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Biotech Science

First DNA Molecule Constructed from Mostly Synthetic Components 188

Posted by ScuttleMonkey from the add-another-helix dept.
ScienceDaily is reporting that Japanese chemists have created the world's first DNA molecule comprised of almost entirely artificial components. The breakthrough could lead to advances in both medicine and technology, possibly utilizing the massive storage capacity of DNA. "In the new study, Masahiko Inouye and colleagues point out that scientists have tried for years to develop artificial versions of DNA in order to extend its amazing information storage capabilities. As the genetic blueprint of all life forms, DNA uses the same set of four basic building blocks, known as bases, to code for a variety of proteins used in cell functioning and development. Until now, scientists have only been able to craft DNA molecules with one or a few artificial parts, including certain bases."
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First DNA Molecule Constructed from Mostly Synthetic Components More

First DNA Molecule Constructed from Mostly Synthetic Components

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  • Well it's been done for many decades. The trick is making the sequence longer & automating the process to not require an army of grad students.

  • For info storage? Nice idea in theory but... (Score:3, Insightful)

    by Viol8 ( 599362 ) on Monday July 07, 2008 @01:02PM (#24085789) Homepage

    .. DNA decomposes from bactierial , chemical and radiative action so can't just be left on its own locked away for years.

    DNA is read slowly by biological means which is hardly easy to interface to digital systems.

    DNA is read sequentially , its not random access at the base level making it useless for most types of database.

    Current technologies could in theory already be pushed to have greater storage density than DNA - eg transistors made from a few atoms.

    So other than an interesting intellectual exercise , whats the point?

    • Re: (Score:2)

      by Ed Avis ( 5917 )

      One property DNA has that transistors don't is that with some enzymes and spare base pairs it can copy itself. You can dissolve lots of copies in a liquid and spray it about to have redundancy. Whether this is useful, I don't know. I doubt that pouring a test tube of synthetic DNA into the ocean and letting it reproduce itself and diffuse around the globe will replace Bittorrent any time soon.

      • Re: (Score:3, Interesting)

        by mikael ( 484 )

        There was article some time where the scientists demonstrated how it was possible to solve the "Travelling salesman problem". Different strands of DNA were constructed to represent the different route segments that were possible and replicated. These were all mixed up together in a container and stirred together. As they were mixed together different strands would join up.

        The solution to the problem was the shortest strand that had the starting point and ending point, along with each and every route destina

        • Re: (Score:3, Informative)

          by FunkyELF ( 609131 )
          I remember that. I didn't RTFA but what you're talking about is DNA computing, not DNA storage. The traveling salesman problem worked with a very, very small graph. I don't remember if the graph was even weighted. Anyway, when you analyze what was going on, they basically did a brute force search which wasn't even guaranteed to find the solution (except for statistics). They basically randomized a ton of DNA which they hoped represented every permutation of the cities the salesman could travel. Then t

    • Re: (Score:3, Informative)

      by backslashdot ( 95548 )

      What "it's sequential at the base level" have to do with anything? Even in a database once you get to the address of a specifc blob of data .. you need to read off a sequence of characters right.

      Unless you mean that to access a specifc data region the DNA must be read sequentially? So if a cell needs to make a protein from say the middle of a chromosome it has to unravel and read through the entire chromosome?

      I don't think so.

      When a protein is needed, a transcription factor is used that attaches to a specif

      • Re: (Score:2)

        by Viol8 ( 599362 )

        So are you going to have an infinite number of transcription factors then for every possible piece of data stored in the DNA?

        I don't think so.

        DNA is a effectively a hard wired database where the required data/protein recipes must exist for the cell to work. The cell doesn't just make up new proteins as it goes along unlike a database which can store any combination of data anywhere in any given amount (up the maximum) at any time and said data can be updated or deleted at any given time.

        Try doing that with

        • DNA is a effectively a hard wired database where the required data/protein recipes must exist for the cell to work. The cell doesn't just make up new proteins as it goes along unlike a database which can store any combination of data anywhere in any given amount (up the maximum) at any time and said data can be updated or deleted at any given time.

