Four New DNA Letters Double Life's Alphabet (nature.com) 67
Joe_NoOne (Slashdot reader #48,818) shares this update from Nature: The DNA of life on Earth naturally stores its information in just four key chemicals -- guanine, cytosine, adenine and thymine, commonly referred to as G, C, A and T, respectively. Now scientists have doubled this number of life's building blocks, creating for the first time a synthetic, eight-letter genetic language that seems to store and transcribe information just like natural DNA.
In a study published on 22 February in Science, a consortium of researchers led by Steven Benner, founder of the Foundation for Applied Molecular Evolution in Alachua, Florida, suggests that an expanded genetic alphabet could, in theory, also support life. "It's a real landmark," says Floyd Romesberg, a chemical biologist at the Scripps Research Institute in La Jolla, California. The study implies that there is nothing particularly "magic" or special about those four chemicals that evolved on Earth, says Romesberg. "That's a conceptual breakthrough," he adds... Benner says that the work shows that life could potentially be supported by DNA bases with different structures from the four that we know, which could be relevant in the search for signatures of life elsewhere in the Universe...
The researchers call the resulting eight-letter language 'hachimoji' after the Japanese words for 'eight' and 'letter'. The additional bases are each similar in shape to one of the natural four, but have variations in their bonding patterns. The researchers then conducted a series of experiments that showed that their synthetic sequences shares properties with natural DNA that are essential for supporting life... Benner's group previously showed that strands of DNA that included Z and P were better at binding to cancer cells than sequences with just the standard four bases. And Benner has set up a company which commercialises synthetic DNA for use in medical diagnostics.
In a study published on 22 February in Science, a consortium of researchers led by Steven Benner, founder of the Foundation for Applied Molecular Evolution in Alachua, Florida, suggests that an expanded genetic alphabet could, in theory, also support life. "It's a real landmark," says Floyd Romesberg, a chemical biologist at the Scripps Research Institute in La Jolla, California. The study implies that there is nothing particularly "magic" or special about those four chemicals that evolved on Earth, says Romesberg. "That's a conceptual breakthrough," he adds... Benner says that the work shows that life could potentially be supported by DNA bases with different structures from the four that we know, which could be relevant in the search for signatures of life elsewhere in the Universe...
The researchers call the resulting eight-letter language 'hachimoji' after the Japanese words for 'eight' and 'letter'. The additional bases are each similar in shape to one of the natural four, but have variations in their bonding patterns. The researchers then conducted a series of experiments that showed that their synthetic sequences shares properties with natural DNA that are essential for supporting life... Benner's group previously showed that strands of DNA that included Z and P were better at binding to cancer cells than sequences with just the standard four bases. And Benner has set up a company which commercialises synthetic DNA for use in medical diagnostics.
hachimoji??? (Score:1)
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This is like going from ASCII to Unicode. But it isn't really "doubling". With four nucleotides, each base pair encodes 2 bits. With eight pairs, it is 3 bits each. So this is only a 50% improvement in information density.
But I am not sure how much this helps. With four nucleotides we already have 64 triples, but there are only 20 amino acids. Add stop and start codons, and that is only 22. So there is already plenty of redundancy.
At least for now, I am sticking with four nucleotides.
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With four nucleotides, each base pair encodes 2 bits. With eight pairs, it is 3 bits each. So this is only a 50% improvement in information density.
3 bits is twice as much information as 2 bits.
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3 bits is twice as much information as 2 bits.
By that measure, 100,000,001 bits per second is twice as much information as 100,000,000 bps. So you must be really happy when your ISP gives you an upgrade.
Well there's an incredible lack of understanding if I ever saw one.
With 2 bits, you can count four possibilities.
00, 01, 10, 11.
With three bits, you can count eight possibilities, twice as many. (All four of the above with a zero added, and all four above with a one added.)
000, 001, 010, 011, 100, 101, 110, 111.
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I think you're mixing two notions of 'bit', and squaring versus doubling (which are the same for 2 but no other number). Eight possibilities per genetic base-pair is twice as many as four. Equivalent representation in binary is another matter, but it would be a whole other coding step.
6 to 8 (Score:4, Informative)
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So is it the new total number of letters 4+2+4, or 4+2+2?
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Don't mistake an entertainment focused presentation like a TED talk for an original research presentation.
