Powered by OpenAIRE graph
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Biophysical Journalarrow_drop_down
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
Biophysical Journal
Article
License: Elsevier Non-Commercial
Data sources: UnpayWall
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
Biophysical Journal
Article . 2013
License: Elsevier Non-Commercial
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
Biophysical Journal
Article . 2013 . Peer-reviewed
License: Elsevier Non-Commercial
Data sources: Crossref
versions View all 3 versions

Characterization of Viscous and Excluded Volume effects on the Folding Kinetics of the Tetraloop-Receptor Motif: Single Molecule Tests of Kramer's Theory

Authors: Dupuis, Nicholas; Nesbitt, David J.;

Characterization of Viscous and Excluded Volume effects on the Folding Kinetics of the Tetraloop-Receptor Motif: Single Molecule Tests of Kramer's Theory

Abstract

It is widely known that there exists a strong relationship between the solvent, including co-solutes (e.g. cations, proteins, nucleic acids), and RNA that cooperatively defines the kinetics of tertiary structure formation. Viscosity, a solvent property that is coupled to dynamics, is critical in RNA folding due to the propensity for populating kinetically trapped species on a rough free energy landscape. Also of importance is the role of macromolecular co-solutes that limit the volume available for molecules to sample (excluded volume effects). The effects of these properties are highlighted by observed in vivo diffusion coefficients that are 4-200x smaller than in aqueous solvents. In this work, Kramers' rate theory is used to describe the viscosity dependence of tetraloop-receptor docking kinetics at the single molecule level. Both rate constants, kfold and kunfold, decrease with increasing viscosity (increasing glycerol %), trends that are predicted by Kramers' theory in the over-damped limit. However, the same measurements made in high molecular weight PEG solutions showed folding rate constants are accelerated by 1-2 orders of magnitude. Scaled particle theory, describing a hard spheres PEG-RNA interaction, quantitatively predicts the stabilizing effect of excluded volume. Temperature dependent measurements show that the thermodynamics of docking are not perturbed (ΔH°= −23(2) kcal/mol and ΔS°= −76(6) cal/mol∗K) even in up to 50% glycerol (∼6 cP) and that solvent activation accounts for 4-6 kcal/mol of the folding enthalpy. In PEG solutions thermodynamics reveal that the folding is stabilized by a reduction in the entropy of the unfolded RNA ensemble (ΔΔS°>0). Thus, these studies validate physical models describing characteristic kinetic and thermodynamic trends for intramolecular structure formation attributed to viscosity and excluded volume.

Keywords

Biophysics

  • BIP!
    Impact byBIP!
    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).
    0
    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.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
Powered by OpenAIRE graph
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!
0
Average
Average
Average
hybrid