APPENDIX I: Proposed Numbering System of Nucleotides in tRNAs Based on Yeast tRNAPhe

Abstract

This compilation presents in a small space the tRNA sequences so far published to enable rapid orientation and comparison. The numbering of tRNA^phe from yeast is used as has been done earlier1 but following the rules proposed by the participants of the 1978 Cold Spring Harbor Meeting on tRNA. This numbering allows comparisons with the three-dimensional structure of tRNA^phe, the only structure known from X-ray analysis. The secondary structure of tRNAs is indicated by specific underlining. In the primary structure, a nucleoside followed by a nucleoside in brackets or a modification in brackets denotes that both types of nucleosides can occupy this position. Part of a sequence in brackets designates a piece of sequence not unambiguously analyzed. Rare nucleosides are named according to the IUPAC-IUB rules (for some, more complicated, rare nucleosides and their identification, see Table 1); those with lengthy names are given with the prefix “x” and specified in the footnotes. Footnotes are numbered according to the coordinates of the corresponding nucleoside and are indicated in the sequence by an asterisk. The references are restricted to the citation of the latest publication in those cases where several papers deal with one sequence. For additional information, refer either to the original literature or to other tRNA sequence compilations.2–6

Table
Table 1Names of some rare nucleosides and citations regarding their identification

NucleosideIdentificationo⁵Uuridine-5-oxyacetic acidmo⁵U5-methoxyuridinemcm⁵U5-methoxycarbonylmethyluridine¹mcm⁵s²U5-methoxycarbonylmethyl-2-thiouridinemam⁵s²U5-N-methylaminomethyl-2-thiouridinei⁶AN-6-(Δ²-isopentenyl)adenosinems²i⁶AN-6-(Δ²-isopentenyl)2-methylthioadenosine³t⁶AN-[9-(β-D-ribofuranosyl)purin-6-ylcarbamoyl]threoninemt⁶AN-[9-(β-D-ribofuranosyl)purin-6-yl-N-methylcarbamoyl]threonineQ₃₄7-(4,5-cisdihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine⁴X3-N-(3-amino-3-carboxypropyl)uridine⁵y^Wwybutosine⁶O₂yW