Molecular Crowding Accelerates Ribozyme Docking and Catalysis
File(s)ja5073146.pdf (1.26 MB)
Published version
Author(s)
Paudel, BP
Rueda, D
Type
Journal Article
Abstract
All biological processes take place in highly crowded cellular environments. However, the effect that molecular crowding agents have on the folding and catalytic properties of RNA molecules remains largely unknown. Here, we have combined single-molecule fluorescence resonance energy transfer (smFRET) and bulk cleavage assays to determine the effect of a molecular crowding agents on the folding and catalysis of a model RNA enzyme, the hairpin ribozyme. Our single-molecule data reveal that PEG favors the formation of the docked (active) structure by increasing the docking rate constant with increasing PEG concentrations. Furthermore, Mg2+ ion-induced folding in the presence of PEG occurs at concentrations ∼7-fold lower than in the absence of PEG, near the physiological range (∼1 mM). Lastly, bulk cleavage assays in the presence of the crowding agent show that the ribozyme’s activity increases while the heterogeneity decreases. Our data is consistent with the idea that molecular crowding plays an important role in the stabilization of ribozyme active conformations in vivo.
Date Issued
2014-11-17
Date Acceptance
2014-11-17
Citation
Journal of the American Chemical Society, 2014, 136 (48), pp.16700-16703
ISSN
1520-5126
Publisher
American Chemical Society
Start Page
16700
End Page
16703
Journal / Book Title
Journal of the American Chemical Society
Volume
136
Issue
48
Copyright Statement
© 2014 American Chemical Society. This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
Subjects
Science & Technology
Physical Sciences
Chemistry, Multidisciplinary
Chemistry
HAIRPIN RIBOZYME
EXCLUDED-VOLUME
RNA
STABILITY
PROTEINS
KINETICS
BINDING
RATES
FRET
Biocatalysis
Fluorescence Resonance Energy Transfer
Magnesium
Molecular Docking Simulation
Polyethylene Glycols
Protein Folding
Protein Stability
RNA, Catalytic
General Chemistry
03 Chemical Sciences
Publication Status
Published