On the Nature of Nucleobase Stacking in RNA: A Comprehensive Survey of Its Structural Variability and a Systematic Classification of Associated Interactions

The astonishing diversity in folding patterns of RNA three-dimensional (3D) structures is crafted by myriads noncovalent contacts, which base pairing and stacking are the most prominent. A systematic comprehensive classification annotation these interactions necessary for a molecular-level understanding their roles. However, unlike case pairing, where widely accepted nomenclature scheme exists public domain, currently available schemes base–base need major enhancements to comprehensively capture features underlying rich RNA. Here, we extend previous based on nucleobase interacting faces introducing structurally intuitive geometry-cum topology-based scheme. Specifically, stack first classified terms geometry described relative orientation glycosidic bonds, generates eight basic geometric families heterodimeric stacks six those homodimeric stacks. Further identity bases region involvement purines (five-membered, six-membered, or both rings) leads enumeration 384 distinct Based our scheme, present an algorithm automated identification crystal analyze context selected structures. Overall, work here expected greatly facilitate structure-based research.