FAME and Steve Benner have been the leaders in this field for a long time. Benner made the first expansion from 4 to 6 bases about 30 years ago. SRI and Floyd Romesberg are very good, but they are following Benner here (and Romesberg is a better public speaker).
You're right, though, that this is from 6 to 8.
Interesting! (Score:3)
How soon before we move to 16 -> 32 -> 64?
Just my 2 cents
8 POSITION, not 8 bit. (Score:2, Informative)
You can only have one of any of the 8 occupying a given strand pair position, meaning that it is 2^3 or 3 bit resolution, up from 2 bit with the previous base pairs. The rest of what you say is correct however.
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The rest of what you say is correct however.
Right, when you double numbers they do get bigger, and the 2 cents is correct.
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OMG, two-bit. Or six-bit per codon.
Re:Interesting! (Score:5, Funny)
It depends if you rely on the marketing departments of NEC, SEGA or Intel.
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Life is 8 bit
It's not. A codon consists of 3 nucleotides, each of which has 4 different values (i.e., distinct chemical composition) equivalent to a two bit encoding. Total: six bits. The artificially extended version adds one bit to the nucleotide range, times 3 nucleotides, total 9 bits. So there is no way to interpret your joke as correct, sorry. It's not about lacking a sense of humour, it just that the numbers need to add up. For example, "life is braille". Which is actually close to the truth when you look at the
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Hmm, correction, the ribosome actually doesn't need to change much if at all for their 3 bit code, mostly they just need some new tRNAs that incorporate their new nucleotides. The natural machinery should be able to handle it with minimal modification. Yikes.
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Please do provide an example of a chemical combination that doesn't "work together", thus reducing the number of bits per codon. (troll detected)
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What an ass.
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You need more than just a decoder. You also need a supply of the nucleotides. If you're doing this as a proof of concept experiment in vitro, you can get away with synthesizing them chemically, but if you want it to work in vivo, you need would need a whole set of enzymes to synthesize, metabolize, and transport those nucleotides. That would probably require dozens of new enzymes, which is way beyond the current state of the art.
Re-reporting news (Score:2)
https://science.slashdot.org/s... [slashdot.org]
At least it's not on the front page anymore...
When Slashdot doesn't dupe (Score:1)
That's noteworthy.
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Are you implying it's a dup? It's not. Different group, different research. Seems to take a similar idea much further, to a specific application.
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If it's a different group, they share the same lead researcher and the name for their new 8-code DNA strands.
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Isn't it easier to just drink Red Bull?
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Mormonism?
One step closer.. (Score:2)
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I, for one, welcome our new S, B, P and Z(ombie) overlords.
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Other letters were probably discarded (Score:5, Insightful)
The answer turns out to be e. 2.718. An alphabet with e characters allows you to represent data the most efficiently and compactly. Obviously you can't have a non-integer number of characters, so the optimal number of characters for a compact language is 3.
Which is probably why DNA only codes 4 different molecules. Since a double helix with conjugate pairs can't be coded with 3 letters, 4 end up being the next step. Likely, DNA/RNA with more base pairs have developed naturally before (probably several times), but were eventually selected out after having to compete with 4-base pair DNA. So as interesting as this is, it probably isn't the first time it's happened like TFA states.
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"Likely, DNA/RNA with more base pairs have developed naturally before (probably several times), but were eventually selected out after having to compete with 4-base pair DNA."
And why would it be selected out? Are you claiming that it could not compete with 4-base pair due encoding efficiency? Please.
search for signatures of life elsewhere... (Score:2)
Benner says that the work shows that life could potentially be supported by DNA bases with different structures from the four that we know, which could be relevant in the search for signatures of life elsewhere in the Universe...
Not sure why anyone would expect to find terrestrial DNA anywhere but Terra. Totally unrelated creatures would use a totally different system. If they did find something like ours, that would mean we were relatives.
Re: search for signatures of life elsewhere... (Score:2)
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Might I suggest you look up "panspermia" ? In it's fullest theories, it's the idea that the most elementary building blocks of life were seeded on Earth from interstellar dust or asteroids, and that they will be seeded on other worlds the same way.
Even if panspermia did not happen. It does not mean that significant amounts of biochemistry, perhaps including some form of DNA, might not exist elsewhere. The nature and extent of parallel evolution surprised Charles Darwin when he originally wrote about evoluti