Quantum mechanical investigation of the nature of nucleobase-urea stacking interaction, a crucial driving force in RNA unfolding in aqueous urea

Abstract

Urea-assisted denaturation of protein and RNA has been shown to be a valuable tool to study their stabilities and folding phenomena. It has been shown that stacking interactions between nucleobases and urea are one of the driving forces of denaturation. In this study, the ability of urea to form unconventional stacking interactions with RNA bases is investigated by performing high-level quantum calculations (RI-MP2/aug-cc-pVDZ level) on a few thousands of model systems. Four systems were considered based on the RNA nucleobases (GUA, ADE, CYT, and URA) for the investigation. For each system, a set of models were designed to study the role of hetero-atoms/groups of the nucleobases on stacking interactions with urea moiety with respect to every possible pair. Several plane-parallel complexes were generated with urea on top of aromatic systems to exhaustively study all possible factors for urea-nucleobases stacking interactions. Energy decomposition analysis (EDA), atoms in molecules (AIM) and natural bond orbital (NBO) analysis were performed to gain better insights on non-covalent stacking interactions. Dispersion component was found to be heavily stabilizing, while the E HF was found to be repulsive for all the four systems indicating lack of hydrogen bonding (HB) type interactions and presence of dispersion type interactions. Amide and carbonyl groups of urea molecule were found to play a major role in favourable stacking interactions. We demonstrate that along with functional groups present on the nucleobases, the orientation of urea molecules plays a vital role in stabilizing the urea-nucleobase non-covalent interactions. The proposed study quantifies and provides a comprehensive theoretical description of urea nucleobase unconventional stacking interactions which helps to unravel urea driven RNA unfolding mechanism.

Energetic, Structural and Dynamic Properties of Nucleobase-Urea Interactions that Aid in Urea Assisted RNA Unfolding

“…As deciphered from spatial density maps analysis, along with conventional hydrogen bonding interactions, urea may be capable of forming NH-π and π-π interactions with nucleobases. Previous studies identified hydrogen bonding and stacking interactions as two main modes of interactions between urea and nucleobases 33,59 . We use certain geometric criteria to quantify these interactions and evaluate their respective probability distributions 37 .…”

Urea-aromatic interactions in biology

“…The quest to answer this challenging riddle has led to a number of experimental and theoretical studies to understand the unfolding mechanism. Earlier studies reported that urea induces changes in nucleic acid structures by forming favorable interactions with exposed surfaces of nucleobases compared with other regions, such as backbone, ribose, and phosphate groups (Hong et al 2004;Lambert and Draper 2012;Guinn et al 2013;Yoon et al 2013;Kasavajhala et al 2015;Miner and García 2017;Alodia et al 2018;Jaganade et al 2019).…”

“…The ability of urea to form strong π −stacking interactions with nucleobases is intriguing. A recent extensive QM calculation investigated the importance of functional groups on nucleobases and studied the effect of urea orientations of the urea-nucleobase stacking interactions (Alodia et al 2018). Noncovalent stacking interactions were found to be the driving forces, and energetically, these interactions are dominated by dispersion effects.…”

“…understand the correct description of the structure and properties of molecules (Meyer et al 2003;Schottel et al 2008;Waters 2002;Riley and Hobza 2012;Wheeler 2012;Daze and Hof 2012;Macias et al 2003;Ma and Dougherty 1997;Dougherty 2012;Tsuzuki et al 2000a, b;Müller-Dethlefs and Hobza 2000). The growing experimental as well as in silico approaches specifically studies of small aromatic model systems (Bissantz et al 2010;Meyer et al 2003;Jarvis and Ouvry 2019;Wang et al 2015a;Bootsma and Wheeler 2018;Toupkanloo and Rahmani 2018;Alodia et al 2018;Jaganade et al 2019;Goyal et al 2017;Casals-Sainz et al 2019) have been providing significant insight into the relative contribution of energetical and geometrical preference of different stacking partners, for example, π −π (Burley and Petsko 1985;Riley and Hobza 2012;Riley et al 2010;Su et al 2014;Scrutton and Raine 1996;Su and Li 2009;Jeziorski et al 1994), anion−π (Schug and Lindner 2005;Schottel et al 2008), cation−π (Dougherty 2012;Salonen et al 2009;Scrutton and Raine 1996), and XH−π (Tsuzuki et al 2000a, b). This knowledge is routinely used in structure-based drug design and molecular recognition.…”