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Starting to Add Letters to Life's Alphabet

Starting to Add Letters to Life's Alphabet

Unread postby Tanada » Sun 14 Dec 2008, 14:19:00

Most people who have had a biology class know that DNA is made up of four basic amino acids commonly expressed as ACGT referring to the first letter of each formula's name. Starting back at the turn of the 21st century labs all over the world including at premier labs in the USA began working to develop additional base pairs that would be compatible with the natural four.

Well as of January 30, 2008 a press release was issued that Scripps Research Institute of La Jolla, California has suceeded in creating the first artificial base pair that can be consistently replicated by natural enzymes in living organisms that already exist.

Dr. Romesberg wrote:With the help of graduate student Aaron Leconte, the group synthesized and screened 3600 candidates. Two different screening approaches turned up the same pair of molecules, called dSICS and dMMO2.

The molecular pair that worked surprised Romesberg. "We got it and said, 'Wow!' It would have been very difficult to have designed that pair rationally."

But the team still faced a challenge. The dSICS base paired with itself more readily than with its intended partner, so the group made minor chemical tweaks until the new compounds behaved properly.

"We probably made 15 modifications," says Romesberg, "and 14 made it worse." Sticking a carbon atom attached to three hydrogen atoms onto the side of dSICS, changing it to d5SICS, finally solved the problem. "We now have an unnatural base pair that's efficiently replicated and doesn't need an unnatural polymerase," says Romesberg. "It's staring to behave like a real base pair."

The team is now eager to find out just what makes it work. "We still don't have a detailed understanding of how replication happens," says Romesberg. "Now that we have an unnatural base pair, we are continuing experiments to understand it better."

In the near future, Romesberg expects the new base pairs will be used to synthesize DNA with novel and unnatural properties. These might include highly specific primers for DNA amplification; tags for materials, such as explosives, that could be detected without risk of contamination from natural DNA; and building novel DNA-based nanomaterials.


"So what?" you may be asking yourself. Well increasing the number of base pairs from four to six increases the possible number of protien coding combinations from 64 to 216. That means that artificial DNA strings with six base pairs have the potential to supply scores of new amino acid synthesizing combinations. Biotech companies desire this abillity because genetically modified bacteria grown in the cultures are by far the cheapest way to attain synthetic Amino Acids.

Now for the rub, if you are altering a common bacterium to act as your Amino Acid supply source that means the codon's have to be stable and replicable by normal living organisms. That being the case it becomes ever more likely that that bacteria with this artificial DNA could escape into the environment and survive there.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby Jotapay » Sun 14 Dec 2008, 14:33:27

This is why I live in (what will be) Raccoon City. :)

I predict that this unregulated and unsupervised tampering with DNA will end very, very badly one day.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby idiom » Sun 14 Dec 2008, 15:08:26

One of the more curios problem in the field of evolutionary biology is why, after several billion years of evolution, are there still only five (ACGT*U*) bases? Why are genes from Archea and humans interchangeable?
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Re: Starting to Add Letters to Life's Alphabet

Unread postby cipi604 » Sun 14 Dec 2008, 18:01:28

idiom wrote:One of the more curios problem in the field of evolutionary biology is why, after several billion years of evolution, are there still only five (ACGT*U*) bases? Why are genes from Archea and humans interchangeable?


Because till today nature didn't need more than that.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby Tanada » Sun 14 Dec 2008, 18:30:46

cipi604 wrote:
idiom wrote:One of the more curios problem in the field of evolutionary biology is why, after several billion years of evolution, are there still only five (ACGT*U*) bases? Why are genes from Archea and humans interchangeable?


Because till today nature didn't need more than that.


Personally I think it is for the same reason we have green plants based on green chlorophyl instead of red xylophyl or black xylophyl. The green got a toehold first and was successful enough that the others never had a chance, though you see the red every year in deciduous bushes and trees whose leaves stay on for a week or three after the chlorophyl is stored by the plant.

Some contend that RNA (The *U* base) came first and DNA evolved from RNA when *T* evolved to replace it in the sequence. *U* & *T* both pair with *A*.

The good news about the artificial base pair is, they bind together by a different mechanism than the other five, therefor niether of them will bind with the natural five, they will only bind with each other.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby GoghGoner » Sun 14 Dec 2008, 23:26:53

idiom wrote:One of the more curios problem in the field of evolutionary biology is why, after several billion years of evolution, are there still only five (ACGT*U*) bases? Why are genes from Archea and humans interchangeable?


originated from whole cells seem to be the likely explanation to me, don't know where they came from. if i did, maybe i would sleep a litte easier or maybe i would just blow my brains out.

of course, we may discover a new life-form that sheds light a different direction. it amazes me how little we know.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby Tanada » Tue 20 Nov 2012, 10:00:42

http://www.nctimes.com/blogsnew/busines ... 68fd6.html
The scientists studied two artificial DNA letters, and found they use a previously unknown property of the DNA replication machinery to be copied, said Romesberg, a Scripps associate professor. This explains findings of earlier research and provides a firm basis for expanding the vast information-carrying capacities of DNA.

