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Scientists Create Synthesized DNA Bases

ScuttleMonkey posted more than 6 years ago | from the and-mother-nature-is-pissed dept.

Biotech 125

Iddo Genuth writes to tell us that researchers at the Scripps Research Institute in San Diego have created two artificial DNA bases in an effort to "expand biology's potential." "In the future, [chemist Floyd] Romesberg envisions manipulating the genetic code of bacteria in order to assemble better drugs or even man-made proteins. Until now, the bases only work in bacteria, so human augmentation is currently not possible. Another option is to use alpha and beta to help construct nanomachines to be used for drug delivery. 'This is like jumping from the Stone Age to the Bronze Age,' Romesberg says. 'It takes time to figure out how best to use metal.'" Update 18:10 GMT by SM: Roger writes to share the NewScientist link with a bit more information. There is also the original release text for consideration.

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I want my Vitamin C! (3, Interesting)

snowgirl (978879) | more than 6 years ago | (#23970497)

Can we get back our Vitamin C gene again? I would love being able to eat less fruit... Scurvy sucks.

I for one... (0, Redundant)

vivin (671928) | more than 6 years ago | (#23970523)

I, for one, welcome our new synthesized DNA-base based overlords.

Re:I for one... (4, Funny)

eviloverlordx (99809) | more than 6 years ago | (#23970819)

The Island of Dr. Moreau called; they want their genetic manipulation with unintended consequences back. I told the caller to take a number.

Re:I for one... (-1, Troll)

Anonymous Coward | more than 6 years ago | (#23970889)

mods cant read timestamps dumb fucks

Re:I want my Vitamin C! (4, Insightful)

twatter (867120) | more than 6 years ago | (#23970571)

This has implications beyond the delivery of drugs. Drugs act at the protein level, but imagine a delivery mechanism that does not require a protein receptor, but instead acts at the DNA filament level.

This is HUGE news.

Re:I want my Vitamin C! (2, Funny)

Sir_Real (179104) | more than 6 years ago | (#23970687)

Can we get back our Vitamin C gene again? I would love being able to eat less fruit... Scurvy sucks.

Apparently a war has already been delcared on Scurvy, and it appears to almost be won [internetwks.com]

Re:I want my Vitamin C! (2, Interesting)

snowgirl (978879) | more than 6 years ago | (#23971167)

Hahahah, it's so funny, because reading about the history of Scurvy, people actually thought this way for awhile.

Personally, I really think it'd be awesome if we could just repair our Vitamin C gene, and generate Vitamin C ourselves again... but then we also need to fix the gene that processes uric acid, so that we don't fill up on stuff doing the job of Vitamin C... since high uric acid levels have been associated with Type II diabetes, it might just effect a reduction in diabetes in humans.

Re:I want my Vitamin C! (3, Funny)

jollyreaper (513215) | more than 6 years ago | (#23971003)

Can we get back our Vitamin C gene again? I would love being able to eat less fruit... Scurvy sucks.

Have you ever tried coconut rum and fresh OJ? You'll never bitch about drinking your fruits again.

Re:I want my Vitamin C! (1)

snowgirl (978879) | more than 6 years ago | (#23971225)

Can we get back our Vitamin C gene again? I would love being able to eat less fruit... Scurvy sucks.

Have you ever tried coconut rum and fresh OJ? You'll never bitch about drinking your fruits again.

Sorry, I prefer my alcohol in the form of Riesling wines. I haven't suffered from Scurvy yet, so I'm apparently getting enough vitamin C, but I don't really eat a lot of fruits and vegetables, so... not so sure.

Anyways, making fruits and veggies a more optional part of our diet, since we can make our own vitamin C might have a positive impact on our quality of life. (Of course, it puts the Vitamin C Herbal Supplement people out of business, but hey, they're just the new patent medicine anyways, so...)

Re:I want my Vitamin C! (3, Funny)

ShieldW0lf (601553) | more than 6 years ago | (#23971545)

If it hasn't been sprayed through a pile of burning rotten vegetation from Scotland, it's shite.

Re:I want my Vitamin C! (2, Funny)

93,000 (150453) | more than 6 years ago | (#23971849)

Pretty reckless with your precious fluilds, there, buddy.

I only drink grain alcohol and rain water.

Re:I want my Vitamin C! (1)

DigitalHammer (581235) | more than 6 years ago | (#23972193)

Have you ever tried coconut rum and fresh OJ? You'll never bitch about drinking your fruits again.

Just wait until he starts bitching about his liver. :P

Re:I want my Vitamin C! (2, Interesting)

snowgirl (978879) | more than 6 years ago | (#23972397)

Have you ever tried coconut rum and fresh OJ? You'll never bitch about drinking your fruits again.

Just wait until he starts bitching about his liver. :P

Why does no one look at my name? Is it just standard presumption that everyone on slashdot is a guy, even when their login is "snowgirl"?

Re:I want my Vitamin C! (0)

Anonymous Coward | more than 6 years ago | (#23972701)

You're not one of those guys who play as a girl on online games are you?

