Аннотация:Stacking interactions of heterocyclic bases of ribonucleotides are one of the most important factors in the organization of RNA secondary and tertiary structure. Most of these (canonical) interactions are formed between adjacent residues in RNA polynucleotide chains. However, with the accumulation of data on the atomic tertiary structures of various RNAs and their complexes with proteins, it hasbecome clear that nucleotide residues that are not adjacent in thepolynucleotide chains and are sometimes separated in the RNA primary structure by tens or hundreds of nucleotides can interact via(non-canonical)base stacking. This paper presents an exhaustive database of such nonadjacent base-stacking elements (NA-BSEs)and their environment in the macromolecules of natural and synthetic RNAs. Analysis of these data showed that NA-BSE-forming nucleotides, on average, account for about a quarter of all nucleotides ina particular RNA and, therefore, should be considered as bona fidemotifs ofthe RNAtertiary structure. We also classifiedNA-BSEs by their location in RNA macromolecules. Itwas shown that the structure-forming role of NA-BSEsinvolvescompact folding of single-stranded RNA loops, transformation of double-stranded bulges into imperfect helices, andbinding of RNA regions distant in the primary and secondary RNA structure.
