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For a presentation of my work I wanted to show a structural representation for dihydrouridine with numbering of the C atoms of the pyrimidine ring, according to this numbering convention.

Then I found this Paper, where the numbering in 5-methylcytidine is consistent with this convention but that in N1-methylpseudouridine is not.

After some more research I found this paper (fig. 1 A), where uridine is numbered according to the nucleotide numbering convention, but pseudouridne is not.

So why is the numbering of modified cytidine according the the convention (m1C), whereas the numbering of pseudouridine (which is a modification of urdine) is not?

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    $\begingroup$ You would probably be best to ask the chemistry SE. $\endgroup$ – bob1 Jun 11 at 10:36
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    $\begingroup$ Welcome to SE Biology. I have answered your question, but can I make a suggestion for improving the way you could have asked it. 1. Your question only showed the numbering for uridine, which made it difficult for readers to know what the situation was with pseudouridine. You should have included a comparative picture — the red dihydro atoms in the diagram you provided are a distraction. 2. Most important, you should then have stated clearly what you thought the numbering convention was that was being applied inconsistently. This might have made you consider whether your assumption was correct. $\endgroup$ – David Jun 11 at 16:14
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Although this question should probably have been asked on SE Chemistry, as the molecules are of biochemical importance — and the question is based on a misconception — I will answer it here.

Answer

The numbering of the carbon and nitrogen atoms in uridine and pseudouridine is perfectly consistent. The numbering is for the pyrimidine ring, which is the same — uracil — in each case. The different positions of attachment to ribose (N1 or C6)) results in two different structures (and hence names) for the resulting nucleoside, but does not alter the numbering of the components.

Numbering of uracil ring in uridine and pseuodouridine

[Modified from https://commons.wikimedia.org/wiki/File:Pseudouridine-synthase.jpg‚ Surundu]

Thus N1-methylpseudouridine has the methyl group attached to the N1:

N1-methylpseudouridine

Basis of numbering

The numbering of the atoms of pyrimidine bases derives ultimately from that of the parent, pyrimidine in which the two (indistinguishable) nitrogen atoms are numbered 1 and 3:

Pyrimidine numbering

The relation of uracil to the parent pyrimidine can be seen from the IUPAC preferred name Pyrimidine-2,4(1H,3H)-dione and a perhaps more easily understood alternative as 2-Oxy-4-oxy pyrimidine i.e. the oxygen substitutions are at positions 2 and 4 (as shown for both uridine and pseudouridine, above).

The preferred IUPAC name for uridine is:

1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4(1H,3H)-dione

and that for pseudouridine is:

5-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4(1H,3H)-dione

i.e. The formal nomenclature for the two nucleosides only differs in the designation of the position of attachment of the base to the sugar ring (1 or 5 — emboldened above).

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