Re:I want my Vitamin C! (1)

snowgirl (978879) | more than 6 years ago | (#23972919)

You're not one of those guys who play as a girl on online games are you?

*sigh* I've apparently found out that such guys don't exist on European servers. It's likely that Europeans being less sex-retentive than us don't provide such fundamental benefits to females that we enjoy here in America that they don't see a benefit to acting like girls to get stuff.

Here's how to tell the boys from the girls when they're both playing female characters: girls don't expect nor ask for stuff from guys. If you give us stuff after we've gotten to know each other, then hey, cool... but if you have a "girl" hounding you online to give her stuff... well, either she's a boy, or a prissy little princess that makes the rest of us look bad. So, just assume it's a guy... you won't hurt anyone that matter's feelings.

Re:I want my Vitamin C! (1)

Moridineas (213502) | more than 6 years ago | (#23974297)

*sigh* I've apparently found out that such guys don't exist on European servers.

That's actually interesting. Would be nice to know more than just one person's experiences though.

It's likely that Europeans being less sex-retentive than us don't provide such fundamental benefits to females that we enjoy here in America that they don't see a benefit to acting like girls to get stuff.

Or maybe European women/girls don't play as many video games as females in the US, throwing things off. Maybe US males are more secure in their sexuality and don't have a problem playing as female characters. Who knows, I'm sure I (and others) could come up with some more equally weird (and probably wrong) theories if I kept trying!

MMORPG (Many Men Online ... (1)

IdeaMan (216340) | more than 6 years ago | (#23975155)

I always play female toons. I figure anyone that enjoys looking at guys for 2000 hours must be gay.

Also I don't usually play just one character, which is why I don't equate myself with my character.

And they gotta have really nice hair, because usually that's what you'll be seeing the most of due to the way the camera zooms in and out on the back of the characters head.

Re:MMORPG (Many Men Online ... (1)

snowgirl (978879) | more than 6 years ago | (#23975579)

I always play female toons. I figure anyone that enjoys looking at guys for 2000 hours must be gay.

... or they're girls... but then we don't really like playing guys so much... while you all may enjoy staring at a girl's butt all day long while you're playing your game... I don't know... it just feels weird to me to pick a character exclusively because I am attracted to it.

Re:I want my Vitamin C! (1)

snowgirl (978879) | more than 6 years ago | (#23975631)

If EU women/girls didn't play as many video games as here in the USA, then there would be a significant lack of female characters on those servers.

The most common reason I hear from guys about why they play a female toon: "If I'm going to stare at a butt for 8 hours a day every day...", that or "girls get free stuff from guys..." Both of those are patently obvious to me that they're driven by the sexually repressive regime.

To link the comment from the other respondent to yours... "Maybe US males are more secure in their sexuality and don't have a problem playing as female characters", however "I figure anyone that enjoys looking at guys for 2000 hours must be gay"... perhaps US males are even LESS secure about their sexuality, and thus feel that they MUST place a female character on their screen, for fear that they might be labeled "gay".

Oddly, presenting an interesting situation... is it more acceptable for a guy to women's clothing at long as they're straight, or more acceptable for them to be gay?

Re:I want my Vitamin C! (1, Funny)

Anonymous Coward | more than 6 years ago | (#23972747)

dude, calm down man.

Re:I want my Vitamin C! (1)

snowgirl (978879) | more than 6 years ago | (#23972801)

lol, funny :P

Re:I want my Vitamin C! (1)

DigitalHammer (581235) | more than 6 years ago | (#23972773)

Girls on slashdot? You must be joking! :P

Re:I want my Vitamin C! (1)

ColdWetDog (752185) | more than 6 years ago | (#23974121)

She's really an FBI agent...

Re:I want my Vitamin C! (2, Funny)

spazdor (902907) | more than 6 years ago | (#23972829)

Nicknames are meaningless. The big giveaway that you're a girl was that you drink Rieslings.

That shit's for ladies and, uh, whoever plays one on the Internet.

Re:I want my Vitamin C! (1)

snowgirl (978879) | more than 6 years ago | (#23972991)

Girls can't enjoy drinking beer? :P Sometimes I do, but usually, unless it's a German light beer, it tastes so bad that I'd usually rather have something that I can stand drinking.

It isn't a "girls drink wine" and "boys drink beer/hard alcohol" world. My friend refuses to drink wine anymore, because she's moved on to strictly vodka. (Personally, I find hard alcohol much too annoying to buy here in Washington what with the state-controlled liquor stores.)

More so, the indicator that I drink Rieslings shows that I have a more refined palette than "meat, potatoes, and beer" which seems to dominate the male diet. *laugh*

Re:I want my Vitamin C! (1)

spazdor (902907) | more than 6 years ago | (#23973387)

Don't get me wrong. I will get into fist fights with dudes who disagree with my many ill-informed opinions about the supremacy of Cabernet Shiraz over all other blended reds. I am a wine asshole of the highest order.

