anticodon and purine

To elucidate the general constraints imposed on the structure of the D and T-loops in functional tRNAs, active suppressor tRNAs were selected in vivo from a combinatorial tRNA gene library in which several nucleotide positions in these loops were randomized. Analysis of the nucleotide sequences of the selected clones demonstrates that most of them contain combination U54-A58 allowing the formation of the standard reverse-Hoogsteen base-pair 54-58 in the T-loop. With only one exception, all these clones fall into two groups, each characterized by a distinct sequence pattern. Analysis of these two groups has allowed us to suggest two different types of nucleotide arrangement in the DT region. The first type, the so-called specific purine trap, is found in 12 individual tRNA clones and represents a generalized version of the standard D-T loop interaction. It consists of purine 18 sandwiched between the reverse-Hoogsteen base-pair U54-A58 and purine 57. The identity of purine 18 is restricted by the specific base-pairing with nucleotide 55. Depending on whether nucleotide 55 is U or G, purine 18 should be, respectively, G or A. The second structural type, the so-called non-specific purine trap, corresponds to the nucleotide sequence pattern found in 16 individual tRNA clones and is described here for the first time. It consists of purine 18 sandwiched between two reverse-Hoogsteen base-pairs U54-A58 and A55-C57 and, unlike the specific purine trap, requires the T-loop to contain an extra eighth nucleotide. Since purine 18 does not form a base-pair in the non-specific purine trap, both purines, G18 and A18, fit to the structure equally well. The important role of both the specific and non-specific purine traps in the formation of the tRNA L-shape is discussed.

Topics: Anticodon; Base Composition; Base Pairing; Codon, Nonsense; Computer Simulation; Hydrogen Bonding; Lac Operon; Models, Molecular; Nucleic Acid Conformation; Purines; RNA, Transfer

Here we report the crystal structures of I.C and I.A wobble base pairs in the context of the ribosomal decoding center, clearly showing that the I.A base pair is of an I(anti).A(anti) conformation, as predicted by Crick. Additionally, the structures enable the observation of changes in the anticodon to allow purine-purine base pairing, the 'widest' base pair geometry allowed in the wobble position.

Topics: Anticodon; Base Pairing; Base Sequence; Crystallography, X-Ray; Models, Molecular; Purines; Ribosomes; RNA, Ribosomal, 16S; RNA, Transfer, Arg

The modified nucleoside (U*) present in the wobble position of Saccharomyces cerevisiae mitochondrial tRNA(Leu) and tRNA(Trp) was isolated by thin-layer chromatography and HPLC. Its chromatographic, UV spectral, and mass spectrometric properties were shown to be identical with those of 5- [[(carboxymethyl)amino]methyl]uridine (cmnm5U). This nucleoside found in yeast mitochondrial tRNAs reading two-codon families ending in a purine permits the selective recognition of A and G in the third codon position.

Topics: Anticodon; Chromatography, High Pressure Liquid; Mass Spectrometry; Mitochondria; Molecular Structure; Purines; RNA, Transfer; RNA, Transfer, Amino Acid-Specific; RNA, Transfer, Leu; RNA, Transfer, Trp; Saccharomyces cerevisiae; Spectrophotometry, Ultraviolet; Uridine