Folding of the Tetrahymena ribozyme by polyamines: Importance of counterion valence and size

Eda Koculi, Nam Kyung Lee, D. Thirumalai, Sarah A. Woodson

Research output: Contribution to journalArticlepeer-review

Abstract

Polyamines are abundant metabolites that directly influence gene expression. Although the role of polyamines in DNA condensation is well known, their role in RNA folding is less understood. Non-denaturing gel electrophoresis was used to monitor the equilibrium folding transitions of the Tetrahymena ribozyme in the presence of polyamines. All of the polyamines tested induce near-native structures that readily convert to the native conformation in Mg2+. The stability of the folded structure increases with the charge of the polyamine and decreases with the size of the polyamine. When the counterion excluded volume becomes large, the transition to the native state does not go to completion even under favorable folding conditions. Brownian dynamics simulations of a model polyelectrolyte suggest that the kinetics of counterion-mediated collapse and the dimensions of the collapsed RNA chains depend on the structure of the counterion. The results are consistent with delocalized condensation of polyamines around the RNA. However, the effective charge of the counterions is lowered by their excluded volume. The stability of the folded RNA is enhanced when the spacing between amino groups matches the distance between adjacent phosphate groups. These results show how changes in intracellular polyamine concentrations could alter RNA folding pathways.

Original languageEnglish (US)
Pages (from-to)27-36
Number of pages10
JournalJournal of molecular biology
Volume341
Issue number1
DOIs
StatePublished - Jul 30 2004

Keywords

  • BD, Brownian dynamics
  • RNA folding
  • counterion condensation
  • group I ribozyme
  • polyamines

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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