Spontaneous Condensation of RNA into Nanoring and Globular Structures

Abstract

The effect of polyvalent cations, like spermine, on the condensation of DNA into very well-defined toroidal shapes has been well studied and understood. A great effort has been made to obtain similar condensed structures from RNA molecules, but so far, it has been elusive. In this work, we show that single-stranded RNA (ssRNA) molecules can easily be condensed into nanoring and globular structures on a mica surface, where each nanoring structure is formed mostly by a single RNA molecule. The condensation occurs in a concentration range of different cations, from monovalent to trivalent, but at a higher concentration, globular structures appear. RNA nanoring structures were observed on mica surfaces 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 in the presence of simple salts. The RNA nanoring formation can be understood by an energy competition between the hydrogen bonding forming hairpin stems—weakened by the salts—and the hairpin loops. This result 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.

RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding

“…These cutting-edge technologies enable the capture of dynamic processes in exceptional detail and provide deeper insight into the behavior of individual molecules. Numerous recent research studies have leveraged AFM to investigate the formation, structure, and heterogeneity of biological condensates within in vitro LLPS systems, by employing high-speed AFM to capture the dynamic surface movements exhibited by biological condensates. − In the specific case of RNA, AFM was able to unveil condensation leading to complex quaternary structures such as nanorings and to investigate the dynamic behavior of RNA nanoparticles …”

Cationic Glucan Dendrimer Gel-Mediated Local Delivery of Anti-OC-STAMP-siRNA for Treatment of Pathogenic Bone Resorption

“…Spermine, an endogenously available polyamine that possesses a strong positive charge, can tightly bind negatively charged nucleic acids, such as DNAs and RNAs. It is also true that spermine can condense DNA and RNA in sperm owing to its strong positive charge in the physiological condition [ 7 , 8 ]. Therefore, spermine-bearing GD gel is expected to hold its molecular cargos, i.e., siRNA, tightly.…”