          That's not true. Retroviruses for example are quite adept at inserting themselves into a specific location within DNA of a host cell. So yeah, it's possible to in

          • Re: (Score:2)

            by Viol8 ( 599362 )

            "Why infinite?"

            Err , because you can choose to search for anything in a database. It doesn't have to actually be in there.

            • That's not an addressing problem though, a search can just go through the whole database incrementally and return the required information when you find it with no need for an address. Kind of like using a limited linked list where you always have to work from the head and can never directly address anything else.

              Besides, if something isn't in the database, there will be no need for an address for it anyway, so you don't need infinite addresses for infinite search terms.

              If you want an infinitely large datab

    • Re: (Score:2)

      by Rei ( 128717 )

      Perhaps computer interfaces may be a bit of a stretch, but the potential for custom DNA sequences, whether it's to make new drugs or do nanoengineering for things like solar panels or battery components, is tremendous.

      While I doubt it would work with artificial bases, since I doubt you could readily get DNA made of artificial bases to reproduce inside an organism one of my favorite potential uses for "ordinary" custom DNA sequences is to eradicate invasive species. You need to make "greedy" (parasitic gene

  • Who cares? (Score:5, Funny)

    by eln ( 21727 ) on Monday July 07, 2008 @01:05PM (#24085831)

    This is nothing new...I created a DNA molecule out of entirely synthetic components for my 5th grade science fair project. Mine was made out of colorful wooden balls glued to wooden sticks. Theirs appears to be sugar-based, which would probably attract ants, so mine is obviously superior.

  • You know, because it'd be nice to know if life can be built on a different set of elements.

    • Re:Can they use silicon in place of Carbon? (Score:4, Informative)

      by clonan ( 64380 ) on Monday July 07, 2008 @01:16PM (#24086013)

      They can...but you wouldn't want to.

      Silicon also has 4 bond sites which you need for the complex chemistry of life. You can make identical molecules except switch silicone for carbon.

      But life will almost certainly NOT do this elsewhere.

      Silicon chemistry takes more energy than carbon chemistry.

      As an example I will point to earth. Silicone is hundreds of times more common than carbon in the crust yet life did not evolve to use Silicone, it instead used the less common carbon.

      • Re: (Score:3, Informative)

        by Relic of the Future ( 118669 )
        I don't normally nitpick, but you made the same confounding error multiple times in one post: silicon and silicone are two different things. One is a chemical element, the other is a group of polymers which contain the element.

      • Yeah, imaging breathing out sand (Mommy-2 style)

      • Under Earth-like environmental conditions, carbon has several advantages. But what happens when you move away from Earth's environment? Suppose that the ambient temperature on LV-426 was substantially higher than on Earth. Put it somewhere favorable to silicon, but disadvantageous to carbon. Are you absolutely certain that carbon would still rule the roost?

        Honestly, I tire of people who are convinced that earth-life is the only possible solution. It works here. Fine. Change the environmental condit

        • Re:Can they use silicon in place of Carbon? (Score:4, Interesting)

          by clonan ( 64380 ) on Monday July 07, 2008 @02:43PM (#24087185)

          Yes...I am still convinced that carbon would rule the roost.

          In order for silicon to even remotely compete, Silicon dioxide would have to be gaseous. At the several hundred degree higher temp, large and complex molecules become unstable.

          In addition silicon is a larger atom which creates a greater limit on structures than carbon.

          Carbon would still be used with Ammonia. Using methane absolutely requires carbon (methane being a hydrocarbon).

          There is no known condition in which silicon would be preferable while still allowing for large complex molecules.

          I get annoyed when people ignore basic physics and chemistry for their own pet beliefs.

        • Re: (Score:2)

          by clonan ( 64380 )

          However on further though let me add that while I don't think life would EVER spontaneously arise using silicon, it would be theoretically possible to artificially create a silicon based life.

        • Re: (Score:2)

          by oni ( 41625 )

          Honestly, I tire of people who are convinced that earth-life is the only possible solution.

          Don't take this personally, but I tire of people whose imaginations outstrip observed evidence. I can imagine all sorts of things - silicon-based life is just one of them.

