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Researchers Design DNA With New Shapes and Structures

Jason Koebler writes: The shape of DNA is a double helix, right? That's what we are taught. Well, now the answer is "not always." Researchers at the Massachusetts Institute of Technology have discovered how to program DNA to be shaped like a bowl, or a spiral, or a ring, or other shapes that aren't found in nature.

It's the latest in a string of discoveries about the underlying structure of life and the building blocks by which it's made. Recently, scientists created new nucleotides that do not exist in nature and inserted them into a living organism. And now, this: DNA can look like just about anything and can be assembled into many shapes.

47 comments

  1. Multipass by RivenAleem · · Score: 4, Funny

    Me fifth element - supreme being. Me protect you.

    1. Re:Multipass by ArcadeMan · · Score: 2

      Autowash.

    2. Re:Multipass by Anonymous Coward · · Score: 0

      Multipass!

  2. Steps to molecular machines? by babymac · · Score: 2

    The next step should be to figure out how to create DNA "tools" to help assemble molecular scale machines!

    --
    "War makes me sad." - Me
    1. Re:Steps to molecular machines? by Anonymous Coward · · Score: 0

      Or replicators. Both the Star Trek and the Stargate variety is fine by me.

    2. Re:Steps to molecular machines? by peragrin · · Score: 1

      That is what DNA does already. It just builds. Macroscopic versions out of the molecules.

      --
      i thought once I was found, but it was only a dream.
    3. Re:Steps to molecular machines? by jbarone · · Score: 1

      Already exist. This is very old news.

  3. Humor by justsomecomputerguy · · Score: 3, Funny

    What do you make of it Johnny?! Well, you can make a hat, a broach, a pterodacty!....

    1. Re: Humor by Anonymous Coward · · Score: 0

      +1

      I'm thinking it's from one of the Airplane movies.

  4. But can this clean up the gene pool ? by Anonymous Coward · · Score: 0

    Because that is the problem facing humanity now.

  5. How long by Anonymous Coward · · Score: 0

    How long until someone creates penis-shaped DNA?

    1. Re:How long by Anonymous Coward · · Score: 0

      Already done if someone has a DNA shaped penis.

  6. dark matters II the hogwash; aired on POT... by Anonymous Coward · · Score: 0

    (Personal Open Terminal). in this episode mutant crown royal dna is composted in the lhc. 'we're going to grow something here' was the official statement? viewers are feeling ill frequently... tbc reruns https://www.youtube.com/results?search_query=nazi+zion+experiments sheesh phewww

  7. This should be a given.. by rahvin112 · · Score: 5, Interesting

    This should be a given, this is how the body makes proteins. The "recipe" is stored in the DNA, the transcriber runs along the DNA making a copy and then it folds into the protein when the copy is complete. A small mistake in the transcription and it doesn't fold into the right protein or doesn't fold at all. This is why protein research is so hard right now, they don't fully understand what governs how the proteins fold.

    This research may give them a leg up on understanding that, very cool that they figured out some of the rules.

    1. Re:This should be a given.. by Anonymous Coward · · Score: 1

      They're folding DNA itself, not proteins.

      In life, DNA gets translated into RNA, RNA is then grabbed by a ribosome which attaches the correct amino acids. Then the amino acids magically fold into a working protein (hopefully).

    2. Re:This should be a given.. by kebes · · Score: 3, Informative

      The base-pair sequence of DNA determines its biological function. As you say, this sequence determines what kinds of proteins get made, including their exact shape (and more broadly how they behave).

      But TFA is talking about the conformation (shape) of the DNA strand itself, not the protein structures that the DNA strand is used to make.

      In living organisms, the long DNA molecule always forms a double-helix, irrespective of the base-pair sequence within the DNA. DNA double helices do actually twist and wrap into larger-scale structures: specifically by wrapping around histones, and then twisting into larger helices that eventually form chromosomes. There are hints that the DNA sequence itself is actually important in controlling how this twisting/packing happens (with ongoing research about how (innapropriately-named) "junk DNA" plays a crucial role). However, despite this influence between sequence and super-structure, DNA strands essentially are just forming double-helices at the lowest level: i.e. two complementary DNA strands are pairing up to make a really-long double-helix.

      What TFA is talking about is a field called "DNA nanotechnology", where researchers synthesize non-natural DNA sequences. If cleverly designed, these sequences will, when they do their usual base-pairing, form a structure more complex than the traditional "really-long double-helix". The structures that are designed do not occur naturally. People have created some really complex structures, made entirely using DNA. Again, these are structures made out of DNA (not structures that DNA generates). You can see some examples by searching for "DNA origami". E.g. one of the famous structures was to create a nano-sized smiley face; others have 3D geometric shapes, nano-boxes and bottles, gear-like constructs, and all kinds of other things.

