Diagnostic Procedure for Detection of Viroids and Viruses with Circular RNAs by "Return"–Gel Electrophoresis

A gel electrophoretic technique for the rapid and sensitive detection of viroids and virusoids is described. Starting from plant material, a typical analysis requires less than 5 hours. Viroid concentrations as low as 800 pg/g tissue can be detected unambiguously without the use of radioactivity, organic solvents, or highly specialized laboratory equipment. The sensitivity may be further increased by introducing additional purification steps. The technique is an essential improvement of the previously published bidirectional gel electrophoretic analysis (Schumacher et al.1983, Anal. Biochem. 135, 288–295). In the new procedure gel electrophoresis is first carried out under native conditions. Before the viroid (or virusoid) bands will leave the gel, conditions are changed to provide denaturing conditions which are achieved by increasing the temperature and changing the buffer. After changing the polarity of the electric field all nucleic acids in the gel “return” in that they now migrate towards their original starting point. Under the denaturing conditions in the second electrophoresis viroids (or virusoids) unfold into the conformation of a circle without in tramolecular base pairs, which structure is unique among the nucleic acids in the gel. The denatured circular viroids migrate in the gel much slower than all other nucleic acids of comparable molecular weight and, therefore stay well separated behind the edge of the other nucleic acids. Thus, viroids can easily be detected on the stained gel as a discrete band.