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Biophysical Journal
Article
License: Elsevier Non-Commercial
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Biophysical Journal
Article . 2008
License: Elsevier Non-Commercial
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Biophysical Journal
Article . 2008 . Peer-reviewed
License: Elsevier Non-Commercial
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Monovalent and Divalent Promoted GAAA Tetraloop-Receptor Tertiary Interactions from Freely Diffusing Single-Molecule Studies

Authors: Fiore, Julie L.; Hodak, Jose H.; Piestert, Oliver; Downey, Christopher D.; Nesbitt, David J.;

Monovalent and Divalent Promoted GAAA Tetraloop-Receptor Tertiary Interactions from Freely Diffusing Single-Molecule Studies

Abstract

Proper assembly of RNA into catalytically active three-dimensional structures requires multiple tertiary binding interactions, individual characterization of which is crucial to a detailed understanding of global RNA folding. This work focuses on single-molecule fluorescence studies of freely diffusing RNA constructs that isolate the GAAA tetraloop-receptor tertiary interaction. Freely diffusing conformational dynamics are explored as a function of Mg(2+) and Na(+) concentration, both of which promote facile docking, but with 500-fold different affinities. Systematic shifts in mean fluorescence resonance energy transfer efficiency values and line widths with increasing [Na(+)] are observed for the undocked species and can be interpreted with a Debye model in terms of electrostatic relaxation and increased flexibility in the RNA. Furthermore, we identify a 34 +/- 2% fraction of freely diffusing RNA constructs remaining undocked even at saturating [Mg(2+)] levels, which agrees quantitatively with the 32 +/- 1% fraction previously reported for immobilized constructs. This verifies that the kinetic heterogeneity observed in the docking rates is not the result of surface tethering. Finally, the K(D) value and Hill coefficient for [Mg(2+)]-dependent docking decrease significantly for [Na(+)] = 25 mM vs. 125 mM, indicating Mg(2+) and Na(+) synergy in the RNA folding process.

Keywords

Base Sequence, Molecular Sequence Data, Sodium, Static Electricity, Biophysics, Diffusion, Kinetics, Tetrahymena, Fluorescence Resonance Energy Transfer, Animals, Nucleic Acid Conformation, RNA, Magnesium, Least-Squares Analysis

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
37
Top 10%
Top 10%
Top 10%
hybrid