      The 'trick' is to violate the assumptions of DNA base-pairing that occur in nature. In living cells, DNA sequences are created as two long complementary strands, which pair up with each other. The idea in DNA nanotechnology is to create an assortment of strands. None of the strands are perfectly complementary to each other, but 'sub-regions' of some strands are complementary to 'sub-regions' on other strands. As they start pairing-up with each other, this creates cross-connections between all the various strands. The end result (if your design is done correctly) is that the strands spontaneously form a ver well-defined 3D structure, with nanoscale precision. The advantage of this "self-assembly" is that you get billions of copies of the intended structure forming spontaneously and rapidly. Very cool stuff.

      This kind of thing has been ongoing since 2006 at least. TFA erroneously implies that this most recent publication invented the field. Actually, this most recent publication is some nice work about how the design process can be made more robust (and software-automated). So, it's a fine paper, but certainly not the first demonstration of artificial 3D DNA nano-objects.

    3. Re:This should be a given.. by Anonymous Coward · · Score: 0

      In living organisms, the long DNA molecule always forms a double-helix

      As always, there are exceptions to that rule.

    4. Re:This should be a given.. by lazy+genes · · Score: 0

      TFP should be in the art section. Protein folding is based on hexagons and is very complex. Glycine and proline are the main reasons why folding is so hard to figure out. My work shows that if you twist the protein hard enough, you will see all the motifs. The problem is that the two problem aminos run off some type of quantum scales.

    5. Re:This should be a given.. by reve_etrange · · Score: 1

      form a structure more complex than the traditional "really-long double-helix".

      I do think TFS is a little misleading, since all the structures are still made out of helices (with bends and junctions and so forth).

      --
      .: Semper Absurda :.
  8. wrong by WindBourne · · Score: 2

    It is still double helix. It is the tertiary structure that is being played with, not the helix. Without the double helix, it would be to easy to have errors. In addition, nature enzymes are designed for double helix and the zipper effect.

    --
    I prefer the "u" in honour as it seems to be missing these days.
    1. Re:wrong by QilessQi · · Score: 1

      Without the double helix, it would be to easy to have errors.

      Can you please elaborate on that? It sounds cool... is there something specific to the shape of the double helix that makes storage or transcription less error-prone?

    2. Re:wrong by quantumghost · · Score: 2

      Double stranded DNA is more resistant to errors, but not immune. At the most basic level, the double helix provides complementary redundancy, the problem then becomes: which strand has the error and which is the true strand. http://en.wikipedia.org/wiki/D...

  9. Spiral is the key by ArcadeMan · · Score: 1

    DNA shaped like a spiral is the key.

  10. Re:Yawn... by pr0t0 · · Score: 1

    Let me know when they can do this: https://www.youtube.com/watch?...
    The Earth needs more Milla Jovovich.

    --
    I'm sorry, but your opinion seems to be wrong.
  11. Re:Yawn... by Anonymous Coward · · Score: 0

    Let me know whey I can visit ill-concieved dinosaur hybrids in Jurassic Park.

    Until then I'm going to stick to spreading my DNA by masturbating into toilet paper.

    Obviously because you'll never get the chance to deposit your DNA in a vagina.

  12. Movies! by dbreeze · · Score: 1

    http://www.nature.com/ncomms/2...
    http://www.nature.com/ncomms/2...

    I gotta figger out how to make screensavers......

    --
    When the king heard the words of the Book of the Law he tore his robes.2Kings22:11
  13. Narf! by Anonymous Coward · · Score: 0

    With this and designed DNA, Pinky and Brain are just one step ahead.

  14. Cosmic DNA? by handy_vandal · · Score: 3, Informative

    Space dust may store information as a double helix.

    A new computer simulation shows that dust immersed in ionized gas (i.e., dusty plasmas) can organize itself into double helixes. The simulations suggested that under conditions commonly found in space, the dust particles first form a cylindrical structure that sometimes evolved into helical structures. Along some spirals, the radius of the helix was seen to change abruptly from one value to another and then back again, providing a mechanism for storing information in terms of the length and radius of a section of a spiral.

    Hessdalen light

    --
    -kgj
  15. Re:Yawn... by Anonymous Coward · · Score: 1

    That's dangerous. Putting DNA in a vagina could lead to pregnancy.

  16. So what? by Anonymous Coward · · Score: 0

    This sounds interesting scientifically, but can it lead to some kind of application that's really interesting, or is this just science for science's sake?

  17. Re:Yawn... by Anonymous Coward · · Score: 1

    I did and this resulted in rapid loss of gathered funds, loss of a job during divorce proceedings, depression and finally loss of a house. In some cases toilet paper or whatever other place you chose to deposit your sperm is better than vagina as this is owned by foreign parasitic species. At least they are foreign and parasitic when sexual organs are important part of a context in which one operates at the moment. At work I do not look at the boobs and arses so I am safe. This of course causes problems too as I was (many times already) taken to be gay because I did not display behaviours characteristic to heterosexual rapists, we all are. I guess we cannot have everything, can we?

