Studies on secondary structure of single-stranded RNA from bacteriophage MS2 by electron microscopy

A method allowing the demonstration and study by electron microscopy of secondary structure of viral RNA has been developed. Single-stranded RNA from the bacteriophage MS2 has been analyzed in the electron microscope in the presence of various concentrations of MgCl2. Depending on the salt concentration, the molecules display one to three large open loops which range in size from 10 to 20% of the total RNA length, and smaller closed loops which are approximately 3-5% of the total RNA length. Within one spreading, the conformation of the molecules is variable. However, the average complexity of the molecules increases with increasing salt, and individual loops which are infrequent at low salt increase in frequency with increasing salt. By analyzing the manner in which the individual loop appeared, it was possible to show that all molecules could be described by one basic pattern of secondary structure formation.