Riesling is pretty much always way too sweet for me though, and I honestly don't know any dudes who feel differently. Same with ice wines.

Re:I want my Vitamin C! (1)

pjt33 (739471) | more than 6 years ago | (#23975183)

There are sweet Rieslings and dry Rieslings. Dry Riesling, preferably from the Moselle region, is my white wine of choice. Well, unless Champagne is on offer.

Re:I want my Vitamin C! (1)

snowgirl (978879) | more than 6 years ago | (#23975809)

My ex-boyfriend drinks a lot of beer now, but pretty much preferred, so called "bitch beers" before being introduced to beer that actually tastes good. (Odd that it could be more acceptable for a guy to drink girlie drinks rather than drink Budweiser, Coors, Miller, et aliae ">cervissiae culae.)

He actually prefers Rieslings, because, well, they taste good if you don't have a distinguished palette. My palette for Rieslings is a little better than "it's sweet", I like a dry component for it to be "refreshing", and if it doesn't have that, it feels a bit like milk in that it coats, but doesn't refresh.

Basically, anyone who doesn't like sweet wines won't like many Rieslings, and Ice Wines, but anyone who has a sweet palette, would definitely like those. My palette isn't dry enough to support drinking most other wines, but I wouldn't say I have a "sweet" palette.

Re:I want my Vitamin C! (1)

Kreigaffe (765218) | more than 6 years ago | (#23972943)

Duh, there are no girls on the internet.

(I for one welcome our mammary-bearing overlords?)

Re:I want my Vitamin C! (1)

bsDaemon (87307) | more than 6 years ago | (#23972977)

Well, since the girls in MMORPGS usually are just fat guys with all their hair on their backs instead of their heads, it probably feeds the stereotype about slashdotters, too.

if it makes any difference, I managed to notice.

Re:I want my Vitamin C! (1)

snowgirl (978879) | more than 6 years ago | (#23975561)

Well, since the girls in MMORPGS usually are just fat guys with all their hair on their backs instead of their heads, it probably feeds the stereotype about slashdotters, too.

if it makes any difference, I managed to notice.

I swear, when I started reading this I expected "in their hands" not "on their backs"... >_ lol

Re:I want my Vitamin C! (1)

Oktober Sunset (838224) | more than 6 years ago | (#23975859)

name? I have no idea what this name thing is, maybe you can explain it to me and how this denotes your gender 978879.


838224.

Re:I want my Vitamin C! (1)

Hatta (162192) | more than 6 years ago | (#23972589)

Are you serious? Could there be anything more delicious than fruit? Try growing your own strawberries some time, they're positively orgasmic. Fruit is the best.

Re:I want my Vitamin C! (2, Informative)

snowgirl (978879) | more than 6 years ago | (#23973025)

I don't hate the fruit! I just hate that every other animal in the world can synthesize their own Vitamin C, but we can't!

It's about EQUALITY, not wanting to get rid of fruit. I do like fruit; I have some cherries right now, and they're absolutely divine.

So, in all, I love fruit, I don't want to get rid of it... I just want to get rid of Scurvy...

Re:I want my Vitamin C! (0)

Anonymous Coward | more than 6 years ago | (#23974529)

Nearing created life and global climate change--Christians must be finding it harder to believe these days...

hehe, made myself laugh there.

It was impossible that the earth was round--until it was undeniable then everyone forgot.
It was impossible that animals used tools--until it was seen, then everyone forgot.
Evolution was not possible under god--so every evidence of evolution has to be explained away as some kind of simple species variety.
God would have no reason to make planets around other stars so they can't exist.
God wouldn't need more than one sun--so the sun can't just be another star.
God said the earth was the center of the universe--until it wasn't (made for a neat model though)
God said only God can create life. That'll last right up until we create some--then they may have to either face it or start killing people. Wonder which they will choose.

--ac because I don't want to be the first killed.

Follow the link at the end of the article (3, Informative)

Sir_Real (179104) | more than 6 years ago | (#23970561)

There is a more technical explanation in the link [scripps.edu] at the end of the article.

Article? (2, Insightful)

Rob Simpson (533360) | more than 6 years ago | (#23970895)

This is a crappy nonsensical blog post about a news story from three years before.

These are bases not amino acids (5, Interesting)

NFN_NLN (633283) | more than 6 years ago | (#23970597)

He's adding new bases which have no coding to amino acids. I don't see the purpose of this. Is it just for adding a trace or marker in DNA?

All the bases do are code for amino acids and it's the amino acid sequence which accounts for a protein's shape. In the end it's the protein's shape that matters for chemical interactions.

Re:These are bases not amino acids (5, Funny)

olyar (591892) | more than 6 years ago | (#23970669)

Mostly they just want to be able to write a technical paper called "All your base (pairs) are belong to us".

Re:These are bases not amino acids (-1, Offtopic)

Anonymous Coward | more than 6 years ago | (#23970977)

Take off every sig.

No, seriously. Everyone, get rid of your signatures. What?

