AbstractWe implement a ϕ4‐model to analyze the localization of energy in collective modes along the sugar‐phosphate backbone of RNA strands. We focus on the relevance of soliton‐like excitations in the site‐specificity of intramolecular nucleophilic attacks leading to transesterifications in the sugar‐phosphate backbone. We provide evidence supporting the view that hot spots for transesterification of catalytic RNA are caused by a combination of two factors: nonlinear energy transfer and intra‐chain folding. In particular, our results might help understanding the physics of covalent cyclization and cycle‐reopening in the catalytic intervening sequence (IVS) of ribosomal RNA fromTetrahymenaand also they might help identifying the nucleophilic agents and cosubstrate in IVS RNA exci