title: Higher-order structure of bovine mitochondrial tRNA(Phe) lacking the 'conserved' GG and T psi CG sequences as inferred by enzymatic and chemical probing.
abstract: Bovine mitochondrial (mt) phenylalanine tRNA (tRNA(Phe)), which lacks the 'conserved' GG and T psi YCG sequences, was efficiently purified by the selective hybridization method using a solid phase DNA probe. The entire nucleotide sequence of the tRNA, including modified nucleotides, was determined and its higher-order structure was investigated using RNaseT2 and chemical reagents as structural probes. The D and T loop regions as well as the anticodon loop region were accessible to RNaseT2, and the N-3 positions of cytidines present in the D and T loops were easily modified under the native conditions in the presence of 10mM Mg2+. On the other hand, the nucleotides present in the extra loop were protected from the chemical modification under the native conditions. From the results of these probing analyses and a comparison of the sequences of mitochondrial tRNA(Phe) genes from various organisms, it was inferred that bovine mt tRNA(Phe) lacks the D loop/T loop tertiary interactions, but does have the canonical extra loop/D stem interactions, which seem to be the main factor for bovine mt tRNA(Phe) to preserve its L-shaped higher-order structure.
authors.affiliation: Department of Biological Sciences, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Wakita
authors.forename: Y
authors.initials: Y
authors.lastname: Watanabe
authors.forename: T
authors.initials: T
authors.lastname: Yokogawa
authors.forename: Y
authors.initials: Y
authors.lastname: Kumazawa
authors.forename: S
authors.initials: S
authors.lastname: Nakamura
authors.forename: T
authors.initials: T
authors.lastname: Ueda
authors.forename: K
authors.initials: K
authors.lastname: Watanabe
authors.forename: K
authors.initials: K
authors.lastname: Nishikawa
mesh_terms: D000818:Animals; D001483:Base Sequence; D002417:Cattle; D004722:Endoribonucleases / Q000378:metabolism; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000648:ultrastructure; D000077278:RNA, Mitochondrial; D012360:RNA, Transfer, Phe / Q000737:chemistry* / Q000648:ultrastructure; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid
chemical_list: D000077278:RNA, Mitochondrial; D012360:RNA, Transfer, Phe; D012313:RNA; D004722:Endoribonucleases; C022543:ribonuclease T(2)