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posted by martyb on Saturday December 02 2017, @02:03AM   Printer-friendly
from the waiting-for-an-off-base-pear dept.

In 2014, scientists engineered Escherichia coli to incorporate new bases they called 'X' and 'Y' in addition to adenine-thymine (A-T) and guanine-cytosine (G-C). Now it has been demonstrated that these synthetic base pairs can be transcribed into RNA and used to produce a protein containing "unnatural" amino acids.

The addition of the new bases could increase the amount of amino acids from 20 to a possible total of 172.

A semi-synthetic organism that stores and retrieves increased genetic information (DOI: 10.1038/nature24659) (DX)

Since at least the last common ancestor of all life on Earth, genetic information has been stored in a four-letter alphabet that is propagated and retrieved by the formation of two base pairs. The central goal of synthetic biology is to create new life forms and functions, and the most general route to this goal is the creation of semi-synthetic organisms whose DNA harbours two additional letters that form a third, unnatural base pair. Previous efforts to generate such semi-synthetic organisms culminated in the creation of a strain of Escherichia coli that, by virtue of a nucleoside triphosphate transporter from Phaeodactylum tricornutum, imports the requisite unnatural triphosphates from its medium and then uses them to replicate a plasmid containing the unnatural base pair dNaM–dTPT3. Although the semi-synthetic organism stores increased information when compared to natural organisms, retrieval of the information requires in vivo transcription of the unnatural base pair into mRNA and tRNA, aminoacylation of the tRNA with a non-canonical amino acid, and efficient participation of the unnatural base pair in decoding at the ribosome. Here we report the in vivo transcription of DNA containing dNaM and dTPT3 into mRNAs with two different unnatural codons and tRNAs with cognate unnatural anticodons, and their efficient decoding at the ribosome to direct the site-specific incorporation of natural or non-canonical amino acids into superfolder green fluorescent protein. The results demonstrate that interactions other than hydrogen bonding can contribute to every step of information storage and retrieval. The resulting semi-synthetic organism both encodes and retrieves increased information and should serve as a platform for the creation of new life forms and functions.

Previously: Scientists Engineer First Semisynthetic Organism With Three-base-pair DNA

Related: How Scientists Are Altering DNA to Genetically Engineer New Forms of Life


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  • (Score: 3, Interesting) by JoeMerchant on Saturday December 02 2017, @04:36AM (13 children)

    by JoeMerchant (3937) on Saturday December 02 2017, @04:36AM (#604140)

    I don't feel like the artificial genes are any better controlled, but they certainly are more identifiable - so we'll know what kills us all came from us.

    There is probably a weakness to the artificial base pairs, otherwise they would have evolved up into normal use along with the common 4 - so, a billion years from now, they may fade away.

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  • (Score: 4, Insightful) by JNCF on Saturday December 02 2017, @05:11AM (2 children)

    by JNCF (4317) on Saturday December 02 2017, @05:11AM (#604142) Journal

    otherwise they would have evolved up into normal use along with the common 4

    Not necessarily; evolution is a bloody mess and it doesn't solve problems in the best way possible, merely incrementally better ways.

    • (Score: 2) by frojack on Saturday December 02 2017, @07:34AM (1 child)

      by frojack (1554) on Saturday December 02 2017, @07:34AM (#604153) Journal

      Never the less, it does seem odd that ALL life on the planet use only the same 4 bases. Given that we have highly isolated life forms cooking in every biological soup in every corner of the planet, it seems you could have bet some odd ball life form would have found it advantageous to encode something unusual.

      If we can imagine it and do it, how long till it becomes mandatory?

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      • (Score: 2) by c0lo on Saturday December 02 2017, @10:09AM

        by c0lo (156) Subscriber Badge on Saturday December 02 2017, @10:09AM (#604200) Journal

        Never the less, it does seem odd that ALL life on the planet use only the same 4 bases.

        Nope. If this is all you can find to eat, you aren'r going to have material to build your DNA from something else.

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  • (Score: 3, Interesting) by sjames on Saturday December 02 2017, @07:39AM (7 children)

    by sjames (2882) on Saturday December 02 2017, @07:39AM (#604155) Journal

    One help is that the bacteria can be made to depend on amino acids that they won't find in nature. If they escape the lab they starve.

    • (Score: 3, Interesting) by takyon on Saturday December 02 2017, @07:45AM (3 children)

      by takyon (881) <reversethis-{gro ... s} {ta} {noykat}> on Saturday December 02 2017, @07:45AM (#604156) Journal

      They might just mutate to remove inhibitory X and Y bases.

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      • (Score: 2) by sjames on Saturday December 02 2017, @08:07AM (2 children)

        by sjames (2882) on Saturday December 02 2017, @08:07AM (#604159) Journal

        That's much less likely when there's no gradient between the 'good' environment and the fatal one. It's also fairly easy to detect a contaminated culture. Transfer a bit to a conventional growth medium. If anything at all grows, destroy it and the tested culture.

        • (Score: 2) by JoeMerchant on Saturday December 02 2017, @06:05PM (1 child)

          by JoeMerchant (3937) on Saturday December 02 2017, @06:05PM (#604333)

          You are talking about best practices. 7 billion people on the planet, say that someday one in a thousand is capable of genetic engineering... that leaves 7 million genetic engineers, if only one in a million is stupid enough to be careless about best practices, that's 7 ground zeroes for escaped bad actors...

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          • (Score: 2) by takyon on Sunday December 03 2017, @10:22AM

            by takyon (881) <reversethis-{gro ... s} {ta} {noykat}> on Sunday December 03 2017, @10:22AM (#604609) Journal

            The focus going forward should be on bolstering human defenses against biological agents rather than trying to regulate amateur biology and suppress citizen science, which will only turn ugly fast.

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    • (Score: 2) by JoeMerchant on Saturday December 02 2017, @06:02PM (2 children)

      by JoeMerchant (3937) on Saturday December 02 2017, @06:02PM (#604331)

      The bacteria can be attempted to be made to depend on amino acids that they won't find in nature. What they actually do after exchanging some DNA in the wild is anybody's guess.

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      • (Score: 2) by sjames on Saturday December 02 2017, @06:22PM (1 child)

        by sjames (2882) on Saturday December 02 2017, @06:22PM (#604341) Journal

        But they won't exchange DNA in the wild since in the wild they will die

        • (Score: 3, Insightful) by JoeMerchant on Saturday December 02 2017, @10:33PM

          by JoeMerchant (3937) on Saturday December 02 2017, @10:33PM (#604438)

          And the wild never gets into the lab where the exotic food is? In real life?

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  • (Score: 2) by maxwell demon on Saturday December 02 2017, @09:29AM (1 child)

    by maxwell demon (1608) on Saturday December 02 2017, @09:29AM (#604173) Journal

    It also means we'd have a better chance to fight those things, by designing a poison that attacks specifically those "unnatural" amino acids.

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    • (Score: 2) by JoeMerchant on Saturday December 02 2017, @06:08PM

      by JoeMerchant (3937) on Saturday December 02 2017, @06:08PM (#604334)

      True, though (however unlikely) if our artificial base pairs are somehow superior to the existing ones, we can have a whole new field of study about the weird things they can do that natural life cannot. We've been studying the basic 4 for thousands of years indirectly, 50 years directly and are just starting to get a handle on them....

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