Insertion of selenocysteine into a growing peptide requires the unusual tRNASec (Zinoni et al., 1987; Stadtman, 1990; Böck et al., 1991). This tRNA has an extended D-stem containing six base pairs, which, in the case of eukaryotic tRNASec (euk-tRNASec), is the key identity element for selenylation and phosphorylation (Wu & Gross, 1994; Amberg et al., 1996). Two secondary structures have been proposed for the euk-tRNASec, which differ in the base pairing of the acceptor/T helical domain (Diamond et al., 1981; Böck et al., 1991; Sturchler et al., 1993). One structure has the normal seven base pairs in the acceptor stem and five base pairs in the T-stem (7/5 structure, Fig. 1, left), and is characterized by an unusually long four-nucleotide unpaired region between the acceptor and D-stems (Connector 1) and an unpaired nucleotide, C64a, in the T-stem. The alternate structure features the normal two nucleotides in Connector 1 and a 13-base pair acceptor/T domain comprised of nine base pairs in the acceptor stem and four in the T-stem (9/4 structure, Fig. 1, right). This 9/4 structure was initially proposed by analogy with the prokaryotic tRNASec (prok-tRNASec), which also contains 13 base pairs in the acceptor/T helical domain. However, in this case, there are eight and five base pairs in the acceptor and T-stems, respectively. The acceptor/T helical domain having 13 base pairs is thought to be a key structural element determining the functionalities pattern of tRNASec in both prokaryotes and eukaryotes (Böck et al., 1991).