Molecular crowding stabilizes folded RNA structure by the excluded volume effect.
Crowder molecules in solution alter the equilibrium between folded and unfolded states of biological macromolecules. It is therefore critical to account for the influence of these other molecules when describing the folding of RNA inside the cell. Small angle X-ray scattering experiments are reported on a 64 kDa bacterial group I ribozyme in the presence of polyethylene-glycol 1000 (PEG-1000), a molecular crowder with an average molecular weight of 1000 Da. In agreement with expected excluded volume effects, PEG favors more compact RNA structures. First, the transition from the unfolded to the folded (more compact) state occurs at lower MgCl(2) concentrations in PEG. Second, the radius of gyration of the unfolded RNA decreases from 76 to 64 A as the PEG concentration increases from 0 to 20% wt/vol. Changes to water and ion activities were measured experimentally, and theoretical models were used to evaluate the excluded volume. We conclude that the dominant influence of the PEG crowder on the folding process is the excluded volume effect.
Kilburn
Duncan
D
T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA.
Roh
Joon Ho
JH
Guo
Liang
L
Briber
Robert M
RM
Woodson
Sarah A
SA
D020627:Azoarcus / Q000201:enzymology; D004305:Dose-Response Relationship, Drug; D015636:Magnesium Chloride / Q000494:pharmacology; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D011092:Polyethylene Glycols / Q000494:pharmacology; D020871:RNA Stability / Q000187:drug effects*; D016337:RNA, Catalytic / Q000737:chemistry*; D053838:Scattering, Small Angle; D014867:Water / Q000737:chemistry; D014961:X-Ray Diffraction
D016337:RNA, Catalytic; D015636:Magnesium Chloride; D014867:Water; D011092:Polyethylene Glycols