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Science Technology

Self-Assembling DNA Pyramids 108

Posted by ScuttleMonkey from the new-and-improved-building-blocks dept.
FleaPlus writes "Physicists in England and the Netherlands have unveiled a technique for constructing rigid DNA pyramids. With the technique, trillions of d4's can rapidly self-assemble from a solution of single-stranded DNA. The scientists also showed that single DNA strands called linkers could be used to attach the tetrahedra to each other, acting as a possible building block for 3D nanofabrication."
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Self-Assembling DNA Pyramids More

Self-Assembling DNA Pyramids

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  • In lay-man's terms this means... (Score:5, Informative)

    by MLopat ( 848735 ) on Monday December 19, 2005 @07:23PM (#14295097) Homepage
    Since the article summary doesn't even begin to explain why this is significant, I'll attempt to.

    First of all, the DNA pyramids are useful because they have some attractive properties, namely they are about 10 nanometers wide and are rigid. They are also tetrahedral in shapre (3 faces and a base) which makes them good building blocks. This all lends itself rather nicely to developing things like three dimensional electronic circuits.

    Today's announcement is simply to say that scientists have fonud a way to do this all in a single step by mixing trillions of the base strands in a mixture to produce the mini-pyramids. However, what is really needed moving forward, is a way to bind all of these pyramids into more complex structures. For more information, check out the article on PhysicsWeb [physicsweb.org]

    • Re:In lay-man's terms this means... (Score:5, Interesting)

      by Hatta ( 162192 ) on Monday December 19, 2005 @09:28PM (#14295813) Journal
      First of all, the DNA pyramids are useful because they have some attractive properties, namely they are about 10 nanometers wide and are rigid. They are also tetrahedral in shapre (3 faces and a base) which makes them good building blocks

      To be precise, a tetrahedron has 4 identical faces. It doesn't make sense to distinguish one as the "base". This is in contrast to an actual "pyramid" shape, like the ones in Egypt, which have a square base, and 4 triangular sides.

      This all lends itself rather nicely to developing things like three dimensional electronic circuits.

      Aren't all electronic circuits three dimensional, since we live in a 3d universe? If not, does going in 3 dimensions let us do anything more? My guess is that a 2d turing complete computer is the same as a 3d turing complete computer, so what's your point?
      • Aren't all electronic circuits three dimensional, since we live in a 3d universe?

        Brilliant. You've clearly out-thunk the parent. Bravo.

        My guess is that a 2d turing complete computer is the same as a 3d turing complete computer, so what's your point?

        Which is why I'm still typing this on my good 'ol 386, what with all turing complete computers being equivalent and all. I don't get why people keep wasting their money on so-called "upgrades".

      • Re:In lay-man's terms this means... (Score:5, Informative)

        by DonGar ( 204570 ) on Tuesday December 20, 2005 @12:16AM (#14296499) Homepage

        This all lends itself rather nicely to developing things like three dimensional electronic circuits.

        Aren't all electronic circuits three dimensional, since we live in a 3d universe? If not, does going in 3 dimensions let us do anything more? My guess is that a 2d turing complete computer is the same as a 3d turing complete computer, so what's your point?


        Most circuits in chips today are 2D designs. Just like the circuits you see traced out on a circuit board, but much smaller. The circuits are '3d' in the sense that the leads have some hight, but no logic is expressed in the z dimension, so that third dimension is uninteresting.

        There are a few exceptions right now were people are building chips that have multiple levels of 2D circuits with a few vertical interconnects, but the third d isn't really being heavily used.

        Having full 3d circuits allows much more complex logic to be expressed in less space with less propogation time. Thus smaller, faster, and less power consumption in the chips for your computer.

        Of course, you are correct in your statement that this doesn't affect the turing completeness of your computer. Thus there is no effect on the types of programs the computer can execute, only how quickly they compute them, how much power is consumed, and how big the machine is that does the computing.

        • Of course, you are correct in your statement that this doesn't affect the turing completeness of your computer. Thus there is no effect on the types of programs the computer can execute, only how quickly they compute them, how much power is consumed, and how big the machine is that does the computing.

          For modern computers, a more relevant abstraction of computational power would be a random-access machine [wikipedia.org], since it models not just what kind of problems can be solved, but also (more realistically) in how much

        • There have been a number of 3D circuit attempts. One of the largest problems to overcome is heat dissipation (particularly from the center of that 3D shape).
      • Aren't all electronic circuits three dimensional, since we live in a 3d universe?

        Yes and no. One of my research projects involves superconducting nanowires, which are essentially one-dimensional. But wait, you say, these so-called nanowires are really wires with cross-sections of a few nanometers, therefore they're really three-dimensional.

