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First DNA Molecule Constructed from Mostly Synthetic Components
ScienceDaily is reporting that Japanese chemists have created the world's first DNA molecule comprised of almost entirely artificial components. The breakthrough could lead to advances in both medicine and technology, possibly utilizing the massive storage capacity of DNA. "In the new study, Masahiko Inouye and colleagues point out that scientists have tried for years to develop artificial versions of DNA in order to extend its amazing information storage capabilities. As the genetic blueprint of all life forms, DNA uses the same set of four basic building blocks, known as bases, to code for a variety of proteins used in cell functioning and development. Until now, scientists have only been able to craft DNA molecules with one or a few artificial parts, including certain bases."
So in other words we can synthesize a variety of sugars.
We can then take these sugars and string them together.
Just for reference, custom oligo DNA chains have been available for purchase for the last 20 years. This is what makes PCR (DNA fingerprinting for example) work.
I call "pointless" on this demonstration.
Tom's Hardware readers want to know.
Well it's been done for many decades. The trick is making the sequence longer & automating the process to not require an army of grad students.
.. DNA decomposes from bactierial , chemical and radiative action so can't just be left on its own locked away for years.
DNA is read slowly by biological means which is hardly easy to interface to digital systems.
DNA is read sequentially , its not random access at the base level making it useless for most types of database.
Current technologies could in theory already be pushed to have greater storage density than DNA - eg transistors made from a few atoms.
So other than an interesting intellectual exercise , whats the point?
This is nothing new...I created a DNA molecule out of entirely synthetic components for my 5th grade science fair project. Mine was made out of colorful wooden balls glued to wooden sticks. Theirs appears to be sugar-based, which would probably attract ants, so mine is obviously superior.
You know, because it'd be nice to know if life can be built on a different set of elements.
We have a sequence of a human genome and are likely to produce more in the future.
We can, albeit presently with difficulty, construct DNA sequences from artificial materials.
We can, in principle, produce viable eggs by nucleus transfer from one egg to another.
If a "human" embryo is produced from synthesized DNA and by nuclear transfer into an egg from artificial or animal sources, the resulting organism will be structurally equivalent to human, without any physical connection to the human race.
Does this organism have a soul? Is it subject to original sin?
Angels and heads of pins aside; this is pretty cool. There is, though, a slightly unpleasant possible outcome of being able to synthesize DNA sequences. Certain viral pathogens, smallpox comes to mind, are very, very hard to get ones hands on. Samples are tightly controlled and generally not allowed out to play. This is a Good Thing. Genetic sequences, however, are public knowledge. In principle, with sufficient expertise in DNA synthesis(and some protein coating wizardry) one could just "compile" some smallpox from source and then go have a smallpox party with the nearest population center. Happy times.
I'm not a biologist, but I've gotten the impression that they've developed a better way to do something that's been done, which makes implementations in biotech more pragmatic TFA: "...This resulted in unusually stable, double-stranded structures resembling natural DNA.... The unique chemistry of these structures and their high stability offer unprecedented possibilities for developing new biotech materials and applications, the researchers say."
Is Transformers music playing in anyone else's head right now?
Can they be translated into proteins by the cells that live in the real world?
If they don't, this seems an intellectual exercise and not to seeming revolution they are promising.
And they talk about these creating "unusually stable, double-stranded structures." I suspect the evolutionary balancing act has lead to stuctures that are stable, but not too stable that they can't be unzipped, and translated into proteins via the mechanisms of the cell.
Why so dour, mod person?
I laughed out loud at that one, myself.
This isn't quite true. DNA is the genetic blueprint for all cellular lifeforms. There are RNA viruses, there are prions... neither of which use DNA as their genetic blueprints.
And to get really nitpick-y, it's incorrect to say that DNA uses the same set of four building blocks. It would be "more" correct to say that DNA uses a set of four building blocks. I mean, it'd be rather ridiculous if every lifeform on the planet had to share just four molecules.
