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Self-Assembling DNA Pyramids

Posted by ScuttleMonkey on 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."

38 of 108 comments (clear)

  1. In lay-man's terms this means... by MLopat · · Score: 5, Informative

    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

    1. Re:In lay-man's terms this means... by Hatta · · Score: 4, Interesting

      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?

      --
      Give me Classic Slashdot or give me death!
    2. Re:In lay-man's terms this means... by DonGar · · Score: 4, Informative


      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.

      --
      plus-good, double-plus-good
    3. Re:In lay-man's terms this means... by wass · · Score: 2, Informative
      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 quantum mechanics, you find that the electronic quantum wave function doesn't want to vary too quickly. Namely - it costs too much free energy if the wave function changes substantially over a length smaller than a length scale called the Coherence Length. So if we craft a wire with cross-sectional lengths shorter than the coherence length, the wave-function won't vary throughout the cross-section. So there really is only one effective dimension when talking about transport throughout the wire. And that opens all sorts of interesting questions.

      So yeah, at a fundamental level, small-enough objects can look purely one or two dimensional if you look at the quantum mechanics. For traditional electronic transport (ie, non-superconducting) you can typically regard things as not having a full dimension if the wavefunctions are 'bound' or 'free'. Namely, do they look like a particle-in-a-box (or harmonic oscillator or other bound potential) with discretely-allowed energy levels, or do they have an effective quasi-continuous band of allowable energy levels? Note that such a reduced dimension can still contribute as a degree of freedom, as represented by a quantum-number n referring to the discrete energy level. But if there aren't quasi-continuous states, it's not really a free dimension in the traditional sense.

      Now back to your original question, one very common reduced-dimensional system is a 2DEG (Two-Dimensional Electron Gas), which is utilized in silicon MOSFET devices. So your computer is exploiting such 2-dimensional devices right now under your nose. (Here is a rough description ).

      --

      make world, not war

    4. Re:In lay-man's terms this means... by Tune · · Score: 3, Interesting
      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, since it models not just what kind of problems can be solved, but also (more realistically) in how much time that solution is found.

      At a practical level, current chips are limited by the distance (lenght of wires) between interacting gates. In normal, planar designs, this distance can be reduced by regrouping interacting gates as close to each other as possible (ie.: making designs more clever), reducing the total number of gates or reducing the gate size (thus reducing the total chip size). Adding a second layer could half the needed die surface, allowing for smaller propagation times, thus higher clock frequency/more complexity/surface.

      However, adding more layers has a lot of practical problems in the current production process. Therefore *any* successful alternative to produce 3D semi conductors is likely to boost processing power.
    5. Re:In lay-man's terms this means... by MancunianMaskMan · · Score: 2, Informative

      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. Disclaimer: We only make the masks not the chips themselves so I don't know the really detailed stuff about the chip making business. Finding a way to assemble elements in proper "3D" fashion would make a big difference: shorter wires, greater complexity, but a complete change in fabrication processes because at the moment it's all done with photolithography, i.e. with a glorified slide projector shining on light-sensitive plastic coating. Changing that would be bad news for me because no-one would want our glorified slides any more! Ok, let them invent the "self-assembling CPU" after they breed the nano-molecule that creeps over the chip in a boiler suit riveting DNA pyramids together! Long live our nano-overlords.

  2. trillions of d4s? by vermox · · Score: 5, Funny

    Man those D&D games are getting complicated!

    Oh... nevermind

    --
    --- /dev/null
    1. Re:trillions of d4s? by mypalmike · · Score: 4, Funny

      Apparently, God DOES roll dice.

      --
      There are 0x40000000 types of people: those who understand 32-bit IEEE 754 floating point, and those who don't.
    2. Re:trillions of d4s? by ShyGuy91284 · · Score: 3, Funny

      And made of DNA? Damn. And I thought pewter or bone dice were fancy (and yes, I know bone has DNA in it, but it still isn't the same).

      --
      In undeveloped countries, the consumer controls the market. In capitalist America, the market controls you.
  3. And Moses said to Pharaoh: by Anonymous Coward · · Score: 5, Funny

    Let my nucleotides go!

  4. So the builders of the pyramids are... by slashname3 · · Score: 4, Funny

    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).

    1. Re:So the builders of the pyramids are... by Oktober+Sunset · · Score: 3, Insightful

      I know that the pyramid/egyptian link is just too easy to resist, but they were square base pyramids, these, being made up of tetrahedrons, will be triangular based.

      --
      What if Tetris was invented by Nazis?
  5. Re:Sounds cool by d.valued · · Score: 2, Funny

    And I thought stat-inflation was bad before...

    "Loknar, roll ten to the eighteenth D4s. And this time, try to keep them all on the table."

