Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations

Kathleen B. Hall, D. Jeremy Williams

Research output: Contribution to journalArticlepeer-review

45 Scopus citations

Abstract

The iron responsive element (IRE) RNA hairpin loop contains six phylogenetically conserved nucleotides, which constitute part of the sequence-specific binding site of the IRE-binding protein. The NMR structure of the loop has been solved, showing that 3 of the 6 nt are poorly constrained. Here, two purine nucleotides in the IRE loop are individually replaced with the fluorescent purine analog 2-aminopurine (2AP). Steady-state and time-resolved fluorescence methods are used to describe the structure and dynamics of 2AP in the IRE loop. The data indicate that 2AP at the position of the adenosine in the loop moves between stacked and unstacked positions, whereas 2AP at the adjacent guanosine is predominantly solvent exposed. Stochastic dynamics simulations are used to provide a physical description of how those nucleotides might move.

Original languageEnglish
Pages (from-to)34-47
Number of pages14
JournalRNA
Volume10
Issue number1
DOIs
StatePublished - Jan 2004

Keywords

  • 2-aminopurine
  • Fluorescence
  • IRE RNA
  • Stochastic dynamics

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