2018
DOI: 10.1063/1.5019939
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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 tetralo… Show more

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Cited by 3 publications
(2 citation statements)
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“…To address this shortcoming, coarse-grained models that include explicit-ion representations have been developed to analyze ion-mediated attraction in DNA. , Explicit-ion models with coarse-grained RNA representations have also been successful in predicting biomolecular stability, , as well as the mechanisms , and energetics of large RNA folding. At a higher level of spatial resolution, ion parameters are available for use with all-atom explicit-solvent simulations. In various applications, these have provided interpretations of ensemble experimental data and insights into the energetics of small RNA systems. While explicit-solvent techniques may be applied to larger systems, the associated computational requirements have limited the accessible time scales to microseconds . As a result, there is not an all-atom model available for which it is tractable to directly connect the properties of diffuse ions with slow (millisecond) conformational processes in large-scale RNP assemblies.…”
Section: Introductionmentioning
confidence: 99%
“…To address this shortcoming, coarse-grained models that include explicit-ion representations have been developed to analyze ion-mediated attraction in DNA. , Explicit-ion models with coarse-grained RNA representations have also been successful in predicting biomolecular stability, , as well as the mechanisms , and energetics of large RNA folding. At a higher level of spatial resolution, ion parameters are available for use with all-atom explicit-solvent simulations. In various applications, these have provided interpretations of ensemble experimental data and insights into the energetics of small RNA systems. While explicit-solvent techniques may be applied to larger systems, the associated computational requirements have limited the accessible time scales to microseconds . As a result, there is not an all-atom model available for which it is tractable to directly connect the properties of diffuse ions with slow (millisecond) conformational processes in large-scale RNP assemblies.…”
Section: Introductionmentioning
confidence: 99%
“…[53][54][55] These have been used to provided interpretations of ensemble experimental data 56 and have provided insights into the energetics of small RNA systems. [57][58][59] Explicit-solvent techniques can be applied to larger systems, though the associated computational requirements have limited the accessible timescales to microseconds. 60 Currently, there is not an all-atom model available for which it is tractable to directly connect the properties of diffuse ions with slow (millisecond) conformational processes in large-scale RNP assemblies.…”
Section: Introductionmentioning
confidence: 99%