But, it's not as if we should expect an article geared towards an ignorant public to be completely accurate... the gist was captured.
Anyway, I think I just managed to pedantically get "the Mondays" out of my system... sorry for the rant.
"Trolls they were, but filled with the evil will of their master: a fell race..." -- J.R.R. Tolkien on Olog-hai
They can...but you wouldn't want to.
Silicon also has 4 bond sites which you need for the complex chemistry of life. You can make identical molecules except switch silicone for carbon.
But life will almost certainly NOT do this elsewhere.
Silicon chemistry takes more energy than carbon chemistry.
As an example I will point to earth. Silicone is hundreds of times more common than carbon in the crust yet life did not evolve to use Silicone, it instead used the less common carbon.
Now I can store pirated music in my DNA!
29 mpg. YMMV.
It's "mostly synthetic" DNA? Does that also mean it is mostly dead and therefore slightly alive? If so, I know a guy named Max who can do some miraculous things with it.
I also detect that some folks may not understand the implications. Right now the given combination of natural DNA base pairs can only code for the 20 base amino acids used in nature. If we could create a DNA system that can code for other types of amino acids (in addition to or instead of), we would be able to make some very interesting proteins that would do gods know what, but would make for some great possibilities.
This isn't a case of synthesizing familiar, natural DNA from scratch. That's been done for years and this research was done on commercial equipment for doing so. These researchers created a new type of DNA using four bases that are each similar to but distinct from the four bases that are found in natural DNA. A new chemistry basically. The article suggests that previous attempts had been unstable but this one is not. This could lead to advances like creating DNA molecules with more bases, to increase the density of storage, or find chemistries that are particularly amenable to manipulation, or who knows what.
No, this isn't ordinary DNA produced by synthetic means. If that were the case, it would be of little interest to anyone but a few specialists.
What's new is that THIS synthetic DNA uses a different set of bases. not the usual C, G, T, and A.
Presumably, therefore, it cannot usefully be read or replicated by the usual cellular machinery. That incompatibility makes it, arguably, less of a biohazard (or maybe more of a biohazard, since it might bind to the cellular machinery and gum up the works).
The potential applications for this synthetic DNA apparently involve using it as a structural component of nanostructures. Theoretically it could be used for high-density data storage, though it's hard to imagine how the information could be either written or read.
God just prefers carbon over silicon.
More evidence that God made everything a 6000 years ago!
Actually, God made carbon that way for this purpose, and silicon for microprocessors.
First steps toward constructing the 5th element, perhaps?
I don't normally nitpick, but you made the same confounding error multiple times in one post: silicon and silicone are two different things. One is a chemical element, the other is a group of polymers which contain the element.
Those who fail to understand communication protocols, are doomed to repeat them over port 80.
Now I can store pirated music in my DNA!
"Care to sample my music collection?"
New slashdot layout sucks.
Maybe it's time to wash your pussy.
It is possible for a very simple "lifeform" with only 54 base pairs to be self-reproducing, but only if it is parasitic. Such "lifeforms" exploit the complex and sophisticated DNA machinery of the host to accomplish reproduction.
I found it amazing that the simplest known lifeform that can reproduce independently is the Mycoplasma genitalium bacteria, with 582970 base pairs! This probably isn't the simplest one that can theoretically exist - it is hard to imagine the right combination out of 4^582970 appearing at random in the pre-life organic soup - but whatever simpler thing existed before it is a mystery, as well as why none of the simpler forms still exist today (if that is the case).
This has been bugging me for some time, and as far as I can tell no one has a good answer.
