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DNA Origami
FleaPlus writes "Caltech scientist Paul Rothemund has developed a new technique for designing and generating self-assembling 2D nanostructures out of DNA. To demonstrate the technique, which is reportedly simple enough that a high-schooler can design with it, Rothemund created patterns like smiley faces, text, and a map of the Americas. The technique might be useful for generating 'nanobreadboard' scaffolds for things like molecular-scale circuitry, protein-based factories, and quantum computers. Rothemund is currently working to extend the technique to 3D nanostructures."
It will be even more exciting when you read it here again in a couple of days.
"Everything you know is wrong. (And stupid.)"
Moderation Totals: Wrong=2, Stupid=3, Total=5.
(I think you need a subscription to see the text of the nature article. I'm hesitant to post the entire thing, but here's the Discussion section, which is IMHO the most interesting part)
The scaffolded self-assembly of DNA strands has been used to create linear structures and proposed as a method for creating arbitrary patterns. But the widespread use of scaffolded self-assembly, and in particular the use of long DNA scaffolds in combination with hundreds of short strands, has been inhibited by several misconceptions: it was assumed that (1) sequences must be optimized20 to avoid secondary structure or undesired binding interactions, (2) strands must be highly purified, and (3) strand concentrations must be precisely equimolar. These three criteria are important for the formation of many DNA nanostructures and yet all three are ignored in the present method. For example, M13mp18 is essentially a natural sequence that has a predicted secondary structure which is more stable (lower in energy) than similar random sequences (Supplementary Note S8). Further, stocks of staples each contained a few per cent truncation products, stock concentrations were measured with at least 10% error, and staples were used successfully at stoichiometries that varied over an order of magnitude.
I suggest that several factors contribute to the success of scaffolded DNA origami (even though the method ignores the normal, careful practices of DNA nanotechnology). These are (1) strand invasion, (2) an excess of staples, (3) cooperative effects and (4) design that intentionally does not rely on binding between staples. Briefly (details are given in Supplementary Note S9), strand invasion may allow correct binding of excess full-length staples to displace unwanted secondary structure, incorrect staples, or grossly truncated staples. Further, each correct addition of a staple organizes the scaffold for subsequent binding of adjacent staples and precludes a large set of undesired secondary structures. Last, because staples are not designed to bind one another, their relative concentrations do not matter.
The method presented here is easy to implement, high yield and relatively inexpensive. Three months of effort went into the design program. In addition, each structure required about one week to design and one week to synthesize (commercially); the mixing and annealing of strands required a few hours. The greatest experimental difficulty was acquiring high-resolution AFM images, typically taking two days per structure. For rigid designs using circular scaffolds (rectangles with patterns, three-hole disks, and sharp triangles), yields of qualitatively well-formed structures were at least 70%. A better understanding of folding will depend on less-destructive imaging and quantification of small ( 15 nm) defects. A possible objection to the routine use of the method is the potential cost of staples; unlike the scaffold, staples cannot be cloned. However, unpurified strands are inexpensive so that the scaffold constitutes 80% of the cost, even when using a 100-fold excess of staples (Supplementary Note S10).
I believe that scaffolded DNA origami can be adapted to create more complex or larger structures. For example, the design of three-dimensional structures should be accessible using a straightforward adaptation of the raster fill method given here. If non-repetitive scaffolds of megabase length can be prepared, micrometre-size origami with 20,000 features may be possible. However, the requirement for unique sequence information means that the method cannot be scaled up arbitrarily; whenever structures above a critical size or level of complexity are desired, it will therefore be necessary to combine scaffolded DNA origami with hierarchical self-assembly, algorithmic self-assembly, or top-down fabrication techniques.
An obvious application of patterned DNA origami would be the creation of a 'nanobreadboard', to which diverse components could be added. The attachment of proteins, for example, might allow novel biological
I can create a dog out of DNA!
God spoke to me.
Responses starting with IAABiochemist are encouraged...
Human being (n.): A genetically human, genetically distinct, functioning organism.
I don't think the article on the Discovery Channel website has any more information, but it does have my favorite quote on the subject..."In a typical reaction, he can make about 50 billion Smiley faces. I think this is the most concentrated happiness ever created."
Aren't programs like Folding@Home spending thousands of hours of computer time trying to come up with the proper shape to get drugs to behave in a desired way? Even if there's more to it (which there probably is; biology is far from my strongest subject), the potential for nanomanufacturing sounds very very interesting.
I'm thinking that, if this can be applied to materials of varying conductivity -- or if these materials can be made to replace certain types of DNA -- you could make super-efficient capacitors, photovoltaic cells, etc.
It wouldn't surprise me at all if this ended up being as important a development as the integrated circuit.
Paleotechnologist and connoisseur of pretty shiny things.
Will the future of geek culture be like this? Instead of bored microelectrical engineers making silicon art, will DNA nano-engineers be making DNA art? :)
keep it serene please
Engineering is the art of compromise.
tis true... its kinda weird when my dad tells me about something like this 5 days before rather than after I see the story here. Its still very interesting though, and I like having the story on slashdot so there are comments :)
By reading this, you have given me brief control of your mind.
