Improved electrophoretic resolution of RNA transcripts by specific homologous oligonucleotide gel retardation

An improved procedure for the resolution of RNA transcripts by electrophoretic gel retardation, mediated by annealing to specific homologous oligonucleotiedes is described. The N and NTN strains of PVY served as a model system. Non-polymorphic but sequence-diverse RNA transcripts were copied from PCR products of the two virus strains. The transcripts were resolved by gel electrophoresis, because of the differential retardation effect caused by the binding of strain-specific homologous oligonucleotides. The two PVY strains were thus differentiated. Applicability of this method to virus strain differentiation in general is discussed.