IIRC the first chemical synthesis of a gene was by Khoran in 1970. What these guys have done is replace the four bases of DNA with different ones, and with a different attachment to the ribose group (having a carbon-carbon triple bond instead of normal DNA's carbon-nitrogen single bond), and have demonstrated double-stranded helix formation. The phosphate deoxyribose backbone is still present in it's usual way. Other groups have modified the backbone of DNA; probably the most famous is peptide-nucleic acid where the backbone is like that of a protein backbone. Also non-standard bases have been introduced by many groups and have been used for years. The paper in the Journal of the American Chemical Society also references these modifications plus some others, notably work simultaneously replacing bases and modifying the sugar groups in the backbone. Still replacing all four bases, changing the base-ribose linkage, and having the resulting product form right-handed duplexes, all of that at the same time, that's pretty cool.
I would like to point out that carbon has properties not reproducible in silicon, such as the fact that carbon dioxide is a gas at temperatures commonly encountered on Earth, while silicon dioxide is a solid. This alone seems to preclude any possibility of silicon being a direct replacement for carbon, at least in these parts.
The silicon atom is also substantially larger and some structures that happily form based on carbon will likely be distorted or stressed in the case of a silicon analogue.
Yeah, imaging breathing out sand (Mommy-2 style)
I do not believe in karma. "Funny"=-6. Do good and forbid evil. Yours, Oft-Offtopic Flamebaiting Troll.
"possibly utilizing the massive storage capacity of DNA"
They could use this technology to create an even BIGGER Blue-Ray Disc!
Under Earth-like environmental conditions, carbon has several advantages. But what happens when you move away from Earth's environment? Suppose that the ambient temperature on LV-426 was substantially higher than on Earth. Put it somewhere favorable to silicon, but disadvantageous to carbon. Are you absolutely certain that carbon would still rule the roost?
Honestly, I tire of people who are convinced that earth-life is the only possible solution. It works here. Fine. Change the environmental conditions such that carbon compounds fall apart readily, or water as a solvent doesn't exist in all three phases. Silicon instead of carbon. Methane or ammonia instead of water. Won't happen on Earth, but it might somewhere else.
Yes...I am still convinced that carbon would rule the roost.
In order for silicon to even remotely compete, Silicon dioxide would have to be gaseous. At the several hundred degree higher temp, large and complex molecules become unstable.
In addition silicon is a larger atom which creates a greater limit on structures than carbon.
Carbon would still be used with Ammonia. Using methane absolutely requires carbon (methane being a hydrocarbon).
There is no known condition in which silicon would be preferable while still allowing for large complex molecules.
I get annoyed when people ignore basic physics and chemistry for their own pet beliefs.
However on further though let me add that while I don't think life would EVER spontaneously arise using silicon, it would be theoretically possible to artificially create a silicon based life.
.... I get my own copy of Leeloo?
Have gnu, will travel.
As other readers have noticed, the authors of this study have used existing DNA synthesis technology to incorporate non-natural bases into DNA. While it is impressive that the authors could design bases with the correct geometry to support a DNA-like double helix, the chemistry is not too novel. However, the ability to customize DNA-like polymers has a few interesting applications.
First, all of the sci-fi applications involving artificial life are not really feasible because one would have to design a huge number of new enzymes to recognize these artificial bases. As the field of enzyme design is still in its infancy, I do not see this happening anytime soon.
The real applications come from non-biological uses of DNA. As previous commenter have noted, biotechnologists are investigating the use of DNA as a tool for computation/data storage. Doi et al. have designed their DNA-like scaffold such that other researchers could relatively easily construct new nucleotide pairs in order to expand the number of nucleotides used in the helix. This ability to expand the number of nucleotides could aid researchers in performing calculations using DNA.
