RNA Secondary Structures in Neurodegeneration

RNA is hierarchically organized, and its 3D structure can be described at different levels. Instead of the long helices formed by two perfectly complementary strands of DNA, an RNA chain folds back on itself to form short stretches of helical regions interrupted by bulges, internal loops, hairpin loops, or multi-way junctions. While RNA plays a significant role in several biological processes, including translation, catalysis, and gene regulation, the RNA secondary structure’s prediction is crucial for the identification and formulation of the RNA functionality. The second level of RNA hierarchical structure is RNA acting as a key factor in the posttranscriptional regulation and the noncoding RNA functions. This chapter reviews the representation, visualization, and mathematical formulation mostly of RNA secondary structures, which can be viewed as steps toward the three-dimensional prediction modeling and their role in neurodegeneration.