Re:These are bases not amino acids (4, Interesting)

Robert1 (513674) | more than 6 years ago | (#23970763)

You're totally right. This is such a non-story and frankly mildly offensive in how full of himself the scientist is with sweeping comments like that.

As it stands currently, the amount of genetic degenerecy in amino acid coding means that they would easily have those double and tripled coded amino acids switched to something else. They could potentially add another 20-30 new amino acids with absolutely no change in the number or form of the base pairs used.

Its like finding a solution to a problem that doesn't exist, will never exist, and serves no purpose even if it was found. But apparently its equivalent from going to the iron age from the bronze age. Ha!

Re:These are bases not amino acids (2, Interesting)

Gat0r30y (957941) | more than 6 years ago | (#23971115)

ahh, come on - this is exactly like the transition from the stone age to the bronze age. If bronze had no additional useful function other than to help keep track of who made a stone.
I'm pretty sure the only use for this is going to be marking genes, probably just to keep track of who owns the patents.
The first genetic DRM?

Re:These are bases not amino acids (1)

buttle2000 (1041826) | more than 6 years ago | (#23974535)

DRM! You just sent his stock value flighing. Nothing like free publicity. Viva!

Re:These are bases not amino acids (1)

doooooosh (1124823) | more than 6 years ago | (#23971137)

You mean like lasers were (a solution to a problem that didn't exist)?

Re:These are bases not amino acids (2, Interesting)

ViperOrel (1286864) | more than 6 years ago | (#23971973)

Actually, even though you have redundancies in the current set, with this new pair you could code for new amino acids (or anything else you wanted to stick in there) without having to worry about disrupting other things those redundancies were already coding for.

My 2c.

Re:These are bases not amino acids (3, Insightful)

Anonymous Coward | more than 6 years ago | (#23972159)

Yeah, while the science here is kind of neat, it's not the biggest news in the world. The article title does not at all reflect what's newsworthy here, anyway. Scientists have been creating synthetic and/or modified nucleotides for decades and successfully incorporating them in to DNA and RNA. The news is that they found a synthetic base that can be copied by DNA polymerase. This is the enzyme that copies your DNA, putting an A next to a T on the opposite strand, a C opposite a G, a T opposite an A, and a G opposite a C. DNA polymerase will now put their new base, 3FB, opposite another 3FB on the opposite strand, and they set up some directed evolution to screen for mutant polymerases that will do a better job of it.

This is kind of neat, but the medical applications of this are pretty limited. First of all, it's unclear if RNA polymerase is able to perform the same reaction, or if only DNA polymerase can. If RNA polymerase can't insert a 3FB base opposite a 3FB base, then this news will basically go nowhere. An expanded genetic code is useless if it's confined to DNA only. The information in the DNA has to get into the RNA before protein can be synthesized, and it takes an RNA polymerase that can insert 3FB in order to do that.

However, even if RNA polymerase or a mutant will perform that addition, there's currently no use for it. There are no natural tRNAs that will pair with a codon containing 3FB, and even if you add some 3FB-containing tRNA genes to an organism, you still have to get an amino-acylation enzyme to strap an amino acid to that tRNA (not a trivial thing), and if you do, it'd have to be a novel amino acid to really mean something. Otherwise, you've just found an extremely difficult way of doing what could have been done with the machinery that's already in place.

This is kind of cool and all, but if Slashdot posted an article every time some scientist found a non-natural function of a given enzyme, it'd completely drown out all the articles hating on the RIAA, and we can't have that.

Re:These are bases not amino acids (1)

redxxx (1194349) | more than 6 years ago | (#23972275)

Seriously, who would ever going to need more than 4 base pairs?

Re:These are bases not amino acids (1)

smellsofbikes (890263) | more than 6 years ago | (#23973825)

I haven't read *extensively* about this but I have read some stuff, including articles about this research in other places.
The goal is to be able to integrate other amino acids -- or just other stuff -- to the standard rna->protein translation so you can put heavier tools in your proteins.
One way to do this is to hijack a current codon. This is being done by a group who are trying to use one of the three 'stop' codons. The problem with this approach is that, while there is redundancy, that redundancy is *used*. There isn't an unused codon. So if you take something that exists, you have to go through that thing's entire DNA and swap all instances of the codon you want to reconfigure, with one of the other synonymous codons. If you don't, you can't use it because all the proteins currently relying on that will break.
So THIS guy has decided to add new codons, rather than hijacking the ones that are already there, because he thinks it's less work. A team has spent several years trying to get one 'stop' codon freed up, and they think they have an E coli that has all the 'stop' codons replaced... but they're not sure and they're still trying to characterize it. Coz, you basically have to sequence the genome *and* know what everything does, every time you think you've managed to get your new bug built.
Building a whole new set of codons means you don't have to worry about that.
Because, in the end, either way you have to build your own new tRNA's with your new weird amino acids or whatever ready to be linked into your protein, but this guy's approach might mean that's *all* you have to do (plus use his patented system) rather than also having to proofread the whole genome repeatedly.

Someone please correct me if I'm wrong, but that's my best understanding of the research.

