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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."

6 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 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.

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    2. 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 ).

      --

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    3. 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. 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.

  3. 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?"