Standard letter for 5-methylcytosine

Question

I'm working on a piece of software that computes melting temperatures for nucleic acid duplexes, and I'm about to add support for 5-methylcytosine as a nucleotide base. At the moment, the bases accepted by the program are adenine, cytosine, guanine, thymine and uracil, with their standard letters A,C,G,T,U. Is there a standard letter for 5-methylcytosine? The only example I've found is this paper, which uses an italic C for 5mc, but I want a distinct letter. The three candidates I've thought of are:

• 5 - for '5-methylcytosine'
• M - for 'methyl'
• B - Since methylation of U gives you T, which is one place earlier in the alphabet, so methylation of C gives B.

Answer 1

Well, don't use M or B, those are already taken (C or A, and not A, respectively). You can see the full list here: http://www.dna.affrc.go.jp/misc/MPsrch/InfoIUPAC.html (The enWiki article on Nucleobases lists a few others but I would ignore those as 1. D is present in both and 2. they are rare and inapplicable)

5-methylcytosine isn't on there. If you want to be pedantic about it, 5-methylcytosine is an epigenetic marker and as such is by definition not a genetic sequence; that remains simply a C and, genetically, the sequence is the same, despite the fact that it may indeed make a difference.

Most of the time people use m⁵C, so I'd go with 5 if I were you. That certainly isn't used for anything else and if you must use a single character most anybody will know what you are talking about.

Answer 2

As Amory suggests the IUPAC "Recommendations on Organic & Biochemical Nomenclature, Symbols & Terminology etc." (http://www.chem.qmul.ac.uk/iupac/) are probably the best place to start. From a quick scan the obviously relevant documents would be:

• "Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents"
• "Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences"

These provide the complete description of the commonly used IUPAC nucleic acid codes, including both the one letter and three letter variants.

Answer 3

Just to fully document the IUPAC advice on this, here is the relevant section from the Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences as reproduced here in the link provided by @Hamish McWilliam.

5.2. Modified nucleotides

In a number of organisms DNA and RNA are modified at certain positions. For instance, the DNA of Escherichia coli is usually methylated on N-6 of the adenine residue in the sequence 5'-GATC-3' [23]. The present nomenclature does not allocate any specific symbol to these modified nucleotides for the following reasons. (1) The presence or absence of a given modification depends upon the location of the DNA. Sequences modified in one organism may not be modified in another. (2) Modification is usually statistical, in that only a proportion of possible sites for modification may actually be utilised in vivo. Modification of a nucleotide or base in a given polynucleotide is not a function of the sequence per se. Although it is recognised that stable RNA species (tRNA and rRNA) often carry a constant pattern of post-translational modification. the present nomenclature is not intended to overlap with or supplant existing systems. It would probably be impossible to devise a simple and logical system that avoided all conflict with previous usage. One should therefore recognise that such conflict is possible and take steps to prevent it from generating confusion, for example in relation to the symbols B, D and S, which have been recommended for 5-bromouridine, 5,6-dihydrouridine and thiouridine respectively [1], or W, which is sometimes used for wyosine.