        Not really. If you look at the quantum mechanics of the superconductor, or even using the Ginzburg-Landau theory which is phemonological and ignores microscopic q

      • Re. 3D circuits: all chips today have one layer of transistors, and no more. You only get one shot at making those in chip fabrication. Then you pile on other stuff, such as 5 or 6 layers of "wires" criss-crossing each other, but after the first layer of trannies it's basically curtains. it's because the transiors all live in the wafer material which is crystalline silicon, and all silicon that you put on afterwards is of relatively poor crystal quality and you can't make good quality transistors out of it.
    • This is an important step in science. We may be looking at organic replacements for electrical circuits sometime in the future. Here is an idea, if it is wrong to genetically modify a human (I know this is looking far into the future but bear with me), then is it wrong to modify something else to better serve our needs? Sounds like something out of star Trek...
    • "by mixing trillions of the base strands in a mixture to produce the mini-pyramids."

      It's a fraud ! You can clearly see the tiny egyptians in the electron microscope pictures, there's even a sphinx in the corner if you squint just right !
    • no, what this really means is we finally know how those pyramids in egypt were made... they constructed themselves!

  • trillions of d4s? (Score:5, Funny)

    by vermox ( 877880 ) on Monday December 19, 2005 @07:27PM (#14295123)
    Man those D&D games are getting complicated!

    Oh... nevermind

  • DNA Civilization. (Score:1, Funny)

    by Anonymous Coward
    "Physicists in England and the Netherlands have unveiled a technique for constructing rigid DNA pyramids."

    Goes perfect with Egyptians created from DNA.

  • And Moses said to Pharaoh: (Score:5, Funny)

    by Anonymous Coward on Monday December 19, 2005 @07:27PM (#14295128)
    Let my nucleotides go!

  • So the builders of the pyramids are... (Score:5, Funny)

    by slashname3 ( 739398 ) on Monday December 19, 2005 @07:30PM (#14295146)
    So the real builders oof the pyramids are nonfrabricators. The Egyptians grew them instead of using slave labor to drag blocks into place or getting help from UFOs.

    Nanu Nanu (obligatory Mork and Mindy reference).

  • Keeps my razor blades sharp? (Score:3, Funny)

    by martinX ( 672498 ) on Monday December 19, 2005 @07:32PM (#14295155)
    So if I store my razor blades under this, will they remain eternally sharp?

  • I knew It (Score:5, Funny)

    by lexxyz ( 939985 ) on Monday December 19, 2005 @07:35PM (#14295180)
    I knew my DNA had to be a pyramid.

    It is more in line with my shape, gets wider the farther you go down!

  • Is it edible? (Score:1, Offtopic)

    by rubberbando ( 784342 )
    If so, then you can call it a food pyramid! :P
    • "If so, then you can call it a food pyramid! :P"

      It's nice to see that graduates of the Bob Saget School of Comedy are still finding time to expand on their art form.

      • It's nice to see that graduates of the Bob Saget School of Comedy are still finding time to expand on their art form.

        Man, that should be a new rating: -1 Saget
      • Bob Saget...

        I think my favorite Bob Saget line was this:

        "Marijuana is not a drug. I used to suck dick for coke. Now that's an addiction, man. Have you ever sucked some dick for marijuana?"

  • pyramids (Score:5, Funny)

    by revery ( 456516 ) <charles@NoSpam.cac2.net> on Monday December 19, 2005 @07:38PM (#14295199) Homepage
    trillions of d4's can rapidly self-assemble from a solution of single-stranded DNA

    In other news, several cheerleaders who were interviewed stated that they were skeptical as pyramids in general are "way hard." They also stated that they doubted the numbers claimed as the largest pyramid they had heard of was composed of 280 or so cheerleaders and that a trillion is "like at least double that."
    • They also stated that they doubted the numbers claimed as the largest pyramid they had heard of was composed of 280 or so cheerleaders and that a trillion is "like at least double that."

      Are these the same cheerleaders who were reading the newspaper headline"TWO BRAZILIAN SOLDIERS KILLED"... and one of them leans over to the other and says, "How many is a brazilian?"

  • old non news (Score:2, Interesting)

    by cinnamon colbert ( 732724 )
    ned seeman at nyu has been doing this for years

    it has little if any practical value; dna is VERY $$, and a delicate molecule that is destroyed by normal shipping temperatures (at least in tuscon)

    the idea that dna will be any sort of industrial material for anything is fantasy
    • So, since you live in Tuscon, all your dna should be gone by now.