While the work is still at the basic research level, Romesberg said the study's finding points the way to applied research with an eye to making products with the technology. In other words, here comes a new form of biotechnology.
Romesberg and colleagues have been studying the two artificial letters, called NaM and 5SICS, for years. They pair in the DNA double helix, similar to how the four natural ones do. In natural DNA, the base adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G), creating what are called base pairs.

The artificial letters are transcribed into the messenger molecule RNA similarly to the natural letters, Romesberg and colleagues had previously found. In nature, RNA carries the instructions from the cell nucleus where DNA resides out into the other parts of the cell where the instructions are carried out, as in making proteins.

Critical question

The key question is whether these artificial base pairs, when spliced into DNA with natural letters, can be faithfully replicated. Research indicated the answer is yes, and almost as efficiently as natural base pairs. However, the molecular mechanism hasn't been identified. That created uncertainty as to whether the results were some sort of fluke, Romesberg said.

That mechanism is what the study has elucidated.

Natural base pairs neatly link by hydrogen bonds, like a molecular-scale version of Legos. The artificial base pairs are held into place by another molecular force, the hydrophobic effect. According to what's called Watson-Crick geometry, this arrangement shouldn't be recognized by DNA polymerase, the molecule that stitches together individual base pairs (the "Lego blocks) to replicate DNA molecules.

The study found that at the moment of replication, DNA polymerase actually grips the artificial base pairs together and places them into a Watson-Crick arrangement. That not only explains how NaM and 5SICS are replicated, it suggests that other artificial base pairs pushed together by hydrophobic forces can also be replicated in the same way. And that leads to the possibility of not just adding two, but many more artificial letters to the DNA alphabet.


Four years ago this was just a glimmer of a possibility, now they have proven that adding these artificial letters can be done with natural replication taking place after insertion.

This will at the very least allow artificial tags of DNA signatures to be added to genetically modified genes so that copyrights can be asserted. Once that becomes commercially prevalent they will be able to "escape into the wild" as genetically modified crops and genetically tagged bacteria used to produce chemical/drug feed stocks like Insulin.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby Tanada » Tue 20 Nov 2012, 10:07:29

http://www.nctimes.com/news/science/unn ... 4bd67.html

Artificial life

Eventually, the scientists say they'd like to perform the much more difficult task of incorporating the unnatural DNA into living cells, creating life forms that never could have existed in nature.

This quest for artificial life is being pursued by several teams of scientists, including one led by famed gene pioneer J. Craig Venter.

Venter's team synthesized the genome of a bacterium in 2008, proving that the complete genetic code of a living creature could be made in the laboratory. In 2010, they put together a bacterial genome with natural and artificial DNA sequences, then inserted the synthetic DNA into a bacterium that had been deprived of its own DNA.

The bacterium's molecular machinery worked with the DNA, or "booted up," as the scientists put it. This creation marked the first time scientists had designed a new life form, however, most of its genes are natural. So it is not a wholly synthetic life form.

Romesberg said Venter's approach differs from his, and that of a friendly rival to his, Steven A. Benner. Venter is designing new genes and combinations of genes, but using the same four letters found in nature, Romesberg said.

Romesberg and Benner's teams are designing new letters for the DNA alphabet that do not appear in nature.

Benner's approach is to create letters that chemically bond to DNA in a similar way to how the natural letters bond. Romesberg, Malyshev and colleagues are working with unnatural letters that are held in place by different forces than those of natural DNA letters. The mechanism is so different than the natural method that the Romesberg team at first feared they had made an error.

According to conventional chemistry, the unnatural letters could not be duplicated by the body's DNA copier, an enzyme called DNA polymerase, because of how they're held in position. However, the Romesberg team found that the enzyme copies the unnatural letters by placing them into the correct position, the so-called "Watson-Crick geometry" that the natural base pairs conform to.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby Tanada » Sun 25 Nov 2012, 00:10:49

Base jumping

Ichiro Hirao, a chemist at the RIKEN Systems and Structural Biology Center in Yokohama, Japan, had been intrigued by the idea of creating unnatural bases ever since reading James Watson's 1968 book The Double Helix as a teenager. Hirao and his colleagues found that they could reduce mispairing by designing shapes that fit awkwardly with natural bases, and by adding negatively charged or electron-rich chemical groups that repel the natural bases' corresponding parts. In 2011, Hirao's team reported that DNA containing an unnatural hydrophobic base pair, called Ds and Diol1-Px, could be copied with 99.77–99.92% fidelity per replication9. The same year, Benner and his colleagues showed that another unnatural base pair — P and Z, which join using hydrogen bonds — achieved fidelity of 99.8% per replication10. And in July, Romesberg's team reported rates of 99.66–99.99% for optimized versions of his bases, called NaM and 5SICS (ref. 11), overlapping with the sloppiest rate for natural DNA. “Our best case is now approaching nature's worst case,” says Romesberg.

