Entropic stabilization of folded RNA in crowded solutions measured by SAXS

Duncan Kilburn, Reza Behrouzi, Hui Ting Lee, Krishnarjun Sarkar, Robert M. Briber, Sarah A. Woodson

Research output: Contribution to journalArticle

Abstract

Non-coding RNAs must fold into specific structures that are stabilized by metal ions and other co-solutes in the cell's interior. Large crowder molecules such as PEG stabilize a bacterial group I ribozyme so that the RNA folds in low Mg2+ concentrations typical of the cell's interior. To understand the thermodynamic origins of stabilization by crowder molecules, small angle X-ray scattering was used to measure the folding and helix assembly of a bacterial group I ribozyme at different temperatures and in different MgCl2 and polyethylene glycol (PEG) concentrations. The resulting phase diagrams show that perturbations to folding by each variable do not overlap. A favorable enthalpy change drives the formation of compact, native-like structures, but requires Mg2+ ions at all temperatures studied (5-55°C). PEG reduces the entropic cost of helix assembly and increases correlations between RNA segments at all temperatures. The phase diagrams also revealed a semi-compact intermediate between the unfolded and folded ensemble that is locally more flexible than the unfolded state, as judged by SHAPE modification. These results suggest that environmental variables such as temperature and solute density will favor different types of RNA structures.

Original languageEnglish (US)
Pages (from-to)9452-9461
Number of pages10
JournalNucleic Acids Research
Volume44
Issue number19
DOIs
StatePublished - Nov 2 2016

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RNA
Temperature
Ions
Untranslated RNA
Magnesium Chloride
Thermodynamics
Metals
X-Rays
Costs and Cost Analysis
GIR1 ribozyme

ASJC Scopus subject areas

  • Genetics

Cite this

Kilburn, D., Behrouzi, R., Lee, H. T., Sarkar, K., Briber, R. M., & Woodson, S. A. (2016). Entropic stabilization of folded RNA in crowded solutions measured by SAXS. Nucleic Acids Research, 44(19), 9452-9461. https://doi.org/10.1093/nar/gkw597

Entropic stabilization of folded RNA in crowded solutions measured by SAXS. / Kilburn, Duncan; Behrouzi, Reza; Lee, Hui Ting; Sarkar, Krishnarjun; Briber, Robert M.; Woodson, Sarah A.

In: Nucleic Acids Research, Vol. 44, No. 19, 02.11.2016, p. 9452-9461.

Research output: Contribution to journalArticle

Kilburn, D, Behrouzi, R, Lee, HT, Sarkar, K, Briber, RM & Woodson, SA 2016, 'Entropic stabilization of folded RNA in crowded solutions measured by SAXS', Nucleic Acids Research, vol. 44, no. 19, pp. 9452-9461. https://doi.org/10.1093/nar/gkw597
Kilburn D, Behrouzi R, Lee HT, Sarkar K, Briber RM, Woodson SA. Entropic stabilization of folded RNA in crowded solutions measured by SAXS. Nucleic Acids Research. 2016 Nov 2;44(19):9452-9461. https://doi.org/10.1093/nar/gkw597
Kilburn, Duncan ; Behrouzi, Reza ; Lee, Hui Ting ; Sarkar, Krishnarjun ; Briber, Robert M. ; Woodson, Sarah A. / Entropic stabilization of folded RNA in crowded solutions measured by SAXS. In: Nucleic Acids Research. 2016 ; Vol. 44, No. 19. pp. 9452-9461.
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