    --
    I used to be someone else. Now I'm someone better.
    Real life is underrated.
  6. Keeps my razor blades sharp? by martinX · · Score: 2, Funny

    So if I store my razor blades under this, will they remain eternally sharp?

    --
    When they came for the communists, I said "He's next door. Take him away. Goddam commies."
    1. Re:Keeps my razor blades sharp? by Locke2005 · · Score: 2, Funny

      As long as your razor blades fit under a 10 nanometer pyramid, then yes, they will be sharp. In fact, they will have a perfect edge on them, plus or minus about 10 nanometers...

      --
      I've abandoned my search for truth; now I'm just looking for some useful delusions.
  7. I knew It by lexxyz · · Score: 5, Funny

    I knew my DNA had to be a pyramid.

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

    1. Re:I knew It by gid13 · · Score: 3, Funny

      You must have some very large feet.

  8. pyramids by revery · · Score: 4, Funny

    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."

  9. Re:Sounds cool by ackthpt · · Score: 5, Funny
    When can I purchase a house made of them?

    Just as soon as you send $1.00 each to the following people, then place your name on the top of the list and delete the last name from the bottom of the list! It's that simple and totally legal!*

    • Fester Bestertester
    • 1050 Karbunkle Ave #7B
    • Finster, NJ

    • Happy Guy
    • 742 Evergreen Terrace
    • Springfield

    • The Pope
    • 1 Pope St.
    • Vatican

    • Sir Alex Ferguson
    • Theater of Dreams
    • Manchester, UK

    • Cowboy Neal
    • 3rd Cardboard Box on the Left
    • Alley behind Rocky Peanut Company,
    • Holland, MI

    * In Antarctica

    --

    A feeling of having made the same mistake before: Deja Foobar
  10. Z Chromosome by JuzzFunky · · Score: 3, Funny

    This explains my mysterious Z chromosome...

    --
    Unexpect the expected!
  11. Re:Dupe by RussG146 · · Score: 2, Funny
    This is a dupe, the egyptians did this millenia ago

    Drat. If I had known that, I wouldn't have spent the last two years making and characterising the bloody things.

  12. Mixing Nano and Bio... by oldzoot · · Score: 2, Insightful

    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.

    --
    enough is too much
  13. Mage hit dice by isomeme · · Score: 4, Funny

    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?

    --
    When all you have is a hammer, everything looks like a skull.
  14. This and Velcro by Capitalist1 · · Score: 2, Funny

    It's nice to see they're finally making use of that captured Goa'uld technology.

    --
    One man's religion is another man's belly-laugh. - LL
  15. Re:old non news by RussG146 · · Score: 5, Informative
    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.

  16. Old news. by Poromenos1 · · Score: 2, Funny

    Bah, watch people mention a million things they can build from this thing. Big deal, I can build a whole person from DNA.

    --
    Send email from the afterlife! Write your e-will at Dead Man's Switch.
    1. Re:Old news. by CupBeEmpty · · Score: 2, Funny

      YOU probably can't build a whole person from your DNA. Highly advanced scientists in the field of cloning may be able to. YOU probably need a girlfriend first.

    2. Re:Old news. by Poromenos1 · · Score: 4, Funny

      Highly advanced scientists in the field of cloning do it asexually.

      --
      Send email from the afterlife! Write your e-will at Dead Man's Switch.
    3. Re:Old news. by leadboot · · Score: 2, Funny

      Now THERE'S a bumper sticker.

  17. No problem here .. by RedLaggedTeut · · Score: 2, Funny

    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.

    --
    I'm still trying to figure out what people mean by 'social skills' here.
  18. Next up... by Urusai · · Score: 5, Funny

    ...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".

  19. Re:old non news by CupBeEmpty · · Score: 4, Informative
    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 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 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 for several years. Is that now "old non news?"

  20. Re:Dupe by jzeejunk · · Score: 3, Funny

    the egyptians did this millenia ago
    But that was never reported on slashdot.

    --
    sarchasm
  21. Obligatory Lego reference by Billy+the+Mountain · · Score: 2, Interesting

    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

    --
    That was the turning point of my life--I went from negative zero to positive zero.
  22. Triangles by Anonymous Coward · · Score: 5, Interesting

    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 http://web.mit.edu/neltnerb/www/bn-triangles-2.jpg 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.

  23. Nanofabrication with organic compounds? by Lisandro · · Score: 2, Interesting

    What would be the life expectancy of such constructions? IIRC, DNA are pretty "fragile" molecules.

  24. Re:Is it edible? by NanoGator · · Score: 2, Funny

    "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.

    --
    "Derp de derp."
  25. Thank you for your submission by Laaserboy · · Score: 5, Funny

    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