Another application involves DNA nanostructures (such as the "DNA origami" designed by Paul Rothemund). DNA is useful for creating nanostructures because it can be easily programmed for self-assembly into arbitrary structures (such as happy faces or long six-helical nanotubes). However, biology is full of enzymes that can degrade DNA, limiting its usefulness. As the authors of this study note, these artificial DNA molecules are resistant to degradation by natural enzymes. Furthermore, it may be possible to alter the mechanical properties of the artificial DNA by tailoring the strength of base-pairing and stacking of the non-natural bases. This could give researchers much greater control over the properties of their DNA nanostructures. One disadvantage of these artificial DNA molecules over natural DNA molecules would be the fact that it is much easier to produce long molecules of natural DNA (the non-enzymatic DNA synthesis technologies used to create the artificial DNA have difficulty creating long [>100bp] strands of DNA). Another caveat is that the authors of the study did not provide a crystal structure of the DNA so we don't yet know its true 3D structure (i.e. whether it forms a helix with the same geometry as regular DNA, although a different geometry could also be interesting).
A real significant advance for DNA nanostructures would be an artificial DNA-like polymer that incorporates a non-natural sugar-phosphate backbone. DNA nanostructures are not stable outside of water which limits their possible applications, in part because water molecules help to stabilize the structure of the sugar-phosphate backbone. Designing a DNA nanostructure that retains its properties outside of water would be a huge boon to the field.
I wonder if on a planet that has no Carbon and an over-abundance of Silicon (obviously an exteme case - but not impossible) if life could evolve using silicon. I mean, when you really come down to it, life could be Germanium, Tin or Lead based by the same arguments, it's just "easier" for Carbon-based to start up. Does anything stop other elements from forming the basis of life? Say Boron (assuming a Boron rich environment void of Carbon and Silicon)?
Even by CowBoyNeal-Natalie Portman-hot grits-frist post standards the whatcoulpossiblygowrong meme is lame as hell. It's attached to absolutely every damn article that is even remotely associated with biology. I'm sick of it. So now every opportunity I get I'll apply that retarded insult to all articles on everything associated with computers and programming. Some wonk over at company X is porting Gentoo to microsoft Access? OMFG! What if s/he/it fucks up and the the the compoooter like becomes self aware and unleashes viruses through the intertubes and n00bs getting pwnd in world of warcraft are actually launching ICBMs???!!!one!!!!!!1111!!!pi!!!!!!? Won't those damn compooter programmers ever learn that they're dealing with forces beyond their control? Better flag that whatcouldpossiblygowrong.
Does slashdot have a dupe checker?
Obviously NO.
Thanks.
Regards,
K. Trout
Life really isn't possible for anything but Carbon or Silicon. The reason I can say that is the number of bonds. 4 bonds allow for extensive and complex networks which complex chemistry requiers. Boron, tin, lead etc can't do this.
We essentially live on a planet with an over abundence of silicon and a virtual absence of carbon. Silicon is so much more plentiful than carbon it is almost silly. On proto-earth the only availible carbon source was the atmosphere and in a water world, like earth, air is a lousy place to get your food.
Silicon COULD be used in life but is very unlikley to arrise spontaneously. We could design life to use silicon in theory.
They talk about using DNA as a data storage device, but I'm worried someone's kinky porn collection might just have the exact data sequence to mutate harmless bacteria into some nasty STD.
Go read the actual JACS paper, it is written a bit more sanely than the synopsis. They synthesized something like DNA with the normal phosphodiester backbone but radically different bases. The design of the bases was about the same as the natural ones, as far as the H-bonding pattern is concerned but with very different attachment chemistry to the deoxy ribose. Cool idea... not hugely more interesting to me than the 5th base that got made a few years back though and here's why.
Synthesizing DNA using these rigs is not a big deal, that there is some other way of positioning the bases seems a bit obvious. Good job to them for figuring it out, and this is a deserved JACS paper but the alarmists and the overly excitable folks can go home. I don't think this tech can be used to amplify the DNA using existing polymerases, the geometry is close but different, and polymerases care. Further, it either doesn't anneal to natural DNA or does so poorly, they don't even discuss mixed oligos (that I saw). The information density arguement would require that this work. As it is they have a new chemistry to get four bases that are very hard to amplify. If one went out and engineered a polymerase to make DNA from these bases, great, but that's a LOT of work to get back to the same information density. It may not actually be possible to end up with a fifth and sixth base pair that pair with high specificity, so this may be a waste of time in that regard.
