title: Entropic stabilization of folded RNA in crowded solutions measured by SAXS.
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 MgCl2and 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.
authors.affiliation: T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Duncan
authors.initials: D
authors.lastname: Kilburn
authors.affiliation: T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Reza
authors.initials: R
authors.lastname: Behrouzi
authors.affiliation: T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Hui-Ting
authors.initials: HT
authors.lastname: Lee
authors.affiliation: T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Krishnarjun
authors.initials: K
authors.lastname: Sarkar
authors.affiliation: Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA rbriber@umd.edu.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Briber
authors.affiliation: T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA swoodson@jhu.edu.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Woodson
mesh_terms: D020627:Azoarcus / Q000235:genetics; D019277:Entropy; D015636:Magnesium Chloride / Q000737:chemistry / Q000494:pharmacology; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry; D011092:Polyethylene Glycols / Q000737:chemistry / Q000494:pharmacology; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding / Q000187:drug effects; D012329:RNA, Bacterial / Q000737:chemistry; D053838:Scattering, Small Angle; D012996:Solutions; D013696:Temperature; D013816:Thermodynamics; D014961:X-Ray Diffraction
chemical_list: D009711:Nucleotides; D012329:RNA, Bacterial; D012996:Solutions; D015636:Magnesium Chloride; D011092:Polyethylene Glycols; D012313:RNA