Everything you need to make this work (1)

MaizeMan (1076255) | more than 6 years ago | (#23975071)

...either way you have to build your own new tRNA's with your new weird amino acids or whatever ready to be linked into your protein, but this guy's approach might mean that's *all* you have to do (plus use his patented system) rather than also having to proofread the whole genome repeatedly.



Here's a list of what you'd have to add to the organism (it's a little complicated, but you've definitely grasped the essentials):

1. A gene using codons incorporating one or both of these new bases to encode your novel protein of interest containing something beyond the standard 20 amino acids.
2. tRNA genes that have the reverse compliment of any new codons you've introduced (otherwise the sequence functions like a stop codon).
3. Gene encoding an amyl transferase protein that binds your novel animo acids to the tail end of your novel tRNAs.
4. Genes encoding the biochemical pathway to synthesize the novel animo acids you were using.
5. Genes encoding the the biochemical pathway to synthesize the two new nucleotide bases developed in this paper.

There's obviously a lot of work left to do before this gets incorporated into synthetic biology, but it'll be very cool when it does.

Re:These are bases not amino acids (2, Informative)

Eponymous Bastard (1143615) | more than 6 years ago | (#23971035)

TFA's TFA mentions information storage in DNA, which makes sense as this basically moves from base-4 to base-5 (The base pairs up with itself, so it's only one new base) thereby improving storage density. They also did some work to evolve a polymerase that replicates the DNA with the new base.

DNA (single strands) and RNA also fold into themselves, and there is some evidence that the folding affects some mechanisms in the cell. Modifying them with these self-binding pairs could probably be hacked up to change the folding patterns. Also, DNA has activation sites and a whole bunch of things other than just the protein coding.

Even without DNA computers, I could see modifying a ribosome to encode a new set of amino acids with the extra base. Also consider, retroviral genetic-therapy style techniques where one of these are inserted into genes to disable them, putting these into introns/extrons to allow for better experiments on DNA transcription, etc.

Interestingly, neither article mentions transcription of this base into RNA, so your concern about amino acids is a little premature.

Re:These are bases not amino acids (2, Informative)

ZackZero (1271592) | more than 6 years ago | (#23971185)

Actually, if you read the second article (or the first link in the updated story), you'll see that the first base would pair up with itself instead of the second synthetic base - its intended pair. They "tweaked" it and it now pairs correctly... supposedly.

However, this makes it base-6 instead of base-5 or the current base-4. If you recall your high-school biology class, the base pairs only exist in two combinations, but in a total of four permutations. There's adenine-thymine, thymine-adenine, cytosine-guanine and guanine-cytosine. Each permutation codes something slightly different. The new bases would add two more permutations, thus making it base-6.

Re:These are bases not amino acids (1)

Eponymous Bastard (1143615) | more than 6 years ago | (#23971733)

Yeah, I read it before the update was posted so didn't see the extra article. I wrote base-5 because the first article made it out to be symmetric, so it was only one extra permutation.

Re:These are bases not amino acids (2, Informative)

Edward Kmett (123105) | more than 6 years ago | (#23971113)

Grossly simplifying, you read off codons (via mRNA, etc.) generating peptides so that you can build up proteins, etc. Some of those codons turn on or off transcription to amino acids.

As noted in the article the fidelity of transcription of these is lower than conventional DNA. So perhaps they could make perfectly suitable markers for areas you want to provoke a mutation at a higher rate, perhaps dropping them into large introns to encourage mutation in those areas.

The 3FB self-pair also expands the vocabulary of base pairs, potentially opening more options for possible nucleases, yielding more ways to cut up the resulting sequences.

The 3FB-3FB pair is symmetric. I'm not sure of any applications of that at this point, but there are people who actually do this stuff for a living who I'm sure can come up with some sort of use for that feature. ;)

Finally the code used need not remain fixed, (i.e. the various mitochondrial DNA codes) so the fact that they don't yield codons in any code we have now, doesn't mean that will always hold. Combined with the fact that transcription error rates are different for them leads to some interesting possibilities.

Re:These are bases not amino acids (2, Insightful)

tempest69 (572798) | more than 6 years ago | (#23971659)

aarrgggg.... intergenic regions of bacteria are reasonably important.. regulation of the production of proteins is a really important process. being able to add an artificial control mechanism to genes that are guaranteed not to exist in nature is a powerful tool.. While temperature sensitive promoters are impressive, they still have some problems. But having a fully artificial promoter sequence should allow for some really impressive experiments once a bit more technology is added to the system. Plus it can make some really big changes in RNA folding..

Storm

Re:These are bases not amino acids (1)

geckipede (1261408) | more than 6 years ago | (#23972111)

Both protein and DNA are partially self assembling polymers, and their purposes can in theory be completely interchangeable. A lot of the most basic functions of metabolism are carried out by RNA-based structures as well as proteins.

I think that what they are proposing is to create a DNA structure that can be replicated when kept artifially fed with these new bases, but which can then be used as a drug in its own right when introduced into humans. Presumably the most common use of it would be to interact with other DNA structures, blocking genes or similar, but there's no reason to believe that you couldn't do other tricks with it.