          But reality is that we're not finding life in places where modern-day earth life could exist, and we're not seeing or hearing evidence of intelligent life elsewhere in the galaxy. I know that we've only begun to search, but we already have enough evidence to say for a fact that life is not ubiquitous.

          So here's what we know: 1) once life

          • Re: (Score:2)

            by clonan ( 64380 )

            I very much agree with you with one exception:

            2) but it's apparently *really* difficult to get life started.

            we don't have the telescope resolution to really see if life exists elsewhere. We can't see earth sized planets and we can't analyze the atmosphere of the ones we do see. Life COULD exist there and we wouldn't know it.

            All we can say is that intelligent life at the industrial age or better (which is when we could have a chance of detecting them) is non-ubiquitous.

            • Re: (Score:2)

              by oni ( 41625 )

              we don't have the telescope resolution to really see if life exists elsewhere.

              Yes, you're right.

          • Hang on a second, and let's examine exactly what predicates "life." You need to have raw materials available. There needs to be an energy gradient. There needs to be a closed-cycle chemical reaction for the transport of energy. There needs to be a solvent for the mechanical transport of chemicals.

            On Earth, we've got the solar influx for the energy gradient, water is the solvent, and the carbon compounds provide the chemical-reaction basis. Environmentally, the Earth's temperature and atmospheric pr

            • Re: (Score:2)

              by oni ( 41625 )

              Why is that such a fantasy?

              What you just said isn't a fantasy, because you were able to back it up with sound reasoning. My complaint is people who talk about silicon for no other reason than that they saw it on star trek.

              • I should further clarify that I'm not suggesting that you could substitute silicon for carbon, and end up with bipedal hominids who strongly resemble us ... only with silver skin. That's Hollywood working within their abilities to map actors into roles. I'm thinking substantially more basic life. Think one-celled critters; bacteria; viruses.

                I was watching some coverage of NASA's recent earthmoving (marsmoving?) efforts, and was stunned at just how stoopid the reporters can be. I expect that the NASA
      • I wonder if on a planet that has no Carbon and an over-abundance of Silicon (obviously an exteme case - but not impossible) if life could evolve using silicon. I mean, when you really come down to it, life could be Germanium, Tin or Lead based by the same arguments, it's just "easier" for Carbon-based to start up. Does anything stop other elements from forming the basis of life? Say Boron (assuming a Boron rich environment void of Carbon and Silicon)?

        • Re: (Score:2)

          by clonan ( 64380 )

          Life really isn't possible for anything but Carbon or Silicon. The reason I can say that is the number of bonds. 4 bonds allow for extensive and complex networks which complex chemistry requiers. Boron, tin, lead etc can't do this.

          We essentially live on a planet with an over abundence of silicon and a virtual absence of carbon. Silicon is so much more plentiful than carbon it is almost silly. On proto-earth the only availible carbon source was the atmosphere and in a water world, like earth, air is a l

      • Re: (Score:2)

        by Pedrito ( 94783 )

        You can make similar molecules using silicon, but you can't make identical molecules. If you took say, a protein, and replaced all the carbons with silicon, that protein would not function. I'm not even certain the protein would remain intact. I'm not aware of any large, complex molecules, on the scale of a protein, made with silicon as the primary backbone. Silicon chemistry simply doesn't lend itself to large, complex, molecules.

  • Entertaining Theological question... (Score:4, Insightful)

    by fuzzyfuzzyfungus ( 1223518 ) on Monday July 07, 2008 @01:09PM (#24085893) Journal
    We have a sequence of a human genome and are likely to produce more in the future.
    We can, albeit presently with difficulty, construct DNA sequences from artificial materials.
    We can, in principle, produce viable eggs by nucleus transfer from one egg to another.

    If a "human" embryo is produced from synthesized DNA and by nuclear transfer into an egg from artificial or animal sources, the resulting organism will be structurally equivalent to human, without any physical connection to the human race.

    Does this organism have a soul? Is it subject to original sin?


