O

yeast tRNALeu. The unmodified U, however, typical of mitochondrial tRNAs.

In some tRNAs, such as tRNAAsp, tRNAAsn, tRNAHis, and tRNATyr of bacteria and animals, the first position of the anticodon contains a hypermodified G derivative, the so-called queuosine (Quo or Q), the chemical name of which is 7-{[(cis-4,5-dioxy-2-cyclopenten-1-yl)amino]methyl}-7-deazaguanosine (see Fig. 3.3).

Hypermodifications are found to be typical of the position of the purine nucleoside adjacent to the anticodon on the 3'-side. For example, the residue flanking the anticodon at the 3'-side is N6-isopentenyl adenosine (i6A) in eukaryotic tRNACys, tRNASer, and tRNATyr; 2-methylthio-N6-

isopentenyladenosine (N6-

isopentenyl-2-methylthioadenosine, ms2i6A) in the analogous bacterial tRNAs; and N6-(threoninocarbonyl)-adenosine (t6A) in tRNAIle, tRNAThr, tRNALys, and tRNAMet of both Eukaryotes and bacteria (Fig. 3.4). This position is even more hypermodified in the tRNAPhe of all Eukaryotes, where it is represented by the so-called wybutosine (yW or Y) or its hydroxy-derivative (oyW) (see Fig. 3.4).

3.2.2. Secondary Structure

An analysis of even the first tRNA primary structure (i.e. tRNAAla of yeast) revealed a number of interesting features concerning possible chain folding into the secondary structure. First of all, the 5'-terminal section (positions 1 to 7) has a marked complementarity with the 3'-end-adjacent section (positions 66 to 72) if the sections are arranged in an antiparallel fashion. In addition, three inner sections of the tRNA chain display self-complementarity when folded upon themselves; because of this they are capable of forming hairpin-like structures. Pairing these complementary sequences results in the structure schematically presented in Fig. 3.1, commonly called a cloverleaf structure. It is remarkable that without exception the nucleotide sequences of all the tRNA species studied so far reveal similar self-complementarity features and correspondingly can be folded into very similar cloverleaves.

The parts of the cloverleaf structure have been designated as follows: the acceptor stem (AA stem), with the universal 3'-terminal sequence CCA which accepts an amino acid residue; the dihydrouridylic arm (D arm), with the corresponding loop varying somewhat in length and containing, as a rule, between one and five dihydrouridylic acid residues; the anticodon arm (AC arm), with an anticodon loop of constant length equal to seven nucleotides; and the thymidyl-pseudouridylic arm (TY arm), which has a loop with the universal GTYCGA or GTYCAA sequence. In addition, the cloverleaf contains a variable loop (V loop) between the anticodon and TY arms; in tRNAAla this loop is only five nucleotides long whereas in other tRNA species it may reach 15 to 20 nucleotide residues in length (the latter is the case for tRNALeu, tRNASer, and bacterial tRNATyr).

In animal mitochondrial tRNAs D-arm or T-arm may be reduced or fully absent.

XH3 "CH3

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