was a friend...nothing to do with me. I'm lucky if I don't trip over my DNA.
  • Compels me to make this stupid joke about the biggest piece of dna once belonging to a Brontosaurus. Why oh why do I listen to my inner class clown?
  • by Anonymous Coward on Friday July 14, 2006 @11:27AM (#15719679)
    You know, I bet if we unravelled that sucker,
    It'd roll all the way down to Fargo, North Dakota
    'Cause it's the biggest DNA in Minnesota
    I'm talkin' 'bout the biggest DNA in Minnesota

    - with apologies to Weird Al Yankovic, Biggest Ball of Twine in Minnesota [com-www.com]
  • exons/introns (Score:5, Informative)

    by smellsofbikes (890263) on Friday July 14, 2006 @11:36AM (#15719749) Journal
    >Scientists once thought of that stuff as junk, but many now believe it may regulate how the genes work or provide some other function.

    To clarify: a stretch of DNA that actually gets turned into RNA and thence into proteins is an exon, and the DNA that lives between exons is called an intron. It's been known for a long time that there are sequences before an exon that control it: regulators, promotors, and repressors, that are activated or deactivated by proteins binding to them during DNA reading, and in some cases there are sections of DNA that are processed into RNA, that help stabilize the RNA and are then clipped out before the RNA becomes protein, so they also have a function. (This is part of the reason that making insulin artificially has been tricky: you can't just stick the DNA into a bacterium and have it crank out insulin because the DNA is in a couple sections and requires post-processing.)

    Also, many of the introns contain echoes of old sequences that used to be useful way back when, and aren't anymore, or bits of viruses that integrated into the genome hundreds or thousands of generations ago and are now widely spread in the population, and some intron bits are designed to facilitate shuffling of chunks of DNA into different orders for proteins that come in a wide variety of flavors with the same start and end sequences. Antibodies, for instance, have long, consistent, identical start and end chunks with wildly variable center chunks. (Think of a key, with differing teeth to fit various locks, but the same end piece, to fit your hand. Likewise an antibody has a hypervariable section that, for each antibody, can adhere to precisely one antigen, and a nonvariable section that signals passing cells that it has/hasn't found any of that antigen.)

    Getting to go play around and make any set of repressor/promoter sequences and change the distances between them is a really nice tool, and being able to make massive sequences like this, helps play with gene interactions and with massive proteins like antibodies. Think of this as the beginnings of the transition from transistors to integrated chips, or maybe it'd be more apt to say from single computers to the beginnings of networks.
    • Re:exons/introns (Score:3, Informative)

      by cnettel (836611)
      Well, isn't the most important part of pro-insulin that it's ONE amino-acid chain that's then cleaved, with retained cystein bindings? Posttranscriptional modifications are easy, "just" give the host a cDNA. Post-translational modificatins are harder.

      Anyway, your description might lead people to assume that most of the DNA present in a human that's not an exon would be an intron or a sequence of direct regulatory use. That's obviously not the case, or at least the regulatory effect is very limited in, for

      • Re:exons/introns (Score:3, Interesting)

        by smellsofbikes (890263)
        A lot of the junk in there IS junk -- detritus from long-past viruses and stuff like that. A lot of it we have no idea. Some of it is clearly regulatory. Now we're beginning to get reliable tools that tell us which is which.
        I just think the summary is misleading in the same way that an extron/intron duality implies: it says that there are two categories of DNA, expressed DNA and junk. That's clearly not true, and it's been known for 50 years that that's not true. The big question is exactly how not tru
        • Consider the possibilty that many of those introns are actually firmware. Code to be used to program the brain.

          • Instinctual behavior comes from somewhere. Fear of falling is not simple: you have to recognize what height is. Sight, abstraction to positional awareness, risk assessment. That's a whole lot of code. (And a lot of code down the drain when you stick the baby in one of those thingies where they can walk around with wheeled support to keep them from falling over, and walk right off the edge of the stairs. It's horrible to laugh at that, but, dude.)
  • Huh.

    I figured this was some sort of bukkake story.

    thank you folks, I'll be here all night. Tip your waiters!
  • I routinely make longer DNA sequences, and give the shorter ones away as gifts to women who I like.
  • I've created customized a string of DNA and put it on a bumper sticker. The genetic sequencing of letters spells out: If you can read this you are too close
  • by exp(pi*sqrt(163)) (613870) on Friday July 14, 2006 @12:40PM (#15720296) Journal
    Isn't it time to stop talking about "junk DNA" as being junk? The idea that it might not be junk has been popular in the popular science press for decades now. Presumably the idea that it's useful has been around for much longer in academia. Every single article I have ever read in the last decade that mentions the stuff points out that it might serve a purpose. So isn't it time to stop saying "Scientists once thought of that stuff as junk" just like you no longer have to preface every discussion about relativity with the statement "people used to think there was an absolute zero velocity with respect to which the aether was at rest". It's kind of insulting, don't you think?
    • Well, just because some of it may have important functions, a lot of it probably doesn't. I mean, with random mutations, viruses inserting their stuff, old genes becoming obsolete, etc, a lot of stuff could end up in your DNA. And unless you believe in continuous divine intervbention at that level, there would really be no efficient mechanism to "clean up" any stuff that does nothing, as long as it does no harm. Why should there? It might be more exposed to loss and damage than other DNA, since it will no
      • there would really be no efficient mechanism to "clean up" any stuff that does nothing
        How do you define "does nothing"? If you mean "isn't transcribed", sure. But DNA can serve structural purposes, act as sites for various types of receptor binding and possibly serve other purposes we haven't figured out yet. People have known for a long time now that untranscribed DNA might serve all kinds of interesting purposes.
  • not as big (Score:2, Informative)

    by Onymous Coward (97719)
    Here's some DNA that's 6" big:
        http://www.bathsheba.com/crystal/dna/big.html [bathsheba.com]

    If that's too big for you, they also have:
        http://www.bathsheba.com/crystal/dna/ [bathsheba.com]
  • To put this in context, a PhD student at the lab I'm working at this summer spent a year and a half constructing a ~7,000 base pair gene for her research using normal cloning methods. I've personally been struggling to clone and express a very small gene construct (~250 bp) for the past month. The ability to synthesize any DNA sequence would be every bit as significant as the recent genomics and bioinformatics revolution. Researchers could study entirely novel and specific variations of natural genes by

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