Tertiary network in mammalian mitochondrial tRNAAsp revealed by solution probing and phylogeny

Nucleic Acids Res. 2009 Nov;37(20):6881-95. doi: 10.1093/nar/gkp697. Epub 2009 Sep 18.


Primary and secondary structures of mammalian mitochondrial (mt) tRNAs are divergent from canonical tRNA structures due to highly skewed nucleotide content and large size variability of D- and T-loops. The nonconservation of nucleotides involved in the expected network of tertiary interactions calls into question the rules governing a functional L-shaped three-dimensional (3D) structure. Here, we report the solution structure of human mt-tRNA(Asp) in its native post-transcriptionally modified form and as an in vitro transcript. Probing performed with nuclease S1, ribonuclease V1, dimethylsulfate, diethylpyrocarbonate and lead, revealed several secondary structures for the in vitro transcribed mt-tRNA(Asp) including predominantly the cloverleaf. On the contrary, the native tRNA(Asp) folds into a single cloverleaf structure, highlighting the contribution of the four newly identified post-transcriptional modifications to correct folding. Reactivities of nucleotides and phosphodiester bonds in the native tRNA favor existence of a full set of six classical tertiary interactions between the D-domain and the variable region, forming the core of the 3D structure. Reactivities of D- and T-loop nucleotides support an absence of interactions between these domains. According to multiple sequence alignments and search for conservation of Leontis-Westhof interactions, the tertiary network core building rules apply to all tRNA(Asp) from mammalian mitochondria.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Databases, Nucleic Acid
  • Humans
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Phylogeny
  • RNA / chemistry*
  • RNA / metabolism*
  • RNA, Mitochondrial
  • RNA, Transfer, Asp / chemistry*
  • RNA, Transfer, Asp / metabolism*
  • Transcription, Genetic


  • RNA, Mitochondrial
  • RNA, Transfer, Asp
  • RNA