Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA

Dynamic and thermodynamic properties of RNA molecules vary across different cellular locations through multiple environmental factors, such as excluded volume interactions of cellular substances, alteration of the physical properties of the surrounding medium, and binding interactions with cellular substances. These environmental factors modulate the energy landscape of RNA transitions, thereby consideration of the effects of the intracellular environment on molecular interactions contributing to RNA folding and RNA-protein complexation is important for understanding RNA structures and their interactions in living cells. This chapter describes the dynamics and interactions of several RNA structures, including functional RNAs such as aptamers and ribozymes, in the environment of molecular crowding, revealed by in-cell, in silico, and in vitro studies. Specifically, in vitro model studies that have used cell-mimicking solutions comprising cellular substances or artificial molecular crowding agents have enhanced our understanding of RNA interactions and their molecular functions under molecular crowding conditions and increased our ability to predict RNA structures in cells. This chapter also provides an overview of the comparison between RNA and DNA interactions because the effects of the environmental factors on DNA are similar to those on RNA.