Unnatural bases still have a lot to prove, however. Researchers haven't shown that polymerases can copy more than four of the paired bases in a row10. The polymerase is “the hard nut to crack”, says Benner. And the solution may be to re-engineer it, too.

http://www.nature.com/news/chemical-bio ... et-1.11863

The above is from a quite long and detailed article on additional DNA letters published November 21, 2012. Highly recommended for anyone who wants to have a clue where genetic engineering is currently headed.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby Subjectivist » Tue 12 Nov 2013, 07:01:54

http://io9.com/5903221/meet-xna-the-fir ... real-thing

. A Step Toward Novel Lifeforms
What mysterious genetic material ruled the world before DNA and RNA?
All living organisms use DNA as the carrier of genetic material and RNA as the messenger molecule directing the expression of genes and creation of… Read…
The implications of the team's findings are numerous and far-reaching. For one thing, the study sheds significant light on the origins of life itself. In the past, investigations into XNA have been largely driven by the question of whether simpler genetic systems may have existed before the emergence of RNA and DNA; the fact that these XNAs appear to be capable of evolution adds to an ever-growing body of evidence of a genetic system predating DNA and RNA both.



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Re: Starting to Add Letters to Life's Alphabet

Unread postby Tanada » Tue 14 Feb 2017, 09:02:04

Scientists create first stable semisynthetic organism

Life's genetic code has only ever contained four natural bases. These bases pair up to form two "base pairs"—the rungs of the DNA ladder—and they have simply been rearranged to create bacteria and butterflies, penguins and people. Four bases make up all life as we know it.

Until now. Scientists at The Scripps Research Institute (TSRI) have announced the development of the first stable semisynthetic organism. Building on their 2014 study in which they synthesized a DNA base pair, the researchers created a new bacterium that uses the four natural bases (called A, T, C and G), which every living organism possesses, but that also holds as a pair two synthetic bases called X and Y in its genetic code.

TSRI Professor Floyd Romesberg and his colleagues have now shown that their single-celled organism can hold on indefinitely to the synthetic base pair as it divides. Their research was published January 23, 2017, online ahead of print in the journal Proceedings of the National Academy of Sciences.

"We've made this semisynthetic organism more life-like," said Romesberg, senior author of the new study.

While applications for this kind of organism are still far in the future, the researchers say the work could be used to create new functions for single-celled organisms that play important roles in drug discovery and much more.

Building a Unique Organism

When Romesberg and his colleagues announced the development of X and Y in 2014, they also showed that modified E. coli bacteria could hold this synthetic base pair in their genetic code. What these E. coli couldn't do, however, was keep the base pair in their code indefinitely as they divided. The X and Y base pair was dropped over time, limiting the ways the organism could use the additional information possessed in their DNA.

"Your genome isn't just stable for a day," said Romesberg. "Your genome has to be stable for the scale of your lifetime. If the semisynthetic organism is going to really be an organism, it has to be able to stably maintain that information."

Romesberg compared this flawed organism to an infant. It had some learning to do before it was ready for real life.

In stepped TSRI Graduate Student Yorke Zhang and Brian Lamb, an American Cancer Society postdoctoral fellow in the Romesberg lab at the time of the study. Together, they helped develop the means for the single-celled organism to retain the artificial base pair.

First, Zhang and Lamb, co-first authors of the study, optimized a tool called a nucleotide transporter, which brings the materials necessary for the unnatural base pair to be copied across the cell membrane. "The transporter was used in the 2014 study, but it made the semisynthetic organism very sick," Zhang explained. The researchers discovered a modification to the transporter that alleviated this problem, making it much easier for the organism to grow and divide while holding on to X and Y.

Next, the researchers optimized their previous version of Y. The new Y was a chemically different molecule that could be better recognized by the enzymes that synthesize DNA molecules during DNA replication. This made it easier for cells to copy the synthetic base pair.

A New Use for CRISPR-Cas9

Finally, the researchers set up a "spell check" system for the organism using CRISPR-Cas9, an increasingly popular tool in human genome editing experiments. But instead of editing a genome, the researchers took advantage of CRISPR-Cas9's original role in bacteria.

The genetic tools in CRISPR-Cas9 (a DNA segment and an enzyme) originated in bacteria as a kind of immune response. When a bacterium encounters a threat, like a virus, it takes fragments of the invader genome and pastes them into its own genome—a bit like posting a "wanted" poster on the off chance it sees the invader again. Later, it can use those pasted genes to direct an enzyme to attack if the invader returns.

