Global flexibility of tertiary structure in RNA: Yeast tRNAPh as a model system

Paul J Hagerman, Marisa W. Friederich, Elsi Vacano

Research output: Contribution to journalArticle

Abstract

The study of RNA structure using x-ray crystallography or NMR has yielded a wealth of detailed structural information; however, such approaches do not generally yield quantitative information regarding long-range flexibility in solution. To address this issue, we describe a solution-based method that is capable of characterizing the global flexibilities of non-helix element in RNA, provided that such elements are flanked by helix (e.g., bulges, internal loops, branches). The "phased τ-ratio" method is based on the principle that, for RNA molecules possessing a set of two variably-phased bends, the relative birefringence decay times depend on the flexibility of each bend, not simply the mean bend angles. The method is used to examine the overall flexibility of the yeast tRNAPhe core (as unmodified transcript). In the presence of magnesium ions, the tRNA core does not appear to be any more flexible than an equivalent length of RNA helix: whereas in the absence of divalent ions, the tRNA core gains flexibility under conditions where its secondary structure is likely to be largely preserved. The phased τ-ratio approach should be broadly applicable to non-helix elements in both RNA and DNA, and to protein-nucleic acid interaction.

Original languageEnglish (US)
JournalFASEB Journal
Volume12
Issue number8
StatePublished - 1998
Externally publishedYes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences (miscellaneous)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Cell Biology

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