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Science

DNA as Construction Equipment 37

Posted by Hemos from the fun-with-building dept.
vivekb writes "Scientists at Ruhr University in Germany are using DNA to assemble microscopic structures. They attached matched DNA strands to construction materials, and use the DNA as an highly selective bonding agent. So far, basic polyhedra have been manufactured using gold spheres. The BBC presents this article. The paper is entitled Self-Assembly of Trisoligonucleotidyls. "
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DNA as Construction Equipment More

DNA as Construction Equipment

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  • .. community on slashdot. First the Unified field theory.. now this! Yippee. When do we get the space hotel announcement?

    This is actually a cool idea. You rip apart DNA strand and place what you want to put together between the strands. Then you allow the strands to reform. Whamo! you have your fabbed object. I wonder how well they can control the operation. Can they build things on the atomic level with this?

    --

  • Every time I see one of these articles, I simultaeneously yelp with joy and quiver with fear. The possibilities for technology this intricate are endless, but at the same time, the risks involved with the raw useful potential make me wonder when we'll finally screw up and cancel ourselves out of the evolutionary race. The one thing that keeps that evil, nasty feeling from getting too far is that it's better to allow for uninhibited expression of creativity than to close doors and burn bridges that we never knew existed in the first place. Go techology!

  • This is actually pretty cool.

    I don't know about you guys (and girls, no sexism here), but I start thinking about other events where a discovery has led to an unexpected area of application; liquid crystals, teflon, microwaves... can anyone think of more examples? Let's hear it for abstract knowledge!

    Hopefully, this will give nanotech a leg up. Using DNA for the actual enzymes and whatnot seems a little bulky to me, but you could probably use the technique to build the nanotech "factories" that are going to assemble the actual nanobots. I imagine von Neumann machines could be built with this as well... DNA is good at self-replication too =)

    // Eärendil
    ---
  • post-it notes and velcro...
  • I can see it now! Micro-Lego(TM)! And it'll reproduce too! Get more for your buck, with Micro-Lego(TM)!
  • ramen noodles and jolt cola

  • This is not much of a story, except that patents in the biotech industry are at least as insane as they are in the software world.
    They synthesised and separated DNA double helixes and then attached the single strands to building materials, such as gold spheres. Then, in solution, the DNA strands found their partners and bound together the components they carried.
    Gold spheres are routinely attached to biomolecules. (quite a useful techniqu in electron microscopy) DNA oligonucleotides are routinely synthesized comercialy. PCR is as basic to biotech as photolithography is to Silicon technology. There is nothing new here.
    They believe the selectivity provided by the DNA pairing will allow complex objects to be assembled. They even speculate such objects could multiply themselves by bio-chemical methods and might be able to optimise their operation through "artificial" evolution.
    This is just absurdity; pandering to the x-files crowd. Thank God these are not the people who will be dealing with the Y2K issues.

  • Thanks -- informed analysis useful (Score:3)

    by Morgaine ( 4316 ) on Monday November 15, 1999 @10:11PM (#1529973)
    We need people with a good overview of the field to make informed comment and separate the wheat from the chaff in areas such as biotech, which is outside of the sphere of competence of many inorganic materials-based nanotech experts.

    How about creating a website devoted to such analysis? It could be a valuable resource.

  • "Only one thing is certain about the future - it is going to be utterly fantastic"
    Quote, Arthur C. Clarke. What a guy!

  • Only on /. period.
    We need people with a good overview of the field to make informed comment and separate the wheat from the chaff in areas such as biotech, which is outside of the sphere of competence of many inorganic materials-based nanotech experts.
    I am uncertain if an inorganic materials-based nanotech expert refers to an expert on nanotechnology that does not involve carbon compounds, or if she is a life force based on germanium. ;-)

    help me.

  • The problem with building things at the nanometer scale is putting them together. We can make individual wires, transistors, bearings, shafts etc. out of atoms, but we can't put them together...

    You really can't get out some tweasers and squint a bit to make a machine that will fit inside a cells nucleus.

    These biotech guys have one way of organising the construction process. It is much easier to use DNA to drag prefabricated components together than to use pure chemistry to build them on site. (You need selectivity to make sure this bit gets made or put here, and not there.)

    Unfortunately, I don't think this will work. DNA is just too big for the parts they are making at the moment. (The parts are made chemically - so they can only be a few hundred atoms or so before the yield drops off.) The way around this is to make successively smaller machines that can build yet smaller machines, and so on. The problem is that I don't see anyone with the blueprints for a universal constructor.

  • Here's an interesting thought: if they can create microscopic objects using DNA strands, they will eventually be able to produce microscopic machines. So how about the idea of Nanomachines, that would be placed inside the human body allowing itself to repair damages, and morph, if you will to develop a needed feature. (ie: gills to live underwater). Sound reasonable?