Re:These are bases not amino acids (3, Informative)

Atmchicago (555403) | more than 6 years ago | (#23972867)

All the bases do are code for amino acids

That's actually not true. A lot of DNA bases are important in mediating binding to proteins, such as RNA or DNA polymerase, histones, etc. Other bases are important in RNA-based regulator mechanisms, such as anti-terminators.

So the truth is that although we can't really say what we can do with these extra bases right now, the possibilities extend way beyond making new proteins and have many implications for regulation. Why is regulation important? Because differential gene expression is the fundamental principle that allows for cell differentiation and mediating responses to external change.

And for the record, IAAB (I am a biologist).

Sweet (1)

kwabbles (259554) | more than 6 years ago | (#23970613)

Now they can get to work on making me a hot Draenei chick with a proper ghetto booty.

Re:Sweet (1)

Kingrames (858416) | more than 6 years ago | (#23970705)

You want to BE one? okay.
But you can already do that, the surgery's just a bit expensive.

Re:Sweet (1)

kwabbles (259554) | more than 6 years ago | (#23970881)

You know that's now what I meant, but now that you mentioned it - I had about a 5 second sick visual that I found strangely exciting, and now I have to go wash my disturbed mind out with soap.

Re:Sweet (1)

Kingrames (858416) | more than 6 years ago | (#23971073)

You know that's now what I meant...

See? it was such a good idea, you decided that was what you meant in the first place after all.

Now I just need a couple more, and a videocamera. PROFIT!

I might be wrong but (0)

Anonymous Coward | more than 6 years ago | (#23970625)

Has this not already been posted?

Re:I might be wrong but (2, Informative)

Spy der Mann (805235) | more than 6 years ago | (#23970867)

Has this not already been posted?

Yes, it has. [slashdot.org]

Tagged oldnews.

Interesting but (1)

dreamchaser (49529) | more than 6 years ago | (#23970635)

Interesting, but I'd rather we have a better understanding of current genetic material and manipulation thereof before we go creating new bases that don't exist in nature.

This might just be an approrpiate time for the 'whatcouldpossiblygowrong' tag.

We'll get beyond DNA (1, Informative)

Anonymous Coward | more than 6 years ago | (#23970641)

Further on, I don't think we'll want to be shackled by our past at all. At some point in posthumanity, you'll just be able to comprehend better systems and think of the DNA-based life as just outdated. We already have far better information density in more stable forms. DNA does happen to do a good job in making use of its own information, but that is not nearly as efficient a process. Think of the early sound and graphics chips that were soldered onto NES cartridges. It did its job, but something else came along and put it in a museum.

Still missing critical information (4, Informative)

Raul654 (453029) | more than 6 years ago | (#23970725)

For those of you who forgot your biology, 3 DNA consecutive DNA base pairs (called a codon) are translated into a single amino acid. (Khorana, Holley and Nirenberg won the 1968 Noble prize in medicine for figuring this out and determining the mapping [codondevices.com] from base pairs to amino acids)

So, after reading the technical article [scripps.edu] , it says that DNA polymerase can bind to the new base pairs (allowing it to replicate), but it doesn't say what amino acids (if any) these new base pairs code for. That's important information because this alleged breakthrough is useless if it doesn't so something useful where proteins are concerned.

Re:Still missing critical information (1)

Dachannien (617929) | more than 6 years ago | (#23971099)

Also keep in mind that the coding for base triplets into amino acids is governed by tRNA, which are short segments of RNA that conform to provide one end that holds an amino acid and the other end (actually the middle, but folded over) that has a three-base segment that binds to mRNA during translation. tRNA are coded in the cell's DNA, so if you really wanted to change the translation table, you would just change the genes that produce tRNA in the first place.

It is possible, however, that the idea here is to form tRNAs that can accommodate new molecules other than the amino acids normally appearing in proteins.

Re:Still missing critical information (1)

Cinnamon Whirl (979637) | more than 6 years ago | (#23974201)

Woah nelly! :)
They can't code for anything, yet.
The point of the article (and the 3 year old link) seemed to be that these base pairs can be built into the DNA as it replicates by standard enzymes. What this means is that we can now build the blueprints, and guarantee a level of control for any new amino acids that are to be produced. That, however, will take a hell of a lot more work.

Wow. (1)

RyanFenton (230700) | more than 6 years ago | (#23970743)

Two new DNA bases? In terms of potential gene expression - this is like the art world getting two new visible base colors, which can mix with the usual red, green, blue, black and white in new ways to create further complex colors... oh, yes it'll take a very long time to figure out what they mean in all these contexts, but the potential there is absolutely huge.

We're still limited to the same physical limits we've ever had - but the potential for efficient complexity and new expressions using genetic systems is what is possibly improved here. Of course, perhaps we'll discover that some non-DNA systems can be more efficient at everything DNA systems do by the time we can really explore these new DNA bases, but at the same time, assuming that these bases will self-replicate in the wild, we've also found new ways for "life to find a way" using good old DNA. This is really, really important science being explored here in any case.