    Angels and heads of pins aside; this is pretty cool. There is, though, a slightly unpleasant possible outcome of being able to synthesize DNA sequences. Certain viral pathogens, smallpox comes to mind, are very, very hard to get ones hands on. Samples are tightly controlled and generally not allowed out to play. This is a Good Thing. Genetic sequences, however, are public knowledge. In principle, with sufficient expertise in DNA synthesis(and some protein coating wizardry) one could just "compile" some smallpox from source and then go have a smallpox party with the nearest population center. Happy times.

    • Re: (Score:3, Interesting)

      by the_brobdingnagian ( 917699 )

      Does this organism have a soul?

      Do you (or anyone else) have a soul? Why would a "synthetic" human be any different?

      • Well, I don't believe in souls or, for that matter, any metaphysical entities; so the question is moot for me. However, I find theology interesting as a theoretical exercise and I would be quite interested to see what a theologian, or even a suitably pious layman, would say on the subject.

        I'm an atheist and a materialist, so such an organism would be little more than a curiosity; but would be considered human because structurally so. It just struck me as an interesting example of something where technolog

        • Re: (Score:2)

          by CODiNE ( 27417 )

          If one is a Jehovahs Witness or Seventh Day Adventist then a "soul" is simply a living, breathing creature such as birds,fish insects and mammals. In the first 2 chapters of genesis "and on the fourth day God created fish", etc... They are all referred to as "living souls". Numbers 6:6 states that touching a "dead soul" makes a person "unclean". In other words a corpse. The bible agrees with your materialist views of physical life, but many bibles have been written to change words to match preconceived reli

      • Do you (or anyone else) have a soul?

        To clarify the common misconception that a "soul" is some ghostly thing inside a person: as CS Lewis once said "You don't have a soul. You are a soul. You have a body."

        You don't have to be religious to believe in the existence of the soul. That word is just a description of that which is emergent from a sufficiently complex neurological system (i.e. thoughts, feelings, personality, etc.).

        • I think I agree with you on the definition of a soul, but many people have a more supernatural definition.
          My point was: "Make op your own mind about what a soul is. Then using your definition of a soul determine if a synthetic human has enough differences with us to make it a soulless being."
          My answer would be: Yes, we have souls and so would these synthetic humans.

    • Does this organism have a soul? Is it subject to original sin?

      More importantly, does this organism have the same rights as other human beings?

      The sane amongst us would probably say "of course it does, it is a living, breathing, thinking human". Unfortunatly the sane aren't always in control. Living, breathing humans have been enslaved, tortured, and murdured throughout our history, often without consequences when one can simply claim "they aren't really human, they're black or jewish or a terrorist...".

    • If we teach 2 other non-standard pairs of bases to code the same 20 aminoacids and be capable to provide an organism with these nonstandard nucleotides and if we will modify DNA polymerase so it will only replicate those non-standard bases-based DNAs, then we will be protected from ALL viruses.

      • If we teach 2 other non-standard pairs of bases to code the same 20 aminoacids and be capable to provide an organism with these nonstandard nucleotides and if we will modify DNA polymerase so it will only replicate those non-standard bases-based DNAs, then we will be protected from ALL viruses.

        You know, that's an awful lot of work. Easier just to boot up a linux distro.

    • If a "human" embryo is produced from synthesized DNA and by nuclear transfer into an egg from artificial or animal sources, the resulting organism will be structurally equivalent to human, without any physical connection to the human race. Does this organism have a soul? Is it subject to original sin?

      I don't see why an artificially created human embryo would not eventually develop a soul (i.e. thoughts, feelings, identity, etc.) like a natural human embryo. If the structure is the same, I don't see why t

    • Re: (Score:3, Insightful)

      by ShieldW0lf ( 601553 )
      If it is capable of breeding true with other humans, then it's human. If it's not, it's not. Pretty simple.
    • Does this organism have a soul? Is it subject to original sin?

