Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop
Abstract
Monovalent salt solutions have strongly coupled interactions with biopolymers, from large polyelectrolytes to small RNA oligomers. High salt concentrations have been known to induce transitions in the structure of RNA, producing non-canonical configurations and even driving RNA to precipitate out of solution. Using all-atom molecular dynamics simulations, we model a monovalent salt species (KCL) at high concentrations (0.1–3m) and calculate the equilibrium distributions of water and ions around a small tetraloop-forming RNA oligomer in a variety of structural arrangements: folded A-RNA (canonical) and Z-RNA (non-canonical) tetraloops and unfolded configurations. From these data, we calculate the ion preferential binding coefficients and Donnan coefficients for the RNA oligomer as a function of concentration and structure. We find that cation accumulation is highest around non-canonical Z-RNA configurations at concentrations below 0.5m, while unfolded configurations accumulate the most co-ions in all concentrations. By contrast, canonical A-RNA structures consistently show the lowest accumulations for all ion species. Water distributions vary markedly with RNA configuration but show little dependency on KCL concentration. Based on Donnan coefficient calculations, the net charge of the solution at the surface of the RNA decreases linearly as a function of salt concentration and becomes net-neutral near 2.5–3m KCL for folded configurations,more »
- Authors:
-
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE Laboratory Directed Research and Development (LDRD) Program
- OSTI Identifier:
- 1440478
- Alternate Identifier(s):
- OSTI ID: 1439393
- Report Number(s):
- LA-UR-17-30875
Journal ID: ISSN 0021-9606; TRN: US1900744
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Chemical Physics
- Additional Journal Information:
- Journal Volume: 148; Journal Issue: 22; Journal ID: ISSN 0021-9606
- Publisher:
- American Institute of Physics (AIP)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 36 MATERIALS SCIENCE; Biological Science
Citation Formats
Miner, Jacob Carlson, and Garcia, Angel Enrique. Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop. United States: N. p., 2018.
Web. doi:10.1063/1.5019939.
Miner, Jacob Carlson, & Garcia, Angel Enrique. Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop. United States. https://doi.org/10.1063/1.5019939
Miner, Jacob Carlson, and Garcia, Angel Enrique. Tue .
"Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop". United States. https://doi.org/10.1063/1.5019939. https://www.osti.gov/servlets/purl/1440478.
@article{osti_1440478,
title = {Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop},
author = {Miner, Jacob Carlson and Garcia, Angel Enrique},
abstractNote = {Monovalent salt solutions have strongly coupled interactions with biopolymers, from large polyelectrolytes to small RNA oligomers. High salt concentrations have been known to induce transitions in the structure of RNA, producing non-canonical configurations and even driving RNA to precipitate out of solution. Using all-atom molecular dynamics simulations, we model a monovalent salt species (KCL) at high concentrations (0.1–3m) and calculate the equilibrium distributions of water and ions around a small tetraloop-forming RNA oligomer in a variety of structural arrangements: folded A-RNA (canonical) and Z-RNA (non-canonical) tetraloops and unfolded configurations. From these data, we calculate the ion preferential binding coefficients and Donnan coefficients for the RNA oligomer as a function of concentration and structure. We find that cation accumulation is highest around non-canonical Z-RNA configurations at concentrations below 0.5m, while unfolded configurations accumulate the most co-ions in all concentrations. By contrast, canonical A-RNA structures consistently show the lowest accumulations for all ion species. Water distributions vary markedly with RNA configuration but show little dependency on KCL concentration. Based on Donnan coefficient calculations, the net charge of the solution at the surface of the RNA decreases linearly as a function of salt concentration and becomes net-neutral near 2.5–3m KCL for folded configurations, while unfolded configurations still show a positive solution charge. Our findings show that all-atom molecular dynamics can describe the equilibrium distributions of monovalent salt in the presence of small RNA oligomers at KCL concentrations where ion correlation effects become important. Furthermore, these results provide valuable insights into the distributions of water and ions near the RNA oligomer surface as a function of structural configuration.},
doi = {10.1063/1.5019939},
journal = {Journal of Chemical Physics},
number = 22,
volume = 148,
place = {United States},
year = {Tue May 29 00:00:00 EDT 2018},
month = {Tue May 29 00:00:00 EDT 2018}
}
Web of Science
Figures / Tables:
Works referenced in this record:
The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
journal, May 1978
- Manning, Gerald S.
