Spontaneous RNA condensation into nanoring structures

Abstract

The effect of polyvalent molecular cations, such as spermine, on the condensation of DNA into very well-defined toroidal shapes have been well studied and understood. However, a great effort has been made trying to obtain similar condensed structures from either ssRNA or dsRNA, which the latter carries similar negative charge density as dsDNA, although it adopts a different helical form. But the analogous condensation of RNA molecules into well-defined structures has so far been elusive. In this work, we show that ssRNA molecules can easily be condensed into nanoring structures on a mice surface, where each nanoring structure is formed mostly by a single RNA molecule. The condensation occurs in a concentration range of different atomic cations, from monovalent to trivalent. The structures of the RNA nanorings on mica surfaces were oberved by atomic force microscopy (AFM). The samples were observed in tapping mode and were prepared by drop evaporation of a solution of RNA in the presence of one type of the different cations used. As far as we know, this is the first time that nanorings or any other well-defined condensed RNA structures have been reported. The RNA nanorings formation can be understood by an energy competition between the hydrogen bonding forming hairpin stems, weakened by the salts, and hairpin loops. This results may have an important biological relevance, since it has been proposed that RNA is the oldest genome coding molecule and the formation of these structures could have given it stability against degradation in primeval times. Even more, the nanoring structures could have the potential to be used as biosensors and functionalized nanodevices.