The wikipedia article about Nucleosides presents a table in which there are three columns — Base, Ribonucleoside and Deoxyribonucleoside — and structures, names and abbreviations for the nucleosides corresponding to the five bases, adenine, guanine, thymine, uracil and cytosine.

The abbreviation pattern for the deoxyribonucleosides is quite regular — they are all termed dN, where N is the first letter of the name of the base and ‘d’ indicates ‘deoxy’ (i.e. dA, dG, dT, dU, dC).

In the case of ribonucleosides, apart from one exception, the pattern is similar — they are all termed N, where N is the first letter of the name of the base (i.e. A, G, U, C). The exception is the ribonucleoside related to the base, thymine, which is not abbreviated T — as one might expect, but as m5U, from its name 5-methyluridine.

  1. What is the reason for this? Why does the abbreviation for ribonucleoside derived from thymine deviate from that for the other bases?

  2. Do people distinguish between m5U and U when referring to RNA, or is the letter U used for both?

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    $\begingroup$ I have simplified your question and removed the reference to alphabet. We are just talking about abbreviations, which by their very nature are imprecise, but arise over time because they are convenient. We are not talking about God creating animals and giving them all names. Think about it in relation to your knowledge of DNA and RNA. $\endgroup$ – David Jan 19 '17 at 21:56
  • $\begingroup$ The m5U isn't a common constituent of RNA, regardless of the nomenclature, and so this notation does not explain why uracil is used in RNA - the answer you linked at the beginning of your post already contains the best explanation for that along with the explanation for why thymidine is found in DNA: simply, it started out as uracil and replacement machinery to deal with thymidine RNA never evolved. $\endgroup$ – Bryan Krause Jan 19 '17 at 22:14
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    $\begingroup$ You say your question is why is T not used in RNA, and not primarily about abbreviations. You certainly fooled me! I have changed the title to reflect this. Have I understood you correctly? If so the question needs revising to say that. And please stop talking about alphabets. I can help you with this (and answer that question). If this is not your question please clarify. Do you understand the roles of the different RNAs in protein synthesis? Are you worried about the fact that the base thymine (5-methyl uracil) is found in some RNA? Do you know where it is found? What books have you read? $\endgroup$ – David Jan 20 '17 at 16:54
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    $\begingroup$ @David No worries, I think we are more or less on the same page of being a bit uncertain about OP's intentions while trying to sort things out. If the new title is indeed what the OP wants answered, then it is a pretty clear duplicate of this question. $\endgroup$ – Bryan Krause Jan 20 '17 at 17:13
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    $\begingroup$ @BryanKrause It may appear to be a duplicate, but the poster is right in saying all the answers answer a different question — why T not U in DNA. So I think we should persist and, eventually andif appropriate make two distinct questions, perhaps by editing the previous one. $\endgroup$ – David Jan 20 '17 at 17:19

From the standpoint of modern molecular biology, one can say that the table in the Wikipedia article would be better if — in the first instance at least — it left blank the entries for the ribonucleoside corresponding to the base thymine and the deoxyribonucleotide corresponding to the base uracil. This is because the thymine ribonucleoside is not a normal constituent of RNA, and the uracil deoxyribonucleoside is not a constituent of DNA.

It would also be more honest if the article explained that the abbreviations used in DNA and RNA databases employ the single letter to represent a deoxyribonucleoside monophosphate residue or a ribonucleoside monophosphate residue, as the case may be, and that only the chemist or student of nucleotide metabolism is likely to be concerned with the abbreviations presented.

It is in metabolism (for which these were named) that the abbreviations make sense. ATP is adenosine triphosphate, so the ‘A’ has to represent the nucleoside, adenosine, and dTTP, deoxy-thymidine triphosphate, is the metabolite that is a DNA precursor used by DNA polymerase. The reason that dU justifies inclusion is that dUMP exists in cells — as a precursor of dTMP (which is then converted to dTTP).

So finally to your Q1 about 5-methyluridine. The answer is that, as far as I am aware, this does not occur in cells as the free nucleoside or the free related base or nucleotide. It can only be considered as occuring at a particular positions in certain transfer RNAs (and ribosomal RNAs) where it is produced by the enzymic modification of the uracil ring by a 5-methyluridine methyltransferase. So in the metabolic era, before the detailed chemical analysis of minor bases in structural RNAs, there was never any reason for biochemists to refer to 5-methyluridine and consider its abbreviation.

You may or may not be aware that there are many minor bases of this type in different tRNAs, all produced by enzymic modification of the four bases occuring in an initial RNA transcript synthesised by RNA polymerase. There are over half a dozen different modifications of uracil, so it was far more meaningful for the scientists working on them to distinguish them with abbreviations that indicated their chemistry, rather than assigning arbitrary single letters to them. The fact that one could logically employ T as an abbreviation for 5-methyluridine would have been of no practical use, and, because of the association of thymine with DNA, could well have led to confusion. Hence, the committee standardizing nomenclature would have been faced with a fait accompli. In such circumstances realism prevails over idealism. (And in any case the names of the bases are a mess — how many students have been confused by adenine/adenosine but cytosine/cytidine.)

Regarding your second question: people don’t talk very much about m5U and U, but when they do they naturally distinguish between them because they are different molecules. Specifically, the databases for tRNA structures will distinguish clearly the different modified bases.

  • $\begingroup$ I think this sentence is unfortunate: "So finally to your Q1 about 5-methyluridine. The answer is that, as far as I am aware, this does not exist as such in cells, and only occurs at a particular position in certain tRNAs". tRNA occurs in cells, ergo m5U occurs in cells. I read here, that it also appears in rRNA. $\endgroup$ – newandlost Jan 23 '17 at 16:18
  • $\begingroup$ "Your second question doesn’t seem to make sense..." It is a simple question and you provided a clear good answer for it: "the databases for tRNA structures will distinguish clearly the different modified bases." No need to be more verbose as necessary. $\endgroup$ – newandlost Jan 23 '17 at 16:24
  • $\begingroup$ @newandlost Ok about the second question. I'll remove the remark. $\endgroup$ – David Jan 23 '17 at 18:32
  • $\begingroup$ @newandlost — Regarding m5U and its occurrence in cells, I'll rephrase the sentence when I have a moment. The "as such" was meant to imply that there is no free ribonucleoside, m5U, or the related base, or any related nucleotide mono-, di- or tri- phosphate in cells. So these molecules are never encountered within cells, and for biologists (rather than chemists) are not discussed and naming is of little concern.m5U can only be considered as part of some tRNAs (and rRNAs) where it is the base that is of interest (rather than the nucleoside or nucleotide residues) as that is what is modified. $\endgroup$ – David Jan 23 '17 at 18:44
  • $\begingroup$ @newandlost — I've made the changes now. I could also add references to the discovery history of the identification of m5U in tRNA and rRNA, and examples of how it is designated in databases, if you really think this would be useful. $\endgroup$ – David Jan 24 '17 at 11:29

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