5 - Classical and Novel Chemical Tools for RNA Structure Probing

Abstract

The techniques used for sequencing and structural probing of nucleic acids, and related techniques, such as foot printing and chemical interference techniques, have their origins in organic chemistry. In particular, alkylating agents are used in an analytical fashion to deduce structural features of nucleic acids. It is the RNA structure itself that influences the extent to which parts of it—that is, nucleotides as a convenient unit—can be modified by a given chemical compound or attacked by a nuclease. If the specificity of the reagent is known, structural features of the RNA can be deduced, given the existence of an efficient detection method for the modification. The validation of RNA structural probing approaches like probing with chemical reagents and probing with nucleases are shown in this chapter. The various probes, targets, and methodology of various probes are shown in detail. Architectural features of RNAs by structural probing covers two- and three-dimensional structures. Probing of RNAs in complexes such as RNA-Protein complexes, RNA-RNA complexes, and RNA-Antibiotic complexes is also presented here.