  18. Mobius! by Chelloveck · · Score: 1

    I so want to see them make Mobius DNA!

    --
    Chelloveck
    I give up on debugging. From now on, SIGSEGV is a feature.
    1. Re:Mobius! by Anonymous Coward · · Score: 0

      Hmm... I wonder what one of those DNA copying enzymes would do when told to copy what is essentially and infinite loop...

  19. Re: Yawn... by Anonymous Coward · · Score: 0

    There's something like a barrel full of DNA in your mom's vagina on any given day. A lot in her stomach, too.

  20. This certainly looks like woven double helix by azav · · Score: 1

    I think the title is misleading.

    It sure looks like they are using the double helix style of DNA and then weaving that into shapes or wound ribbons.

    Am I missing something here?

    --
    - Zav - Imagine a Beowulf cluster of insensitive clods...
    1. Re:This certainly looks like woven double helix by Anonymous Coward · · Score: 0

      Nope. It's an article written by someone who never paid attention to picture observation in 1st grade.

    2. Re:This certainly looks like woven double helix by gx5000 · · Score: 1

      Oh well then, I guess I can cancel the move to Iceland then, Thanks.

      --
      End of Line.
  21. Does this qualify as an intelligent design? by Anonymous Coward · · Score: 0

    I guess we are back to egg or chicken debate.

  22. Different levels of structure by damn_registrars · · Score: 1

    The primary structure for double-stranded DNA is most often a double helix. Single stranded will try to form similarly complementary structures to minimize unbalanced charges. However from the primary structure you can get into secondary, tertiary, and quaternary structures that go well beyond that. One really good example is the structure of a chromosome which starts with double-stranded DNA (as a double helix) wrapping around histones to form chromatin. From there it condenses further, eventually reaching the level of a chromosome with several steps along the way.

    We also know that DNA can form interesting shapes as single-stranded forms that can bind to a lot of non-nucleic-acid molecules (Aptamers being good examples of these).

    --
    Damn_registrars has no butt-hole. Damn_registrars has no use for a butt-hole.
  23. Re: Yawn... by Anonymous Coward · · Score: 1

    I'd buy several

  24. New shapes and structures? by Rinikusu · · Score: 1

    I will not be satisfied until they spell out METALLICA in DNA. (pre-black album metallica, you know)

    --
    If you were me, you'd be good lookin'. - six string samurai
  25. Dig a big hole and get ready by gx5000 · · Score: 1

    " that do not exist in nature and inserted them into a living organism"

    GMO's aren't the problem, how we use them is.....now this ?
    There's a reason to believe in the complexity of Evolution's tests and trials.
    When we start mucking around with building blocks like this let's hope we remember that we don't
    really know how this lego set will act once it's built up....really interesting though I must admit.

    (GMOs belongs in Labs and Cures, not in crops or Livestock)

    --
    End of Line.
  26. Prediction is only novel part of this research by jbarone · · Score: 1

    This isn't even remotely new. People have been doing DNA origami for years. This article isn't about building anything new, it's about software that can better predict how the DNA will fold given a certain construction method.

    DNA origami is mostly novelty, anyways. Most researchers have moved on to using DNA to build structures that actually do useful things, rather than just look pretty.

  27. design is not the same as produce. by Chikungunya · · Score: 1

    I think is still too early to celebrate the technique, this are mostly just computer predictions that have not yet been proven in the lab, there are a lot of things in biology that are supposed to happen based in computer simulations that simply don't in a flask. If you have a million compounds and dock them to a single active site in a protein you may get around a thousand that are predicted to work inhibiting that site, when you test them you are lucky if a couple really have some kind of significant inhibition. Here they are talking about predicting a shape using hundreds or even thousands of this interactions in a single molecule, I would expect most of this predictions to result false and even those that get it right will do it only on a few cases out of many trials.

    1. Re:design is not the same as produce. by jbarone · · Score: 1

      Actually, the current roadblock isn't in silico->in vitro, it's in vitro->in vivo. There are plenty of really cool mechanical or "electronic" devices built with DNA/RNA/proteins in wetlabs. You are absolutely correct that the stochasticity makes the goal reaction(s) unreliable, but that's why they make extensive use of amplifiers to replicate desired outputs to the point that they will reliably continue the reaction or report the result. It takes a lot of redundancy and it's not fast (at least as compared to artificial nanotech), but it has the advantages of being dirt cheap, self-correcting in many ways (biological systems have eons of fine tuning while artificial systems have, at most, decades), and very scalable.

      The problem is getting these methods to work in actual cellular environments, as the aforementioned eons of fine tuning also mean that there are a lot of mechanisms dedicated to identifying and destroying unusual DNA in cells.