      If you're a materialist, the answer is simple: no, because we don't either. If you're not, however, I think the question is equivalent to whether or not it's a philosophical zombie. The good news for that standard is that it's universal: a truly conscious AI has just as much a soul as a human. The bad news is that you can't measure it (unless there are some things philosophical zombies just can't do, which would also give a reason for why evo

  • the SAME building blocks?! (Score:4, Informative)

    by Red Flayer ( 890720 ) on Monday July 07, 2008 @01:16PM (#24086005) Journal
    I know it's nitpick-y, but

    As the genetic blueprint of all life forms, DNA uses the same set of four basic building blocks, known as bases, to code for a variety of proteins used in cell functioning and development.

    This isn't quite true. DNA is the genetic blueprint for all cellular lifeforms. There are RNA viruses, there are prions... neither of which use DNA as their genetic blueprints.

    And to get really nitpick-y, it's incorrect to say that DNA uses the same set of four building blocks. It would be "more" correct to say that DNA uses a set of four building blocks. I mean, it'd be rather ridiculous if every lifeform on the planet had to share just four molecules.

    But, it's not as if we should expect an article geared towards an ignorant public to be completely accurate... the gist was captured.

    Anyway, I think I just managed to pedantically get "the Mondays" out of my system... sorry for the rant.

    • Re: (Score:3, Informative)

      by ComaVN ( 325750 )

      Viruses and prions are not, generally, considered to be alive.

      • That's still a topic of debate, wrt viruses especially.

      • I admit my immense ignorance of everything cellular biological but I don't quite get what you're saying.

        Viruses possess an ability for locomotion and propagation. They also feed, discriminate against certain agents and other cells.

        They are also 'squishy'(the best definition of life as I know it so far).

        How is a virus not alive simply because it doesn't have adenine, thymine, cytosine, and guanine all twisted up inside a cell nucleus like a cheese string?

        (Not being snarky, I'm honestly curious.)

        Prions I get

    • Re: (Score:2)

      by hyfe ( 641811 )

      As the genetic blueprint of all life forms, DNA uses the same set of four basic building blocks, known as bases, to code for a variety of proteins used in cell functioning and development.

      This isn't quite true. DNA is the genetic blueprint for all cellular lifeforms. There are RNA viruses, there are prions... neither of which use DNA as their genetic blueprints.

      I'm not a native speaker, so the definitions in english might not be entirely the same, however viruses aren't generally considered to be alive si

  • Now I can store pirated music in my DNA!

  • Stress on base pairs (Score:4, Informative)

    by Orleron ( 835910 ) on Monday July 07, 2008 @01:20PM (#24086083) Homepage
    I don't think the summary stresses the base pairs enough. We have been able to synthesize DNA from the regular naturally occurring base pairs for a long time. This article is special because it talks about synthesizing DNA from unnatural base pairs, which several labs are working on, albeit with bacteria not chemical synthesis.

    I also detect that some folks may not understand the implications. Right now the given combination of natural DNA base pairs can only code for the 20 base amino acids used in nature. If we could create a DNA system that can code for other types of amino acids (in addition to or instead of), we would be able to make some very interesting proteins that would do gods know what, but would make for some great possibilities.

    • Re: (Score:3, Interesting)

      by comm2k ( 961394 )
      The current 4 bases allow 64 combinations (codons). Yet they're only 20 (actually 1 or 2 more) amino acids coded by them (- stop). Introducing new bases does not overcome this limit - the limit is in the tRNAs which are complementary to more than 1 codon. You would also have to create tRNAs complementary to your new codons and for that to be efficient you would need compatible enzymes loading these tRNAs with your new amino acid.
      The latter part is actually far more work then creating this type of 'artific

  • Not Synthetic, Artificial (Score:4, Informative)

    by burris ( 122191 ) on Monday July 07, 2008 @01:21PM (#24086099)

    This isn't a case of synthesizing familiar, natural DNA from scratch. That's been done for years and this research was done on commercial equipment for doing so. These researchers created a new type of DNA using four bases that are each similar to but distinct from the four bases that are found in natural DNA. A new chemistry basically. The article suggests that previous attempts had been unstable but this one is not. This could lead to advances like creating DNA molecules with more bases, to increase the density of storage, or find chemistries that are particularly amenable to manipulation, or who knows what.