Knowing this, the researchers designed their organism to see a genetic sequence without X and Y as a foreign invader. A cell that dropped X and Y would be marked for destruction, leaving the scientists with an organism that could hold on to the new bases. It was like the organism was immune to unnatural base pair loss.

"We were able to address the problem at a fundamental level," said Lamb, who now serves as a research scientist at Vertex Pharmaceuticals.

Their semisynthetic organism was thus able to keep X and Y in its genome after dividing 60 times, leading the researchers to believe it can hold on to the base pair indefinitely.

"We can now get the light of life to stay on," said Romesberg. "That suggests that all of life's processes can be subject to manipulation."

A Foundation for Future Research

Romesberg emphasized that this work is only in single cells and is not meant to be used in more complex organisms. He added that the actual applications for this semisynthetic organism are "zero" at this point. So far, scientists can only get the organism to store genetic information.

Next, the researchers plan to study how their new genetic code can be transcribed into RNA, the molecule in cells needed to translate DNA into proteins. "This study lays the foundation for what we want to do going forward," said Zhang.


https://phys.org/news/2017-01-scientist ... hetic.html
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Re: Starting to Add Letters to Life's Alphabet

Unread postby dissident » Tue 14 Feb 2017, 09:33:55

This all so cool from a science geek perspective. But in reality it is insane games with fire. Yeah, let's create bacteria with more DNA information storage capacity that, given their rapid adaptation cycle, can become super pathogens. If we have a problem with finding antibiotics now, then think of how hard it will be in the brave new world of enhanced DNA bacteria.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby Cog » Tue 14 Feb 2017, 10:13:47

I for one welcome are six-pair genome overlords.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby Subjectivist » Tue 14 Feb 2017, 12:07:56

Wow in nine years they have gone from experimental chemistry to an actual viable bacteria.

What happens when someone builds artificial viruses using these synthetic DNA pairs? Will you immune system even recognize them?
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Re: Starting to Add Letters to Life's Alphabet

Unread postby KaiserJeep » Tue 14 Feb 2017, 12:58:30

Subjectivist wrote:Wow in nine years they have gone from experimental chemistry to an actual viable bacteria.

What happens when someone builds artificial viruses using these synthetic DNA pairs? Will you immune system even recognize them?


It's a favorite meme with internet conspiracy buffs already. "Weaponized" versions of HIV, Ebola, Influenza, Zika, Anthrax, Smallpox, etc. are claimed by these nuts, usually as a racial conspiracy to kill off black and brown populations, or perhaps GLBTQ people. We don't even need the extra amino acids for the conspiracy theories to multiply over the internet.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby Plantagenet » Tue 14 Feb 2017, 19:35:00

KaiserJeep wrote:It's a favorite meme with internet conspiracy buffs ….. "Weaponized" versions of HIV, Ebola, Influenza, Zika, Anthrax, Smallpox, etc.


Is that an unfounded conspiracy theory….or is concern about research on chemical and biological WMDs in various chem warfare labs in China, Russia, Raqqa, and other such places a perfectly reasonable concern?

china bio chem WMDs

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Chinese_propaganda_poster_biowarfare
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Re: Starting to Add Letters to Life's Alphabet

Unread postby Tanada » Wed 15 Feb 2017, 08:26:54

Plantagenent raises a valid point, if you can add stable DNA sequences to an existing bacteria there is no reason you could not add synthetic DNA sequences to an existing virus sequence to possibly make it stealthy and harder for your immune system to combat. On the other hand a virus has such a short sequence it doesn't have room for a lot of unnecessary DNA/RNA so adding extra bit might have the opposite effect and make it easier for your immune system to recognize.

Either way I am sure of two things, because the technology exists someone out there is playing with it. I really with they wouldn't, the risk/reward ratio is far far too high.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby diemos » Wed 15 Feb 2017, 10:48:05

Famous last words:

" What could go wrong?"

Almost as good as, "Here, hold my beer." or "Watch this!"
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Re: Starting to Add Letters to Life's Alphabet

Unread postby dissident » Wed 15 Feb 2017, 19:34:16

Funny "logic". Some schizophrenic nutjob touches on the same subject, so the whole subject must be tin foil hat nonsense. I now know why KJ denies global warming.
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Re: Starting to Add Letters to Life's Alphabet

Unread postby dissident » Wed 15 Feb 2017, 19:40:08

diemos wrote:Famous last words:

" What could go wrong?"

Almost as good as, "Here, hold my beer." or "Watch this!"


The arrogance is incredible. As if they are gods who know all the future eventualities.

I bet that this research is funded heavily by money from certain special interests.

As for biowarfare research, the US and Israel are front and center in this regard.

https://en.wikipedia.org/wiki/Israel_In ... l_Research

http://www.businessinsider.com/military ... ons-2016-9
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