Cation enrichment in the ion atmosphere is promoted by local hydration of DNA

Abstract

Electrostatic interactions are central to the structure and function of nucleic acids, including their folding, condensation, and interaction with proteins and other charged molecules. These interactions are profoundly affected by...

Spectroscopic Fingerprints of Cavity Formation and Solute Insertion as a Measure of Hydration Entropic Loss and Enthalpic Gain

“…This is consistent with a population increase in the hard‐librations and a loss in population of soft‐librations, as observed experimentally. We want to mention that a similar absorption increase in the THz spectra at frequencies >400 cm −1 has been previously reported for hydration water molecules as a result of strong interactions with ions or with polar groups of biomolecules [43–45] . In order to quantify this effect, we take the slope of the absorption increase in the 450–600 cm −1 region and we compare it for different alcohols in Figure 3C.…”

“…We want to mention that a similar absorption increase in the THz spectra at frequencies > 400 cm À 1 has been previously reported for hydration water molecules as a result of strong interactions with ions or with polar groups of biomolecules. [43][44][45] In order to quantify this effect, we take the slope of the absorption increase in 450-600 cm À 1 region and we compare it for different alcohols in Figure 3C. Remarkably, a similar slope is measured for EtOH, PrOH and BuOH, which are all primary alcohols (i.e.…”

Spectroscopic Fingerprints of Cavity Formation and Solute Insertion as a Measure of Hydration Entropic Loss and Enthalpic Gain

“…We want to mention that a similar absorption increase in the THz spectra at frequencies > 400 cm À 1 has been previously reported for hydration water molecules as a result of strong interactions with ions or with polar groups of biomolecules. [43][44][45] In order to quantify this effect, we take the slope of the absorption increase in the 450-600 cm À 1 region and we compare it for different alcohols in Figure 3C. Remarkably, a similar slope is measured for EtOH, PrOH and BuOH, which are all primary alcohols (i.e.…”

RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis

“…This work explores how RNA electrostatics are used in ribozyme active sites to recruit monovalent and divalent metal ions that promote catalysis. The study of the solvation and ion atmosphere around nucleic acids, including enzymes, has been a subject of great fundamental interest and research effort both experimentally and computationally. , Experimental approaches have been reviewed, , and include so-called “ion counting” experiments, − anomalous small-angle X-ray scattering , and wide-angle X-ray scattering , and NMR. , …”

“…The study of the solvation and ion atmosphere around nucleic acids, including enzymes, 12 been a subject of great fundamental interest and research effort both experimentally 13 and computationally. 9,14 Experimental approaches have been reviewed, 7,15 and include so-called "ion counting" experiments, 16−18 anomalous small-angle X-ray scattering 19,20 and wide-angle X-ray scattering 21,22 and NMR. 23,24 Here we consider four metal-dependent RNA-cleaving nucleic acid enzymes: the hammerhead (HHr), pistol (Psr), and Varkud satellite virus (VSr) ribozymes, and the 8−17 DNAzyme (8−17dz).…”