Finally, on the information storage discussion... DNA isn't bad. Current DNA archiving systems are ridiculously easy to use and cheap. Lifetimes are at least five years at room temp with pretty lax humidity requirements (probably decades)... so this is better than CDR's at least. And one can think of this as a really high redundancy system, if you wanted the infoback from a really old card, just use the modern sequencing methodology on the mix recovered from the card with ~10x over reading and you'll (with high confidence) recover the original sequence even if there's been some degradation.
The big advantage of the articles technology isn't lifetime or information density (as far as I'm concerned), but that it is tolerant of biological contamination (which is everywhere). You could get the info off the card decades later, and with some care reconstruct even a degraded sample, but a contaminated sample is much harder to deal with. This approach gives you (if they could ever make a polymerase specific for these bases) the ability to get the info back, even with degradation and contamination. So halfway maybe.
cheers-
-sk
No message here.
My other sig is a BMW
Since you guys seem to be very "up" on this "DNA" stuff, I shall posit a question...
From the Apex of my complete ignorance about Synthetic DNA, does this discovery mean I should:
A) Begin stocking up on weapons, ammunition and food in a highly defensible bunker for the inevitable Solanum virus outbreak and subsequent zombie horde plague.
B) Begin boning up on my virtual gaming ability as our new Synthetic DNA Overlords encapsulate all of humanity in a virtual world until such time as The One frees us all.
C) Ignore this as yet another pointless discovery which shall lead to nothing, and just go have another [insert food or beverage of choice].
D) ???
E) Invest large amounts of money into the company these scientists work for and make PROFIT!
Anyone?
Bueller? Bueller? Bueller?
Official Heretic from the "Church of Global Warming". Proven right thanks to whistle blowers. AGW = Flat Earth Theory
Honestly, I tire of people who are convinced that earth-life is the only possible solution.
Don't take this personally, but I tire of people whose imaginations outstrip observed evidence. I can imagine all sorts of things - silicon-based life is just one of them.
But reality is that we're not finding life in places where modern-day earth life could exist, and we're not seeing or hearing evidence of intelligent life elsewhere in the galaxy. I know that we've only begun to search, but we already have enough evidence to say for a fact that life is not ubiquitous.
So here's what we know: 1) once life gets started, it is very tenacious and difficult to snuff out. 2) but it's apparently *really* difficult to get life started. Those two facts combined suggest that yes, earth-like life might be the only possibly solution. I don't mean *exactly* earth like. I mean carbon and oxygen based.
To me, it is reasonable to speculate alien life with an extra nucleotide or two. It's reasonable to speculate about novel amino acids or DNA with a left hand twist. But to me, it's pure unfounded fantasy to suggest that life can be based on silicon.
You can make similar molecules using silicon, but you can't make identical molecules. If you took say, a protein, and replaced all the carbons with silicon, that protein would not function. I'm not even certain the protein would remain intact. I'm not aware of any large, complex molecules, on the scale of a protein, made with silicon as the primary backbone. Silicon chemistry simply doesn't lend itself to large, complex, molecules.
and soon after that it became self aware...
You forgot to mention that a significant amount is covered by DD and FFF brassieres making access difficult.
Silicon, on the other hand is under less constraint (heh).
Hey, somebody had to say it.
I very much agree with you with one exception:
2) but it's apparently *really* difficult to get life started.
we don't have the telescope resolution to really see if life exists elsewhere. We can't see earth sized planets and we can't analyze the atmosphere of the ones we do see. Life COULD exist there and we wouldn't know it.
All we can say is that intelligent life at the industrial age or better (which is when we could have a chance of detecting them) is non-ubiquitous.
we don't have the telescope resolution to really see if life exists elsewhere.
