Dispersion Interactions between Urea and Nucleobases Contribute to the Destabilization of RNA by Urea in Aqueous Solution

Abstract

Urea has long been used to investigate protein folding and, more recently, RNA folding. Studies have proposed that urea denatures RNA by participating in stacking interactions and hydrogen bonds with nucleic acid bases. In this study, the ability of urea to form unconventional stacking interactions with RNA bases is investigated using ab initio calculations (RI-MP2 and CCSD(T) methods with the aug-cc-pVDZ basis set). A total of 29 stable nucleobase-urea stacked complexes are identified in which the intermolecular interaction energies (up to −14 kcal/mol) are dominated by dispersion effects. Natural bond orbital (NBO) and atoms in molecules (AIM) calculations further confirm strong interactions between urea and nucleobases. Calculations on model systems with multiple urea and water molecules interacting with a guanine base lead to a hypothesis that urea molecules along with water are able to form cage-like structures capable of trapping nucleic acid bases in extrahelical states by forming both hydrogen bonded and dispersion interactions, thereby contributing to the unfolding of RNA in the presence of urea in aqueous solution.

Effect of temperature perturbation on hydrogen bonding in aqueous solutions of different urea concentrations

“…The SKSS model [31][32][33] proposed by Schellman, Kresheck, Sheraga, and Stokes suggest that urea is present in dimerized or oligomerized form in aqueous solution by selfaggregation. On the basis of such speculations, researchers illustrate that, urea denatures the protein by direct interaction with different group of protein 47 and supported by NMR 48 , calorimetry 49 , and dielectric spectroscopy 50 . Research to date suggests that both the self-aggregated form of urea and water-urea clusters are present in aqueous solution [33][34][35][36] .…”

Cation‐Induced Stabilization and Denaturation of DNA Origami Nanostructures in Urea and Guanidinium Chloride

“…The interaction of urea with nucleic acids is well studied and involves stacking interactions and hydrogen bonding of urea with the nucleobases, resulting in a reduction of the melting temperature T m . Less is known about DNA denaturation by GdmCl, which has mainly been investigated with regard to its effect on protein structure .…”

“…Due to the extraordinarily high density of negative charges in DNA origami nanostructures, it appears likely that the Gdm + cations interact with the negatively charged phosphates in the DNA backbone, thereby reducing the destabilizing electrostatic repulsion between neighboring helices. In contrast, urea is a neutral molecule that does not participate in electrostatic interactions and denatures DNA via the aromatic nucleobases . This explains the higher stability of the DNA origami nanostructures in GdmCl at low cation concentrations, whereas much higher cation concentrations are required to achieve a similar stability in urea.…”

Exploring the potential for rosacea therapeutics of siRNA dispersion in topical emulsions

“…Urea is known to interact with charged biomolecules and RNA. [59,60] The observed interphasic localization of the RNA in the emulsion suggests a surfactant effect, presumably effect of multiple interactions with the functional groups of the components in the emulsion (Figure 3). [61] Mechanisms for urea-dependent skin permeability enhancement were previously discussed [14] ; for ex- macromolecules up to a size of few nanometres.…”