His personal page is promising more details by last thursday... (oops). He's out to lunch right now (OK: Supper), so It'll be at least a couple of hours before he gets the update installed (he has been given the heads up).
Free Software: Like love, it grows best when given away.
Forget RTFA, we need a new one for someone who doesn't even read the title.
God spoke to me.
I might sound like a Luddite, but I would have thought that the earth was already sufficiently littered with waste organic compounds.
Wait till the FDA or whoever declares DNA smileys to be a suspected carcinogen. Who'll be smiling then?
This story was on Digg 2 days ago. No wonder the Yahoo CEO is predicting Slashdot will die like BSD
I'm not a scientist, but a geek interested in computer graphics and 3D modeling and just thought of share this tip with you guys hoping it may be useful.
When you design 3D graphics, you need a software tool to design your artwork in 3D and render it to get the final output. The Blender is one of the best open source 3D modeling and rendering tool. See the 'Art Gallery' section in the Blender home page to understand what you can do with it.
Another very useful 2D vector graphic design tool is Inkscape, this is similar to Adobe Illustrator, and again its open source.
The Gimp is similar to Adobe Photoshop and again this too open source.
Latest versions of these software are included into Tomahawk Desktop, this is a very useful multimedia Linux OS.
isn't origami 3-d, not 2-d as the stuff in the submission says? I'm not trying to troll, but I don't see any 2-d origami anywhere on the net. If someone can point me out to 2-D origami, please do, I want to learn!
Still waiting on Serviscope_minor to wake up to fucking reality and realize that Jessica Price isn't going to fuck him.
If DNA twists... is it 3D or 2D? I'm confused. At what point in 'nano-speak' does something go from 2D to 3D? Okay, molecules on a plane -- 2D. Molecules by themselves -- 3D. It all sounds so... jargoned. Real Life! Now in 3D!!!
7h3$3 4r3n'7 7h3 Ðr01Ð$ ¥0 4r3 £00|{1n9 f0r. M0v3 4£0n9. --OB1
If you are interested in DNA nanotech, definitely check out the SciAm article by Ned Seeman (the founder of the field). Here are some links to lab pages:
Ned Seeman
William Shih
Eric Winfree
John Reif
...we can now create viruses on our computer?
I love humanity, it is people I hate
I have posted here before being generally critical of many "nano"
results as bullshit or hype, however these results here are for real,
they are a big deal, and they do legitimately go under the moniker of
nanotechnology. One of the few times when the public gets fed stuff as
exciting hype and it is actually exciting underneath.
Why is there no image gallery of this stuff? I need new desktop wallpaper!
"No live organism can continue for long to exist sanely under conditions of absolute reality;..."
And we are just finding ways to write code for it. The Matrix of the future is right here, under our feet.
Computational Chemistry will not mean computer simulations of drugs, but the ability to write software in physical hardware, complex chemical structures (DNA) providing a processing capability that will enable us to create physical structures out of software.
Software that processes and generated a physical form for itself.
Just when you swallow a red pill labelled 'windows artery' just remember, viruses and trojans will become physioware too, and just don't get backdoored (ouch) and that next slice of cake you eat could induce and orgasm.
Actually, that sounds great.
#hostfile 0.0.0.0 primidi.com 0.0.0.0 www.primidi.com 0.0.0.0 radio.weblogs.com
The Virus strand:
The virus strand serves as the basic starting material for the origami. It's a single stranded, 7000 base long piece of DNA from a virus that attacks bacteria. There are only two reasons the virus strand is used:
1. It is nonrepeating. This is important because every group of 8 bases have a pretty much random sequence of DNA, and can therefore serve as a unique address for a particular position along the length of the virus strand (you get 4^8 = 65536 possible addresses). Thus, in this way, you can address ~1000 distinct points along the length of this viral DNA.
2. It's readily available. Since you can harvest the DNA from the virus, it's cheap to produce. In fact, this strand is commercially available.
DNA staples:
To actually make the virus fold into position, you need several hundred pieces of DNA to serve as staples that stitch together specified positions along the virus strand. Each staple is 32 bases long. Say that you want to stitch together positions A, BC, and D on the virus strand. You then make a staple whose first 8 bases are complementary to those at position A on the virus, whose next 16 bases are complementary to position BC, and whose final 8 bases are complementary to D. The DNA staple will then bind to those positions in solution and staple positions A, BC, and D together into a rigid, tightly packed structure.
You can buy any 32 base long sequences of DNA that you specify from the internet, so getting several hundred distinct strands is no big deal.
Okay, now how do I make a shape?