Yes, you're right.
[insert witty Pamela Anderson joke here]
Have you driven a fnord... lately?
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Call me a sci-fi nut but it seems like these synthetic molecules (or the future versions of them) would be ideal for DNA computing. If it ever becomes viable it would be beneficial to have the DNA be non-standard. If you can engineer them from the ground up you can make sure there is no cross contamination and no mechanisms to cause a viral-like replication scheme. Look at viroids and viruses and prions. The last thing you want is a stray computer DNA to get into a cell. If it is in the same natural DNA structure it can either end up reproducing itself to the detriment of the host, or end up spewing nonsensical proteins causing damage or possibly cancers. If it is in a form of DNA that the cell cannot utilize it will merely be floating junk matter and hopefully not interact with the host body in any way. Same for vice versa. If you have a computer that only uses synthetic DNA for storage the processes to retrieve and store data won't be (hopefully) screwed up by cellular/viral DNA trying to replicate. Also you would probably have to worry less about microorganisms trying to eat the data of your DNA computer.
Hang on a second, and let's examine exactly what predicates "life." You need to have raw materials available. There needs to be an energy gradient. There needs to be a closed-cycle chemical reaction for the transport of energy. There needs to be a solvent for the mechanical transport of chemicals.
On Earth, we've got the solar influx for the energy gradient, water is the solvent, and the carbon compounds provide the chemical-reaction basis. Environmentally, the Earth's temperature and atmospheric pressure put us near the solvent's triple point, with the majority of the solvent in the liquid phase.
Could you conceive of a place where ammonia is the solvent? You'll need environmental constraints such that there's an abundance of the solvent in a form conducive to mechanical transport. You might still have carbon-based life forms, but they wouldn't be using the water-cycle we know here on Earth. Why is that such a fantasy?
If you're going to argue that "I haven't seen it yet, therefore it can't possibly exist," I'd recommend some introspection on the definition of the word "preconception."
> DNA decomposes from bactierial , chemical
Wron. You can use PNA or Nylon based "DNA".
> DNA is read slowly by biological means which is hardly easy to interface to digital systems.
[X] You have no idea how DNA could be used for computer chips.
Hint: Intal and IBM puting money into this!
Use DNA to self-assemble single walled carbon nano tubes and we are talking business.
> DNA is read sequentially , its not random access at the base level making it
s. above.
If you have no idead what you are taling about it is sometimes better to just shut up.
...and when I was a kid we used the colored balls and wooden sticks. Isn't that the same? ;O I didn't realize we were so smart.
Perhaps, then, there was a geological period when silicon-based life existed on molten Earth? Perhaps it still exists bellow the crust? Perhaps someday THE ELDERS will come over here and punish us for our disrespectful saprophytic usage of their bodies' remains for our glassware, electronics and boobs enlargement?
That does it! I am establishing a cult.
Why is that such a fantasy?
What you just said isn't a fantasy, because you were able to back it up with sound reasoning. My complaint is people who talk about silicon for no other reason than that they saw it on star trek.
I should further clarify that I'm not suggesting that you could substitute silicon for carbon, and end up with bipedal hominids who strongly resemble us ... only with silver skin. That's Hollywood working within their abilities to map actors into roles. I'm thinking substantially more basic life. Think one-celled critters; bacteria; viruses.
I was watching some coverage of NASA's recent earthmoving (marsmoving?) efforts, and was stunned at just how stoopid the reporters can be. I expect that the NASA folks do understand that life doesn't have to play by the earth-based ruleset, but that it's a good place to start. It's very likely that all the inner planets have some form of cross-contamination (i.e. localized exogenesis.) I wouldn't expect critters from Earth to fare well on either Mars or Venus, but some molds might. I've got some tenacious mold growing in my crawlspace, and that's a pretty inhospitable place. The stuff keeps coming back in spite of my best "scorched earth" efforts.
Can they make Splenda taste better?