Electrostatics Explains the Position‐Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes

Abstract

International audienceIn the RNA realm, non‐Watson Crick base pairs are abundant and affect either the RNA 3D structure and/or its function. Here we investigated the formation of RNA kissing complexes where the loop‐loop interaction is modulated by non‐Watson‐Crick pairs. Mass spectrometry, surface plasmon resonance and UV‐melting experiments show that the G • U wobble base pair favors the kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modelling, including molecular mechanics Poisson–Boltzmann surface area (MMPBSA) thermodynamics calculation and PBSA calculation of the electrostatic potential surfaces. Modeling reveals that the G • U stabilization is due to a specific electrostatic environment defined by the base pairs of the entire loop‐loop region. The loop is not symmetric, and therefore the identity and position of each base pair matters. Predicting and visualizing the electrostatic environment created by a given sequence can help designing specific kissing complexes with high affinity, for potential therapeutic, nanotechnology or analytical applications

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

“…The control sequence with mutated GUGG loop indicated only the formation of a monomeric hairpin and absence of dimeric structures. Later, Abi-Ghanem et al reported the effect of wobble base pairs on the formation of RNA kissing complexes by native ESI-MS . The results revealed that the position and the nature of G·U wobble base pairs in the loop could influence the formation of kissing complexes due to the electrostatic phenomena of the entire loop region.…”