Simple and Analytical Model of RNA Collapse
- 25 June 2020
- journal article
- research article
- Published by American Chemical Society (ACS) in The Journal of Physical Chemistry B
- Vol. 124 (25), 5149-5155
- https://doi.org/10.1021/acs.jpcb.0c03584
Abstract
An analytical model for the free energy change during collapse of an RNA molecule from an extended to a compact conformation is proposed. It considers explicit binding of water and ion molecules to the RNA and the exchange of these molecules with the aqueous solution. Microscopic states of the system are captured on a two-dimensional square lattice and evaluated using contact energies. We compute the free energy as a function of a collapse variable and the number of ions bound to the RNA. The major driving force to the collapse of the RNA chain is the gain in water entropy once expelled from the surface of the RNA molecule illustrated by decomposing the free energy into species contributions and their energy and entropy components. The sensitivity of the conclusions of the model to variations in parameters is computed and appears to be weak.Funding Information
- Welch Foundation (F-1896)
- National Institute of General Medical Sciences (GM59796)
This publication has 18 references indexed in Scilit:
- Molecular Simulations of Ion Effects on the Thermodynamics of RNA FoldingThe Journal of Physical Chemistry B, 2018
- Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix–Junction–Helix SystemsJournal of the American Chemical Society, 2018
- RNA Structural Modules Control the Rate and Pathway of RNA Folding and AssemblyJournal of Molecular Biology, 2016
- Tuning RNA Flexibility with Helix Length and Junction SequenceBiophysical Journal, 2015
- Thermodynamic Origins of Monovalent Facilitated RNA FoldingBiochemistry, 2012
- Entropic origin of Mg 2+ -facilitated RNA foldingProceedings of the National Academy of Sciences of the United States of America, 2012
- The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and NetworksAccounts of Chemical Research, 2011
- SAXS Studies of Ion–Nucleic Acid InteractionsAnnual Review of Biophysics, 2011
- Role of counterion condensation in folding of the Tetrahymena ribozyme II. Counterion-dependence of folding kineticsJournal of Molecular Biology, 2001
- The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotidesQuarterly Reviews of Biophysics, 1978