- Quarterly Reviews of Biophysics, Vol. 11, Issue 2
Parameters of Monovalent Ions in the AMBER-99 Forcefield: Assessment of Inaccuracies and Proposed Improvements
journal, October 2007
- Chen, Alan A.; Pappu, Rohit V.
- The Journal of Physical Chemistry B, Vol. 111, Issue 41
Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements
journal, June 2015
- Meisburger, Steve P.; Pabit, Suzette A.; Pollack, Lois
- Biophysical Journal, Vol. 108, Issue 12
Quantifying the ion atmosphere of unfolded, single-stranded nucleic acids using equilibrium dialysis and single-molecule methods
journal, April 2016
- Jacobson, David R.; Saleh, Omar A.
- Nucleic Acids Research, Vol. 44, Issue 8
Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin
journal, January 2008
- Garcia, Angel E.; Paschek, Dietmar
- Journal of the American Chemical Society, Vol. 130, Issue 3
Evaluation of the Donnan model for polyelectrolytes using the composite Poisson-Boltzmann equations
journal, July 1994
- Ohshima, H.; Miyajima, T.
- Colloid & Polymer Science, Vol. 272, Issue 7
Canonical sampling through velocity rescaling
journal, January 2007
- Bussi, Giovanni; Donadio, Davide; Parrinello, Michele
- The Journal of Chemical Physics, Vol. 126, Issue 1
All-atom polarizable force field for DNA based on the classical drude oscillator model
journal, April 2014
- Savelyev, Alexey; MacKerell, Alexander D.
- Journal of Computational Chemistry, Vol. 35, Issue 16
High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations
journal, September 2013
- Chen, A. A.; Garcia, A. E.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 42
A Network of Heterogeneous Hydrogen Bonds in GNRA Tetraloops
journal, December 1996
- Jucker, Fiona M.; Heus, Hans A.; Yip, Ping F.
- Journal of Molecular Biology, Vol. 264, Issue 5
The Ionic Atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulations
journal, February 2012
- Kirmizialtin, Serdal; Silalahi, Alexander R. J.; Elber, Ron
- Biophysical Journal, Vol. 102, Issue 4
Simulating water with rigid non-polarizable models: a general perspective
journal, January 2011
- Vega, Carlos; Abascal, Jose L. F.
- Physical Chemistry Chemical Physics, Vol. 13, Issue 44
Free-energy landscape of a hyperstable RNA tetraloop
journal, May 2016
- Miner, Jacob C.; Chen, Alan A.; García, Angel E.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 24
Cosolvent Effects on Protein Stability
journal, April 2013
- Canchi, Deepak R.; García, Angel E.
- Annual Review of Physical Chemistry, Vol. 64, Issue 1
The Donnan equilibrium: I. On the thermodynamic foundation of the Donnan equation of state
journal, April 2011
- Philipse, A.; Vrij, A.
- Journal of Physics: Condensed Matter, Vol. 23, Issue 19
Specific Ion Effects at the Air/Water Interface
journal, April 2006
- Jungwirth, Pavel; Tobias, Douglas J.
- Chemical Reviews, Vol. 106, Issue 4
Molecular Simulation Studies of Monovalent Counterion-Mediated Interactions in a Model RNA Kissing Loop
journal, July 2009
- Chen, Alan A.; Draper, David E.; Pappu, Rohit V.
- Journal of Molecular Biology, Vol. 390, Issue 4
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
journal, February 2008
- Hess, Berk; Kutzner, Carsten; van der Spoel, David
- Journal of Chemical Theory and Computation, Vol. 4, Issue 3
Ion Counting from Explicit-Solvent Simulations and 3D-RISM
journal, February 2014
- Giambaşu, George M.; Luchko, Tyler; Herschlag, Daniel
- Biophysical Journal, Vol. 106, Issue 4
Molecular dynamics with coupling to an external bath
journal, October 1984
- Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.
- The Journal of Chemical Physics, Vol. 81, Issue 8
SAXS studies of RNA: structures, dynamics, and interactions with partners: SAXS studies of RNA
journal, April 2016
- Chen, Yujie; Pollack, Lois
- Wiley Interdisciplinary Reviews: RNA, Vol. 7, Issue 4
How RNA folds
journal, October 1999
- Tinoco, Ignacio; Bustamante, Carlos
- Journal of Molecular Biology, Vol. 293, Issue 2
Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components
journal, July 2002
- Timasheff, S. N.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 15
Interpretation of preferential interaction coefficients of nonelectrolytes and of electrolyte ions in terms of a two-domain model
journal, March 1995
- Record, M. T.; Anderson, C. F.