    • Re:old non news (Score:5, Informative)

      by RussG146 ( 940088 ) on Monday December 19, 2005 @08:14PM (#14295403)
      ned seeman at nyu has been doing this for years

      That's certainly true - Ned Seeman is definitely the 'founding father' of the field, and has lab continues to be a driving force in this sort of research. However, while I'm not exactly an objective observer, I believe this paper offers a number of practical advances in the field, such as yield, ease of synthesis, rigidity, and adaptability.

      it has little if any practical value; dna is VERY $$, and a delicate molecule that is destroyed by normal shipping temperatures (at least in tuscon)

      This simply isn't true. DNA is shipped all over the place at room T (we ordered the DNA for this experiment from America), and in lyophilised form is very stable. It's less stable in solution, but you can make modifications to increase its stability. DNA tetrahedra in my experience are very stable. As for cost, you can buy the DNA for this kind of synthesis relatively cheaply, and DNA gets cheaper every year.

    • Re:old non news (Score:5, Informative)

      by CupBeEmpty ( 720791 ) on Monday December 19, 2005 @08:27PM (#14295484)
      Well that is all a question of environment. We get lyophilized primers (~15-25bp) sent to us at room temperature all the time. In fact, we incubate long strands of DNA at temperatures of 95C all the time. We even do the same with long strands of RNA (the 10,000 bp RNA genome of Hepatitic C Virus). Brian Sykes at Oxford even made a big splash by exctracting 9,000+ year old mitochondrial DNA [isogg.org] from the "Cheddar Man," not to mention other famous historical figures.

      Making a blanket statement like "DNA is a delicate molecule" or "this will never be useful" is not necessarily correct. It is more correct to say "DNA can be delicate in the wrong conditions" and "this does not have applications, yet." Now, will we overcome the cost of synthesizing DNA? Perhaps. The cost of DNA synthesizing oligonucletides (15-20bp) has dropped dramatically in the last few years. Now will this be useful in making nano-toaster ovens or other more "industrial" tech? Probably not, but neither article really proposes anything like that. Also DNA is a lot less expensive than certain chemicals that are used in trace amounts in all sorts of tech and industrial applications. The field really seems to be wide open.

      Ned Seeman's work [nyu.edu] is slightly different but along the exact same lines. Also, of course he has been doing it for years! A lot of people have been working on this for years. The scientific community is all for competition. Simply because Dr. Seeman has been working on this doesn't somehow invalidate this study. People have also been working on broadband over powerlines [slashdot.org] for several years. Is that now "old non news?"

      • What is $$
        In plastics, a buck a pound is typical for commodity PS; super $$ peek is 13 dollars a pound. I don't know what the cost of oligos is, but a hundred bucks a gram is the cheapest i have ever heard.

        DNA is NOT stable lyophilized; you only think that cause you don't have good analytical tools like dggge or sscp or maldi, and your enzymes filter out the bad stuff
        Sure, dna may possibly be usefull for some esoteric or trace apps, but as an industrial base material - nah (and don't quote pcr barcode olig
      • Are you saying that it is environment in the normal cell that necessitates all the repair mechanisms?

        (The halflife for a normal RNA molecule in the cell kernel is quite short, right?)

        If you have a use with controlled temperature (and no hungry bacteria around!) in a given solution, DNA is stable enough to make applications?

        (With or without DNA modifications?)

        Would it be easy to vary the sequence on the DNA so you could have enzymes cutting up the pyramids in specific places?

    • the idea that dna will be any sort of industrial material for anything is fantasy

      Don't know about tuscon but over here we've been making all kinds of durable critters and even people with it for years.

      We don't even need a lab. :)
    • Strangely, I ship my DNA around through all sorts of temperatures. I grew up in Ohio and have been in subzero winters, and now live in Texas where summers reach over 100 degrees F. Somehow, I've managed not to degrade into a pile of bubbling goo.

      Remember folks, nanotechnology WILL work. The proof is in the question. Are you able to think about nanotechnology? If so, then the trillions of nanomechanical, nanoelectrical, and nanochemical actions going on in your body are working well (more or less), and
      • Well, if you don't have analytical tools like DGGE (lerman and fisher) SSCP, MALDI or electrospray, you don't really know much about the chemical nature of your DNA

        for instance, it is well known, except to "scientists" who post on /. that a large fraction of the oligo you get from your fav vendor (IDT/genosys/etc etc) has some form of covalent modificatin, such as non removed deprotecting groups,etc

        You are simply not aware of this, as various filters (Taq, transformation) remove the junk

        Similarly, when you

  • Z Chromosome (Score:3, Funny)

    by JuzzFunky ( 796384 ) on Monday December 19, 2005 @07:52PM (#14295282)
    This explains my mysterious Z chromosome...

  • Mixing Nano and Bio... (Score:3, Insightful)

    by oldzoot ( 60984 ) <morton.james@com ... inus threevowels> on Monday December 19, 2005 @07:53PM (#14295293)
    Seems kind of scary to use Bio building blocks to do nano-tech construction. Will the industrial use of DNA nano-blocks have biosafety scrutiny? I hope that some wonderfully usefull industrial nano-object does not end up with a potent lethality, particularly if it somehow can replicate in the wild.
    • I can assure you bio nano-building blocks are not the least scary. I am working with them every day.