  • DNA, RNA and BBC (Score:4)

    by jw3 ( 99683 ) on Monday November 15, 1999 @11:32PM (#1529978) Homepage
    1. There is a saying in polish, which seems apriopriate in this case. You could say, BBC "discovered America". This usage of DNA they describe isn't anything new at all - DNA as a "velcro" to attach molecules has been used in mol. biol. since many years. DNA pairing is not an issue. They completly missed the point regarding Kiedrowskis research.
    2. Kiedrowski is one of the guys who's research led to the discovery of rybozymes - self-modifying, RNA-based molecules, which can even in a certain way replicate themselves. RNA research is much more promissing at this point than DNA research - RNA molecules tend to have a much more complicated structure and sometimes carry enzymatic activities. It is now a widely accepted view that the life started with self-replicating and self-encoding RNA molecules. For the difference between DNA and RNA molecules only one oxygene atom is responsible, lacking in DNA (therefore, deoxyribonucleic acid). He re [natureasia.com] is an abstract of an article by Kiedrowski about self-replicating molecules.
    3. Both DNA and RNA are prone to enzymes called nucleases. RNA is especially fragile - it is enough to touch the cap of a propylene tube containing RNA sample with a bare finger - and there goes a week of your research, because there are plenty of RNases (enzymes digesting RNA) on your fingers. DNA is much more stable, but still you have to store it in -20 in a buffer containing EDTA, a chemical which binds to metall iones, which are necessary for DNases to work (RNases are very hard to get rid off: boiling, cleaning with ethanol doesn't help).
    4. This [ruhr-uni-bochum.de] is an abstract of the research report written by Kiedrowski himself. English translation is lower down the page.
    5. As for "velcro" properties of DNA for constructing nanobots, I have a better proposition - there is a type of synthetic molecules, which are called "peptide-nucleic acids" (PNAs). In this molecules, instead of the riboze (which is a sugar) and phosphoric acid residues, the "spine" of a moleucle consists of a pseudopeptide. In fact, PNAs are not acidic - and this is very important. When two single strand DNA molecules bind, they have to overcome the negative charge they bear. In fact, to make them do it, you have to provide sufficient salt concentration in the solution where the binding (hybridization) takes place. PNAs are not acidic => have no charge at all => can even bind in water. And they are much more stable than other nucleic acids. On this [horizonpress.com] page you can find many sources of information about PNAs.
    6. There are much better sources of easy-to-read, but scientifically sound articles about current research in biology and other fields - Nature Science Update [nature.com] - a very good site for a start, updated daily.

    Regards,

    January

    P.S. When /. posts a reference to an article about computers, it is usually worth reading. When /. posts a reference to an article about biotech, don't bother.

  • If the DNA would be flexible enough you could make clothes out of it. That could be neat...

  • It already happened. The properties of DNA are heavily used in.. ...uhmm... DNA research, mostly :-) Or, molecular biology - generally speaking. Basically, you can tag a molecule with a certain sequence, and fish it out later from a mixture of other molecules with a complementary strain of DNA attached to, for example, a magnetic bead.

    Personally, I think that two large fields of application will stem from a) RNA research (self-modyfying, or even evolving molecules) and b) PNA research (see my other post - "DNA, RNA and BBC"), which are much more stable then DNA molecules itself.

    As for DNA, I know that there are people trying to use DNA as a conductor, so you could build molecular-sized wires (see this fascinating artic le [upenn.edu] from The Scientist about the first DNA nanomachines; another idea is to use nanotubes).

    Don't dream about using DNA or RNA attached to anything which could get dirty: there are so much nucleases from bacteria, or even from your fingers, that it wouldn't last more then, say, a couple of hours, maybe minutes.

    As for building nanobots repairing DNA in your cell, well, we have them, every living cell has them - complicated repair mechanisms. So it would be a much better idea to use what already works, and maybe make it work a little better - your genes are not as interested in an infinite prolongation of your cells life as you are, they have to care about spreading and replicating as well, so they do not invest all the available energy for repairing what is not supposed to last forever.

    Regards,

    January

  • Pandering to the X-file crowd? Well, how about evolving RNA molecules? The group from Yale (Altman - Nobel prize for ribozymes, Dorit, Breaker - engineering new RNA and DNA enzymes by in vitro evolution) - you can lookup their homepage here [yale.edu].

    Of course, it is about RNA, and not DNA, but still, the article wasn't basically wrong.

    Regards,

    January

  • Isn't the "there are things Man was not meant to know" spiel getting just a wee bit old? They said it about electricity for crying out loud...
  • I have often wondered whether a machine could be built that could build a copy of itself. The issue here is the component parts that the machine must construct itself from... in the case of biological life these component parts are rather complex molecules, these are fortunately in abundence on our planet. The question is whether a machine could be constructed which could use simple elements to construct a copy of itself (or something more complex than itself).

