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Nucleic Acids Research Advance Access originally published online on August 21, 2008
Nucleic Acids Research 2008 36(17):5472-5481; doi:10.1093/nar/gkn529
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Nucleic Acids Research, 2008, Vol. 36, No. 17 5472-5481
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Core flexibility of a truncated metazoan mitochondrial tRNA

Ashley A. Frazer-Abel1 and Paul J. Hagerman2,*

1National Jewish Health, Denver, CO 80206 and 2Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, CA 95616, USA

*To whom correspondence should be addressed. Tel: +1 530 754 7266; Fax: +1 530 754 7269; Email: pjhagerman{at}ucdavis.edu

Received May 29, 2008. Revised July 29, 2008. Accepted August 1, 2008.

Secondary and tertiary structures of tRNAs are remarkably preserved from bacteria to humans, the notable exception being the mitochondrial (m) tRNAs of metazoans, which often deviate substantially from the canonical cloverleaf (secondary) or ‘L’-shaped (tertiary) structure. Many metazoan mtRNAs lack either the T{psi}C (T) or dihydrouridine (D) loops of the canonical cloverleaf, which are known to confer structural rigidity to the folded structure. Thus, the absence of canonical T{psi}C–D interactions likely results in greater dispersion of anticodon-acceptor interstem angle than for canonical tRNAs. To test this hypothesis, we have assessed the dispersion of the anticodon-acceptor angle for bovine mtRNASer(AGY), which lacks the canonical D arm and is thus incapable of forming stabilizing interarm interactions. Using the method of transient electric birefringence (TEB), and by changing the helical torsion angle between a core mtRNA bend and a second bend of known angle/rigidity, we have demonstrated that the core of mtRNASer(AGY) has substantially greater flexibility than its well-characterized canonical counterpart, yeast cytoplasmic tRNAPhe. These results suggest that increased flexibility, in addition to a more open interstem angle, would allow both noncanonical and canonical mtRNAs to utilize the same protein synthetic apparatus.


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