Think of how you would draw a smiley face with a CRT screen. Your computer has the outlines of the smiley face in memory, and raster-fills the shape. In the case of a virus origami, you first specify the outlines of the shape, then you raster-fill it with the virus strand by running the virus strand side to side from top to bottom. You then figure out all the staples you need to hold your raster-filled shaped together. Finally, you get the sequences, buy them over the internet, throw them together with the virus strand in a solution, and wolah, you get the world's smallest smiley face.
Is this important?
Paul Rothemund may get a trip to Stockholm some day.
Damn, and I just started reading Neal Stephenson's Diamond Age...
Maybe we deserve this world ?
The article mentions that, basically, you can use this technique to create arbitrary 2D shapes out of 6nm pixels.
.5cm. The unusuable inner ring has a diameter of less than 3cm. So the usable surface area of a standard optical disc is at least:
10,000,000nm per cm.
Divide by 6, gives you 1,666,666 pixels (rounding down) per cm.
Squared gives you 2,777,777,777,776 pixels per cm^2.
Divide by 8 bits per byte gives you 347,222,222,222 bytes per cm^2.
Now, this isn't quite accurate, because you can't have disjoint groups. However, there are ways around that: You could create two contiguous groups which XOR to create the data array, giving you 173,611,111,111 bytes per cm^2.
161GB in a square centimeter.
Standard optical discs (CDs/DVDs) are 12cm in diameter. The unusuable outer edge is not greater than
(pi*5.25^2)-(pi*1.5^2) which gives us about 80cm^2 of usable data space on a standard optical disc.
80cm^2 * 161GB/cm^2 gives us 12.5TB per DNA disc.
Happiness is relative, Based upon the way we live.
And tommorow they'll be learning how to make a Christmas Tree with Stem Cells! Woot!
:D
Oh one more thing... you know what this means right? Many years down the road, we will all have our own living mini-pacman.....
This article immediately reminded me of research on how to control DNA remotely using radio waves I read about a few years ago. Adding gold nanoparticles to the "DNA staples" of the current work should allow the creation of I/O devices to get from our human scale to this nanoscale to build true supercomputers.
There's a long delay from binary file to programmed DNA while the staple strands are readied. It's read-only. It gets harder, less efficient and more error-prone as you scale it to larger arrays. DNA can be destroyed by all sorts of chemical reactions. Maybe it could somehow be used for bulk reproduction of the same data - like printing CDs today, but I predict that we'll find more useful technologies.
Instead, think of it more like a way to do chip patterns. No one would store their mp3s on a chip using optical lithography, but it's hugely useful anyway. This thing may very well be used for patterning all sorts of useful components - CPUs, nanowire processors, chemical sensors and maybe some kind of storage device. There's still plenty of room at the bottom :-)
Any sufficiently advanced libertarian utopia is indistinguishable from government.
Lazy Genes was the first to link oragami with dna.Does anybody remember this? I will show you how to use this with proteins.Its all about the h-bonds.Of coarse this is not free.
Lazygenes
Okay...not real versed on DNA, RNA, etc, but...
Is there a risk that changing things around like this, runs the risk of forming some form of virus that could be quite deadly if not handled properly..
Eric B
ebresie@gmail.com
I know that it's a little late in the day, but since I didn't see anybody mention the costs involved - the short answer is thousands of dollars.
The cost of (buying) DNA varies dramatically depending on the length and the purity of a sample, largely because DNA samples of different length are produced by different methods. The cost purification can also add up to more than that of the production. This is one of the reasons why the Nature article specifically mentions common assumptions about the requirements for DNA components that can be used in this type of programmed self-assembly - essentially he has demonstrated that this can be done a lot cheaper than people have assumed.
The short "staples" in this case are synthetic single-stranded DNA (also called oligonucleotides or oligos). These can be ordered on-line, and the price is typically described as 1$/base. Each oligo is synthesized by adding one base at a time and each time there is about 1% chance of an error - the exact number will depend on the process, but one vendor (IDT) explains that for a 27-mer about 30% of the sample will contain mistakes. Purifying the sample to keep only the correct 70% of the oligos can make it 2-3 times more expensive, hence the article specifically mentions that the proposed method works with cheap unpurified staples. But still, a hundred of different staples each about 30 bases long will be about 3000$.
Even from the short description above, it is clear that the same method can not be used to produce the template that is 1000's of bases long, so they use a natural sequence that can be multiplied by cloning - a relatively cheap process, although with extraction and purification the costs add up - 80% of the total cost according to TA.
Adding up the above estimates, my educated guess is that the total cost of materials in this work adds up to about 10k $ quite easily - custom synthesized and purified DNA is still more expensive than gold on a per gram basis, but then again, so are most nanomaterials. The saving grace is that in some cases you need very little of them to improve or make a product, but until we find a way to make custom-designed nanomaterials on an industrial scale, none of this stuff will be affordable for projects outside of research labs.
And should being coarse ever be free, I ask you ? Of course not, you answer, since you know that there are ladies present.
(Sorry about that, still on my first cup of coffee, just couldn't resist it)
How many beans make five, anyhow ?
I think there might be a typo in your sig.
Is this a rhetorical question?