Ryan Fenton

Re:Wow. (1)

not_potable (916929) | more than 6 years ago | (#23971101)

What a shitty article. The reference it links claims there's only one new base that pairs with itself, 3-flourobenzene. "Alpha" and "beta", my ass.

assuming that these bases will self-replicate in the wild,

Since (I think it's safe to assume, based on the use of "unnatural") current organisms do not have a metabolic pathway for synthesizing the artificial base, unless it's bacteria grown in media supplied with some there's no way for a replicating genome to conserve the altered structure.

Two new DNA bases? In terms of potential gene expression - this is like the art world getting two new visible base colors, which can mix with the usual red, green, blue, black and white in new ways to create further complex colors... oh, yes it'll take a very long time to figure out what they mean in all these contexts, but the potential there is absolutely huge.

Colors? No. As other people have mentioned, the article says nothing about what tRNA can read codons containing the novel base. Either they can be read by current tRNAs' sloppy matching and would therefore not change the resulting amino acid structure, or there is no tRNA that can interact with the base so translation would not be able to progress and you'd just be knocking out genes. A better art analogy would be comparing this to a slightly different paintbrush from what everyone's using already. There isn't even great potential to use this for labeling, since that's already done quite well with modified natural bases or nucleic acid analogues.

Re:Wow. (1)

RyanFenton (230700) | more than 6 years ago | (#23971427)

Cool - If that's all that is, then yeah, not quite the potential I thought it could be.

Ryan Fenton

Re:Wow. (1)

my $anity 0 (917519) | more than 6 years ago | (#23972119)

Except it would be like 2 new colors that no one could see. There would have to be significant amounts present as rNTPs to transcribe it, and it would have to bond to specific tRNAs It would, in computer terms, be like adding two instructions, but the processor can't quite handle them.

Alpha and Beta? (1)

EriktheGreen (660160) | more than 6 years ago | (#23970781)

They should have just gone ahead and called them ADAM and EVE :)

Re:Alpha and Beta? (1)

I(rispee_I(reme (310391) | more than 6 years ago | (#23971929)

Or, since the Neocons are bound to oppose this anyway (due to its scientific nature), ADAM and STEVE.

Alpha and Beta (1)

ProfessionalCookie (673314) | more than 6 years ago | (#23970821)

If we're synthesizing bases you'd think that we could come up with better names than Alpha and Beta. If you work in biology at all you know that these designations are already overused. If you don't, this is essentially naming the bases "one" and "two". BwwaaahhhhH!! Hopefully these are on

Old News (3, Interesting)

dwye (1127395) | more than 6 years ago | (#23970903)

We have seen this before. The new bases just make new STOP codons, until someone creates new types of MRNA and/or TRNA to let the mitochondria process them to add a matching amino acid.

Where is the whatcanpossiblygowrong tag, like last time? Have the Luddites left, already?

Re:Old News (0)

Anonymous Coward | more than 6 years ago | (#23971201)

As you just said, nothing could possibly go wrong.

Re:Old News (0)

Anonymous Coward | more than 6 years ago | (#23971409)

Ribosomes, not mitochondria.

From the 4004 Age to the 8008 Age (-1, Flamebait)

Doc Ruby (173196) | more than 6 years ago | (#23970931)

This technique might mark a jump from Stone Age to Bronze Age in the techniques. But in the products, it's more like a jump from the original Intel 4004 [wikipedia.org] , the first commercial microprocessor, to the 8008, which was when chips with an instruction set really came of age. Because DNA bases are the basic instructions for the ribosomes (which are the "nanoprocessors" of the DNA instructions into amino acids, and thereby into the proteins that do the work expressing traits).

This advance has humans now varying the instruction sets to more precisely craft "living nanotech" devices to the tasks to which we set them. Hopefully a few generations down the road we'll do something better than DOS.

Bronze Age (3, Insightful)

wcrowe (94389) | more than 6 years ago | (#23970953)

'It takes time to figure out how best to use metal.'

I don't think it took too much time to figure out that the best use of bronze was to make it sharp and run someone through with it.

Re:Bronze Age (1)

dotmax (642602) | more than 6 years ago | (#23971177)

mod parent up insightful

Re:Bronze Age (1)

oodaloop (1229816) | more than 6 years ago | (#23971315)

Boy, hindsight sure is great isn't it?

When you're used to working with just stone, how to make stuff with metal would not neccessarily be intuitively obvious.

In the brave new world of patented genetics ... (2, Funny)

winomonkey (983062) | more than 6 years ago | (#23970989)

... all your base are belong to us.

all yor dna base are belong to us (0)

Anonymous Coward | more than 6 years ago | (#23971165)

nuff said

I for one... (1)

Synchis (191050) | more than 6 years ago | (#23971203)

Welcome our new genetically modified bacterial overlords...