      Ok, so it is a big strange that my left leg has turned a solid grey-bluish color, but it works just as well as the initial one and I've gotten used to it solving math questions faster than me.

  • Mage hit dice (Score:5, Funny)

    by isomeme ( 177414 ) <cdberry@gmail.com> on Monday December 19, 2005 @08:12PM (#14295392) Journal
    Should I be more embarrassed that I get my news from a source that calls tetrahedra "d4s", or that I immediately knew what that meant?
  • It's nice to see they're finally making use of that captured Goa'uld technology.
  • So it wasn't the aliens...

  • Old news. (Score:3, Funny)

    by Poromenos1 ( 830658 ) on Monday December 19, 2005 @08:18PM (#14295437) Homepage
    Bah, watch people mention a million things they can build from this thing. Big deal, I can build a whole person from DNA.

  • Next up... (Score:5, Funny)

    by Urusai ( 865560 ) on Monday December 19, 2005 @08:23PM (#14295469)
    ...entire self-assembling DNA-based organisms. Scientists are working hard on the technology, but research is hampered by a mysterious and poorly understood preliminary stage called "sex".

  • Obligatory Lego reference (Score:3, Interesting)

    by Billy the Mountain ( 225541 ) on Monday December 19, 2005 @08:42PM (#14295562) Journal
    If you ever thought you might like to get paid for playing with Lego's this looks like the closest you are going to get.

    How about this idea: You tag blocks with flourescent dyes and assemble them according to a computer voxel model one color at a time (using whatever method pleased you the most ;) Then when you turn on the light, and view under a microscope, you'd see your model rendered in color.

    BTM
  • ... using socks or tissues as foundations, of course.

  • Triangles (Score:5, Interesting)

    by Anonymous Coward on Monday December 19, 2005 @09:46PM (#14295913)
    This is awesome, I accidentally produced something that I suspect is very similar to this no more than 8 months ago using DNA to self-assemble gold nanoparticles. The pictures are gorgeous (but inconclusive, unfortunately). http://web.mit.edu/neltnerb/www/bn-triangles-1.jpg [mit.edu] http://web.mit.edu/neltnerb/www/bn-triangles-2.jpg [mit.edu] Sorry, I have no particular desire to register an account here for my very rare posts. And Kuna, don't laugh. I promise, I'm not a total dork. But DNA self assembly is still cool.

  • Nanofabrication with organic compounds? (Score:3, Interesting)

    by Lisandro ( 799651 ) on Monday December 19, 2005 @09:59PM (#14295985)
    What would be the life expectancy of such constructions? IIRC, DNA are pretty "fragile" molecules.
    • If you look close at the picture in the article, and follow the colors around the edges, notice that each face is intertwined with neighboring faces. I would imagine that gives it some strength, but you have to wonder about those corner bonds.

      I would be curious to know how "strong" this is compared to 10 cubic nanometers of iron or salt crystal or titanium or aluminum etc. Though I suppose for its strength it could have ease of manufacture over say, 10 nanometer titanium d6s.
  • Thank you for your submission of a new [x] nanostructure [ ] transistor [ ] laser

  • Thank you for your submission (Score:5, Funny)

    by Laaserboy ( 823319 ) on Tuesday December 20, 2005 @12:47AM (#14296600)
    THANK YOU for your submission of a new
    [x] nanostructure
    [ ] laser
    [ ] transistor
    using
    [ ] straw and bailing wire
    [x] DNA strands
    [ ] silicon
    This is a bad idea, because
    [x] a 3-D structure is difficult to heat-sink
    [x] scientists likely never will produce a transistor this way
    [ ] this is a case of outright fraud
    The problem however is not to make circuits
    [ ] out of lasers
    [x] 3-D
    [x] self ordered
    But the problem is to make them
    [x] reliably
    [x] at low cost
    [x] faster
    Further this article was published in
    [ ] Science
    [ ] New Scientist
    [ ] Nature
    [x] Science News
    which is primarily a publicity-seeking mag, and not a great peer-reviewed journal for physics.
    I can say this because I have a
    [ ] BS
    [ ] MS
    [x] PhD
    in
    [x] Physics
    [ ] Electrical Engineering
  • And in fifty years we can read:

    "Yet another entire biota was wiped out by the pyramidal prions. Earlier this week we could see how Puerto Rican biota was wiped out by the ever growing pyramidal prions. The island state was literally covered with small, inch high grey pyramids. The US Government now fears the pandemic will spread onto mainland US and has banned all border crossing, in or out, and the import of any organic matter. It is believed that once the pyramidal prions enters living tissue it starts re

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