An international team of researchers has created a semisynthetic organism, based on E. coli, with 6 base pairs: A, C, T, G, and two artificial nucleotides called X and Y (dNaMTP and d5SICSTP). The researchers had to modify normal cellular chemistry to facilitate accurate replication. The research was published in pnas on the 23rd Jan. They’d previously inserted the nucleotides into the organism, but growth was slow, and the unnatural base pair was excised after several generations.

btm said:

An international team of researchers has created a semisynthetic organism, based on E. coli, with 6 base pairs: A, C, T, G, and two artificial nucleotides called X and Y (dNaMTP and d5SICSTP). The researchers had to modify normal cellular chemistry to facilitate accurate replication. The research was published in pnas on the 23rd Jan. They’d previously inserted the nucleotides into the organism, but growth was slow, and the unnatural base pair was excised after several generations.

Wow. A huge step forwards. Wish I’d thought of it.

“All natural organisms store genetic information in a four-letter, two-base-pair genetic alphabet. The expansion of the genetic alphabet with two synthetic unnatural nucleotides that selectively pair to form an unnatural base pair would increase the information storage potential of DNA, and semisynthetic organisms that stably harbor this expanded alphabet would thereby have the potential to store and retrieve increased information. Toward this goal, we previously reported that Escherichia coli grown in the presence of the unnatural nucleoside triphosphates dNaMTP and d5SICSTP, and provided with the means to import them via expression of a plasmid-borne nucleoside triphosphate transporter, replicates DNA containing a single dNaM-d5SICS base pair. To fortify and vivify the nascent organism, we engineered the transporter, used a more chemically optimized base pair, and harnessed the power of the bacterial immune response by using Cas9 to eliminate DNA that had lost the base pair. The organism grows robustly, constitutively imports the unnatural triphosphates, and is able to indefinitely retain multiple unnatural base pairs in virtually any sequence context. This organism is thus a form of life that can stably store genetic information using a six-letter, three-base-pair alphabet.

Not long ago, I had a close look at the standard base-pairing shown below:

with the view of exploring the possibility of creating a third base-pairing by “standard” means (purine-pyrimidine bonding via OHN or NHN hydrogen bonding (note that the third base-pairing of the opening post is non-standard)). If one considers the three bonding locations of Guanine as either donating or accepting, with the corresponding bonding locations of Cytosine as complementary, then one might consider that there are 2³ = 8 possible combinations of donating or accepting locations. But valency and aromaticity constraints prevent the nature of the three bonding locations being independent. Thus, two existing base-pair configurations are really the only ones possible.

It’s interesting to note that one could add an NH₂ group to Adenine to produce three bonding locations, or remove an NH₂ group from Guanine to produce two bonding locations, and that nature chose one base-pair with two bonding locations and one base pair with three bonding locations rather than both with two bonding locations or both with three bonding locations.

Looking at the standard base-pairing shown below:

one may question why tautomerisation followed by hydrolysis doesn’t cause more problems with regards to the stability of the information contained in DNA. Note that such reaction would reverse the order of the donating and accepting character for the top two bonding locations of Adenine and Cytosine. However, Guanine has an NH₂ group that the degraded Adenine does not, and Thymine has a CH₃ group that the degraded Cytosine does not. Thus, if these bases were degraded, it would be possible in principle to repair the damage.

KJW said:

Looking at the standard base-pairing shown below:

one may question why tautomerisation followed by hydrolysis doesn’t cause more problems with regards to the stability of the information contained in DNA. Note that such reaction would reverse the order of the donating and accepting character for the top two bonding locations of Adenine and Cytosine. However, Guanine has an NH₂ group that the degraded Adenine does not, and Thymine has a CH₃ group that the degraded Cytosine does not. Thus, if these bases were degraded, it would be possible in principle to repair the damage.

> tautomerisation followed by hydrolysis

Can you spell that out in more detail? Which double bond, which hydrolysis?
Wikipedia says “Adenine forms several tautomers”. It also says that adenine can also bond with “D” and “ψ”, whatever they are.
“Guanine has two tautomeric forms”.

I’m still at the stage of wondering why uracil gets used in RNA as opposed to thiamine in DNA. Uracil does occasionally occur in DNA, but rarely.
It’s even more confusing to me because cytosine can lose it’s amino group to become uracil in DNA or it can become methylated.

mollwollfumble said:

> tautomerisation followed by hydrolysis

Can you spell that out in more detail? Which double bond, which hydrolysis?
Wikipedia says “Adenine forms several tautomers”. It also says that adenine can also bond with “D” and “ψ”, whatever they are.
“Guanine has two tautomeric forms”.

I’m still at the stage of wondering why uracil gets used in RNA as opposed to thiamine in DNA. Uracil does occasionally occur in DNA, but rarely.
It’s even more confusing to me because cytosine can lose it’s amino group to become uracil in DNA or it can become methylated.

It would seem that I should have looked at uracil before writing my second post in this thread. Uracil (shown below):

which bonds to adenine in RNA, is the product formed by the tautomerisation followed by hydrolysis of cytosine. This degradation of cytosine to uracil is well-known and is rapid enough to be a problem if uracil were used instead of thymine in DNA. However, since RNA is a short-term storage of information, in contrast to DNA which is long-term, the degradation of cytosine in RNA would be less of a problem. Because uracil is simpler than thymine, it was probably the original form of the base chosen by life. Selection pressure would likely have caused a shift to thymine for long-term storage, but for short-term storage, the selection pressure would have been minimal, allowing uracil to persist.

In the case of adenine, its degradation by tautomerisation followed by hydrolysis would be similar to the degradation of cytosine. But, unlike for cytosine, I was not able to find any information about the degradation of adenine. I was also not able find out anything about the molecule that would be formed by the degradation of adenine, including any common name. I was only able to find out that guanine degrades to xanthine.

> Because uracil is simpler than thymine, it was probably the original form of the base chosen by life. Selection pressure would likely have caused a shift to thymine for long-term storage, but for short-term storage, the selection pressure would have been minimal, allowing uracil to persist.

I agree.