Variation of the acceptor-anticodon interstem angles among mitochondrial and non-mitochondrial tRNAs

A cloverleaf secondary structure and the concomitant "L"-shaped tertiary conformation are considered the paradigm for tRNA structure, since there appears to be very little deviation from either secondary or tertiary structural forms among the more than one dozen canonical (cloverleaf) tRNAs that have yielded to crystallographic structure determination. However, many metazoan mitochondrial tRNAs deviate markedly from the canonical secondary structure, and are often highly truncated (i.e. missing either a dihydrouridine or a TΨC arm). These departures from the secondary cloverleaf form call into question the universality of the tertiary (L-shaped) conformation, suggesting that other structural constraints may be at play for the truncated tRNAs. To examine this issue, a set of 11 tRNAs, comprising mitochondrial and non-mitochondrial, and canonical and non-canonical species, has been examined in solution using the method of transient electric birefringence. Apparent interstem angles have been determined for each member of the set, represented as transcripts in which the anticodon and acceptor stems have each been extended by ∼70 bp of duplex RNA helix. The measurements demonstrate much more variation in global structure than had been supposed on the basis of crystallographic analysis of canonical tRNAs. In particular, the apparent acceptor-anticodon interstem angles are more obtuse for the metazoan mitochondrial tRNAs that are truncated (missing either a dihydrouridine or a TΨC arm) than for the canonical (cloverleaf) tRNAs. Furthermore, the magnesium dependence of this interstem angle differs for the set of truncated tRNAs compared to the canonical species.