(sorry... I had to...)

mod Up (-1, Troll)

Anonymous Coward | more than 6 years ago | (#23971249)

Do and doinG what Volume of NetBSD

Oblig. (0)

Anonymous Coward | more than 6 years ago | (#23971253)

All your DNA base are belong to us...

It also takes time... (1)

actionbastard (1206160) | more than 6 years ago | (#23971359)

"It takes time to figure out how best to use metal."
to figure out how long you can stretch out your research funding so you can keep your plush job. Usually this is accomplished by publishing just enough of your findings every few years so that it impresses the prols and convinces the patrons to keep funding you because a 'breakthrough' is RSN.

mo3 Up (-1, Redundant)

Anonymous Coward | more than 6 years ago | (#23971473)

may also 3ant

Maybe good for nanotech, but probably not genetics (1)

paratiritis (1282164) | more than 6 years ago | (#23971483)

otherwise evolution would already be using them. After all nature has already produced uracil [wikipedia.org] but does not use it in DNA. I don't see why it would not have produced and used these bases as well if they were useful.

So I don't think that there will be any breakthroughs in producing new proteins the classical way (DNA->RNA->mitochondria->proteins).

The sources also mention nanotech. This could be more promising, as the standard rules don't apply and any new material would multiply the available options.

Re:Maybe good for nanotech, but probably not genet (2, Insightful)

ChromaticDragon (1034458) | more than 6 years ago | (#23973925)

I would suggest your logic here is flawed or at the very least belies a bit of a gap in understanding how evolution works.

All the other folk who have commented that this is like giving artists new colors nobody can see are perhaps a bit closer.

Once we got started with anything even close to DNA, I would imagine we were more or less locked into that pattern. Evolution branches more so than tries all permutations and possibilities. It seems far more likely that once life got going with all the support systems (RNA, tRNA, etc.) and current coding mechanisms that it would have been very difficult to "back up" and try something new. Evolutionary history is full of examples like this where for what a lifeform is doing at the moment something else would be a bit better (human eye and blind spot?) but there is no going back, per se.

Silly Scientists (0)

Anonymous Coward | more than 6 years ago | (#23971729)

Can't they just play with the Spore Creature Creator like everyone else?

Re:Silly Scientists (1)

spazdor (902907) | more than 6 years ago | (#23972965)

You, AC, win the thread.

Overkill (1)

naoursla (99850) | more than 6 years ago | (#23971877)

The use of four base sequences probably optimizes the generation complexity to the coding/mainentance complexity. Six or eight base sequences are probably less energy efficient or less stable or something.

Although that might be a good approach for making new life forms that don't escape and outcompete native lifeforms.

Dear Slashdot +1, Informative (0)

Anonymous Coward | more than 6 years ago | (#23971949)


The Slashdot Editorial board has been obviously spending too much time on their stupid book and hardware reviews.

This is VERY OLD NEWS.

Please sell this URL to Microsoft.

Cordially,
Kilgore Trout

Something similar already done (1)

phaed2 (1205828) | more than 6 years ago | (#23972221)

Something similar has already been done as early as 2001. A team of researchers in Japan was able to demonstrate that artificial amino acids (instead of nucleotides) could be incorporated into the yeast translational machinery using five-base codons (instead of three). http://nar.oxfordjournals.org/cgi/reprint/29/17/3646 [oxfordjournals.org]

"DNA Origami" (2, Informative)

peter303 (12292) | more than 6 years ago | (#23972415)

Nanotechnology can coerce the DNA sugar (ribose) into exotic chapes like tri-helicies, platonic solids, etc. However there are no known biological applications of these exotic molecules. They mainly demonstrate the increasing skill of nanotechnology.

In many ways... (1)

Bobby Mahoney (1005759) | more than 6 years ago | (#23972627)

...alphabeta never left- they've continued to offer the same great service and selection at every day affordable prices!

Reasonable Fidelity? (1)

Pedrito (94783) | more than 6 years ago | (#23974633)

From the scripps article: While the polymerase does not replicate the unnatural DNA with the same fidelity observed in nature, (roughly one mistake for every 10 million bases of DNA copied), its fidelity is reasonable (typically making only one mistake for every 1000 base pairs).

Fidelity is reasonable? Maybe for bacteria, but not in my body! You'd get this in you in the morning and you'd probably have cancer before dinner. Okay, maybe that's a bit of an exaggeration... Still, they ever get this thing working with eukaryotes, and I'm gonna be concerned.

The only mutations are in the synthetic bases (1)

MaizeMan (1076255) | more than 6 years ago | (#23975165)

Even if I transformed a new gene incorporating these bases into cells in your body, the higher mutation rate is only going to affect the specific positions where the new bases are present. It wouldn't do anything to change the mutant rates of the proto-oncogenes and cancer-suppresser genes that are still encoded with normal As Cs Ts and Gs.

And this doesn't even get into the complication that sequences with the new bases could only be replicated in vivo as long as there's a supply of the new bases being synthesized in the cell.

Key point: synthetic dna bases aren't going to give you cancer.
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