- Biophysical Journal, Vol. 68, Issue 3
Understanding Nucleic Acid–Ion Interactions
journal, June 2014
- Lipfert, Jan; Doniach, Sebastian; Das, Rhiju
- Annual Review of Biochemistry, Vol. 83, Issue 1
Equilibrium Denaturation and Preferential Interactions of an RNA Tetraloop with Urea
journal, January 2017
- Miner, Jacob C.; García, Angel E.
- The Journal of Physical Chemistry B, Vol. 121, Issue 15
Salt dependence of oligoion-polyion binding: a thermodynamic description based on preferential interaction coefficients
journal, July 1993
- Anderson, Charles F.; Record, M. Thomas
- The Journal of Physical Chemistry, Vol. 97, Issue 27
Comparison of simple potential functions for simulating liquid water
journal, July 1983
- Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
- The Journal of Chemical Physics, Vol. 79, Issue 2
Experimental and computational studies of the G[UUCG]C RNA tetraloop11Edited by I. Tinoco
journal, April 2000
- Williams, D. Jeremy; Hall, Kathleen B.
- Journal of Molecular Biology, Vol. 297, Issue 5
A-Z-RNA conformational changes effected by high pressure
journal, January 1994
- Krzyżaniak, Andrzej; Barciszewski, Jan; Fürste, Jens Peter
- International Journal of Biological Macromolecules, Vol. 16, Issue 3
Precipitation of RNA impurities with high salt in a plasmid DNA purification process: Use of experimental design to determine reaction conditions
journal, June 2003
- Eon-Duval, Alex; Gumbs, Karlene; Ellett, Christopher
- Biotechnology and Bioengineering, Vol. 83, Issue 5
Interactions of polyelectrolytes with simple electrolytes. II. Donnan equilibria obtained with DNA in solutions of 1-1 electrolytes
journal, July 1967
- Strauss, Ulrich P.; Helfgott, C.; Pink, H.
- The Journal of Physical Chemistry, Vol. 71, Issue 8
Extracting water and ion distributions from solution x-ray scattering experiments
journal, June 2016
- Nguyen, Hung T.; Pabit, Suzette A.; Pollack, Lois
- The Journal of Chemical Physics, Vol. 144, Issue 21
Counterion binding in polyelectrolyte theory
journal, December 1979
- Manning, Gerald S.
- Accounts of Chemical Research, Vol. 12, Issue 12
Competitive interaction of monovalent cations with DNA from 3D-RISM
journal, August 2015
- Giambaşu, George M.; Gebala, Magdalena K.; Panteva, Maria T.
- Nucleic Acids Research, Vol. 43, Issue 17
The Hofmeister series: salt and solvent effects on interfacial phenomena
journal, August 1997
- Cacace, M. G.; Landau, E. M.; Ramsden, J. J.
- Quarterly Reviews of Biophysics, Vol. 30, Issue 3
Preferential Interaction Coefficient for Nucleic Acids and Other Cylindrical Polyions
journal, February 2007
- Trizac, Emmanuel; Téllez, Gabriel
- Macromolecules, Vol. 40, Issue 4
Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity
journal, May 1978
- Record, M. Thomas; Anderson, Charles F.; Lohman, Timothy M.
- Quarterly Reviews of Biophysics, Vol. 11, Issue 2
Salt- and solvent-dependent conformational transitions of ribo-CGCGCG duplex
journal, August 1985
- Adamiak, Ryszard W.; Gałat, Andrzej; Skalski, Bohdan
- Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, Vol. 825, Issue 4
Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions
journal, January 2014
- Strulson, C. A.; Boyer, J. A.; Whitman, E. E.
- RNA, Vol. 20, Issue 3
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
journal, October 2002
- Winkler, Wade; Nahvi, Ali; Breaker, Ronald R.
- Nature, Vol. 419, Issue 6910
Counting the ions surrounding nucleic acids
journal, December 2016
- Jacobson, David R.; Saleh, Omar A.
- Nucleic Acids Research
Preferential interaction coefficient for nucleic acids and other cylindrical poly-ions
text, January 2007
- Trizac, E.; Tellez, G.
- arXiv