    --

  • OK, I was thinking about creating such a webpage for a long time. Unfortunatelly, my english is... pathetic. Nevertheless, I did a primer, an alpha version, a grin-duck-and-run page:

    The Biogeek [uni-heidelberg.de] page. Well, if anybody is interested, I might get on with the idea... although... I really don't know... What do you think?

    Regards,

    January

  • File Not Found

    The requested URL /acf/pubs/connect/sprint97/SciVisSeemNanoSp97.html was not found on this server.

    j.

  • ...controlled by Micro-Lego Micro-Mindstorms...which is of course a DNA computer...oh, nevermind.
    --
  • This is the same technology that causes a stamp to stick to an envelope after it's been licked...

    human://billy.j.mabray/
  • It's my fault :-) I was too quick - eventually, after looking at the connect homepage, I figured it out... :-)

    Regards,

    January

  • ...and then some fool will come along and try to figure out a "software copy protection" scheme for DNA. Wait! Someone already has!

    http://www.greens.org/s-r/17/17-21.html [greens.org]

    http://thewinds.org /archive/newworld/terminator_seeds04-98.html [thewinds.org]

  • Nature prooves that this is possible: a simple, autotrophic bacterium needs an electron acceptor, an electron donor and some anorganic molecules (carbon dioxide, water, microelements and such). Simple, isn't it? And bacterial cells can be very tiny - the bacterium I'm working with can pass even through so-called "bacterial retaining filters" :-)


    Regards,


    January

  • Not really? Nanos are JUST MACHINES. Thats IT. They build what you need, but building and testing is the last part of any proccess. (Ok, maintance is the very last part.) First you have to design the damn things. Gills are easy because so many creatures have them. Now, where do you put them? Replace you lungs? Where are you during this phase? You need extremely detailed plans on this..where will you store them? Will you be carrying aound the designs for every possible thing your nanites can do?

    Repair damages, I can see hospitals for this. Sure, you have nanites with you, but are you carrying 'Bonerepair Ver 3.4' on you? The hospital carries the latest plans. You do have the latest version with you? Well the hospital is still better, they have the equipment to make sure your nanites are saturated in the materials they need, plus assistance on a macro level (Setting the bone) will speed the procces greatly.

    The amount of knowlege required to use nanites effectively is beyond what we know now.

    Later
    Erik Z
  • On the other hand we can correct bad things that happens in a natural way if we learn enough... Cancer, HIV, you name it.
  • I personally find these types of articles very interesting. Granted, they impart a Diamond Age feeling, but I think that is more of a sign of Neal Stephenson's insight rather than just sci-fi hype. (Comsat?)

    The fact is nanotechnology is making great strides lately, even if only in terms of public perception(or media hype, whatever). That in itself is good. The more people become aware of what could be, the more likely people are going to start funding/supporting nanotech so that it will be. This is all relevant to Slashdot because nanotech will change computing drastically once it arrives in full force.

    Since when was computing the domain of silicon only? Keep it coming.

    Scarpa
  • If the DNA would be flexible enough you could make clothes out of it. That could be neat...

    Oh, DNA is flexible enough...the problem isn't that it's inflexible, but that it degrades/dissolves so rapidly. You don't want your clothes to fall apart when you wear them out in the sun or spill something on them, do you?

    But not to worry. There's actually plenty of DNA in your clothes already, unless you're wearing synthetics. Wool is chock-full of (probably quite degraded) sheep DNA. Cotton has cotton DNA, hemp has hemp DNA, linen has flax DNA, and leather has DNA from whatever animal the skin came from. Enjoy!
  • Hehe, good question! :-)

    I was of course referring to materials scientists, inorganic chemists, solid-state physicists and all the related engineering types who are avidly absorbing nanotech-related news and even contributing to the research, but who typically lack an in-depth background in biotech, organic chemistry or genetic engineering.

    It's a difficult subject largely because of its multidisciplinary nature, so any help that can be offered by more biotec-aware folk would be extremely useful and welcome.
  • wow, does this mean that were going to have extremely small little CAT Earthmovers and Cranes? hehe, that'd be c00l but it would totally suck/be cool if something went wrong and the DNA mixed and found some host-like thing to grow on and spawn off.... but that wouldnt happed....them scientist are smart! but you never know.... we might have people making Gold Sphere Creatures.... heh heh heh
  • DNA can actually be a nasty poison since it easily becomes airborne, and can be taken up by your human cells in vitro. Presumably it could also be taken up by a living body through mucous membranes for example if inhaled.

    If there was enough DNA floating around in the environment, who knows how much of it might end up integrated randomly into your own DNA. Since it'd be "junk" DNA designed for structural rather than genetic properties it wouldn't code for anything specific, but random insertion of arbitrary DNA strings into your genome is genetic damage pure and simple.

    Consciousness is not what it thinks it is
    Thought exists only as an abstraction
  • oh shoo
    disregard this
    i'm just fiddling with /.

    ;-)

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