Single-molecule approach to study RNA nanoparticles

The application of RNA nanotechnology in cancer therapy has received more and more interest in recent years (Guo et al., 2010; Guo, 2010; Shu et al., 2011). RNA nanoparticles can be designed to carry drugs or siRNA for treatment of diseases. The study of the intra- and intermolecular interactions, conformations, and functions of RNA nanoparticles is of fundamental importance, as it provides insights into improving the designs, the stability, and functionalities of these nanoparticles. The development of fluorescence imaging at the single-molecule level provided a convenient way to directly visualize and study biological samples in their physiological environment one molecule at a time (Weiss, 1999; Ha, 2001; Yanagida and Ishijima, 2003; Chu, 2003). Compared to ensemble studies, single-molecule techniques have the advantages of differentiating subpopulations in heterogeneous mixtures or unsynchronized reactions, as well as localization with nanometer precision and stoichiometry determination of subunits in biological complexes. When applied to RNA, imaging at the single-molecule level has been able to reveal detailed information for each individual RNA molecules such as stoichiometry or distances in a mixture and to study the kinetics and thermodynamics during RNA folding and function (Rueda et al., 2004; Bokinsky and Zhuang, 2005; Ditzler et al., 2007; Karunatilaka and Rueda, 2009).