  • Doesn't anyone RTFA? (Score:5, Informative)

    by mck9 ( 713554 ) on Monday July 07, 2008 @01:24PM (#24086143) Homepage

    No, this isn't ordinary DNA produced by synthetic means. If that were the case, it would be of little interest to anyone but a few specialists.

    What's new is that THIS synthetic DNA uses a different set of bases. not the usual C, G, T, and A.

    Presumably, therefore, it cannot usefully be read or replicated by the usual cellular machinery. That incompatibility makes it, arguably, less of a biohazard (or maybe more of a biohazard, since it might bind to the cellular machinery and gum up the works).

    The potential applications for this synthetic DNA apparently involve using it as a structural component of nanostructures. Theoretically it could be used for high-density data storage, though it's hard to imagine how the information could be either written or read.

  • The mystery of "life" (Score:5, Interesting)

    by ortholattice ( 175065 ) on Monday July 07, 2008 @02:02PM (#24086655)
    There is a long, long way to go before a self-reproducing organism results from a random combination of DNA, artificial or not.

    It is possible for a very simple "lifeform" with only 54 base pairs [ucr.edu] to be self-reproducing, but only if it is parasitic. Such "lifeforms" exploit the complex and sophisticated DNA machinery of the host to accomplish reproduction.

    I found it amazing that the simplest known lifeform that can reproduce independently is the Mycoplasma genitalium bacteria [wikipedia.org], with 582970 base pairs! This probably isn't the simplest one that can theoretically exist - it is hard to imagine the right combination out of 4^582970 appearing at random in the pre-life organic soup - but whatever simpler thing existed before it is a mystery, as well as why none of the simpler forms still exist today (if that is the case).

    This has been bugging me for some time, and as far as I can tell no one has a good answer.

    • but whatever simpler thing existed before it is a mystery,

      If you have the time and inclination, you might want to wander through the first four of these lectures [rockefeller.edu]. They talk about using simple RNA chemistries as tools for coming with with potential progenitors to Life As We Know It. Quite interesting and of course rather speculative.

    • I found it amazing that the simplest known lifeform that can reproduce independently is the Mycoplasma genitalium bacteria, with 582970 base pairs! This probably isn't the simplest one that can theoretically exist - it is hard to imagine the right combination out of 4^582970 appearing at random in the pre-life organic soup - but whatever simpler thing existed before it is a mystery, as well as why none of the simpler forms still exist today (if that is the case).

      Of course if you put it that by saying "4^5

  • still cool, but a bad summary. (Score:4, Informative)

    by Bowling Moses ( 591924 ) on Monday July 07, 2008 @02:04PM (#24086675) Journal
    IIRC the first chemical synthesis of a gene was by Khoran in 1970. What these guys have done is replace the four bases of DNA with different ones, and with a different attachment to the ribose group (having a carbon-carbon triple bond instead of normal DNA's carbon-nitrogen single bond), and have demonstrated double-stranded helix formation. The phosphate deoxyribose backbone is still present in it's usual way. Other groups have modified the backbone of DNA; probably the most famous is peptide-nucleic acid where the backbone is like that of a protein backbone. Also non-standard bases have been introduced by many groups and have been used for years. The paper in the Journal of the American Chemical Society also references these modifications plus some others, notably work simultaneously replacing bases and modifying the sugar groups in the backbone. Still replacing all four bases, changing the base-ribose linkage, and having the resulting product form right-handed duplexes, all of that at the same time, that's pretty cool.
  • .... I get my own copy of Leeloo [imdb.com]?

  • As other readers have noticed, the authors of this study have used existing DNA synthesis technology to incorporate non-natural bases into DNA. While it is impressive that the authors could design bases with the correct geometry to support a DNA-like double helix, the chemistry is not too novel. However, the ability to customize DNA-like polymers has a few interesting applications.

    First, all of the sci-fi applications involving artificial life are not really feasible because one would have to design a hug

  • They talk about using DNA as a data storage device, but I'm worried someone's kinky porn collection might just have the exact data sequence to mutate harmless bacteria into some nasty STD.

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