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1.7 Nomenclature and Abridged Formulas of Nucleosides

The available structural data indicate that the purine nucleosides isolated from hydrolysates of nucleic acids are essentially 9-b-D-ribo- or 9-b-2'-deoxyD-ribofuranosides of adenine and guanine, while the isolated pyrimidine nucleosides are 1-b-D-ribo- or 1-b-2'-deoxy-D-ribofuranosides of cytosine, uracil and thymine. The numbering of atoms in pyrimidine and purine nucleosides is shown in the following formulas:

Tables 1-2 and 1-3 list the structural formulas and names of the major nucleosides of RNA and DNA. In view of the fact that difficulties arise when complete structural formulas of nucleosides are used in writing those of nucleic acids and their large fragments, abridged structural formulas are used instead as well as abbreviated (one- or three-letter) symbols which are also listed in Tables 1-2 and 1-3.

If abbreviated letter symbols of nucleosides occur in a text, they normally consist of a single letter, although such symbols coincide with one-letter symbols of the constituent pyrimidines or purines (see Table 1-1). In cases where bases of nucleic acids are mentioned in the same text along with nucleosides without using formulas (complete or abridged), three-letter symbols of nucleosides may be used to avoid confusion.

An abridged structural formula (see Tables 1-2 and 1-3) represent the sugar as a vertical line (a modified borrowing from the chemistry of carbohydrates) with the abbreviated symbol of the base constituting the nucleoside added on top. The hydroxyl groups are represented by horizontal lines with the OH group (the latter is omitted sometimes) - on the right in the case of 2'- and 3'-hydroxyl groups or on the left to denote the 5'-OH group. For the 2'- and 3'-hydroxyl groups to be represented correctly, the vertical line is mentally divided into three parts with a horizontal line associated with the 2'-hydroxyl being connected to the end of the first part and a line associated with the 3'-hydroxyl being connected to the end of the second part.

Table 1-2. Structure, Name and Symbols of Major Pyrimidine and Purine Nucleosides Isolated from RNA

The difference between the abridged structural formulas of adenine ribo- and deoxyribonucleosides (adenosine and deoxyadenosine) is in the absence of a horizontal line with an OH group, which indicates that the 2'-hydroxyl group is absent:

When structural formulas are written in this way, the presence of cyclic oxygen is always implied.

Table 1-4 lists pyrimidine nucleosides of some phage DNAs in which they replace the major nucleosides (see Tables 1-2 and 1-3).

Table 1-3. Structure, Name and Symbols of Major Pyrimidine and Purine Nucleosides Isolated from DNA

 

Table 1-4. Structure and Name of Pyrimidine Deoxyribonucleosides Constituting DNAs of Some Phages

Table 1-4. (Continued)