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

An improved procedure for the resolution of RNA transcripts by electrophore tic gel retardation, mediated by annealing to specific homologous oligonucl eotiedes is described. The N and NTN strains of PVY served as a model syste m. Non-polymorphic but sequence-diverse RNA transcripts were copied from PC R products of the two virus strains. The transcripts were resolved by gel e lectrophoresis, because of the differential retardation effect caused by th e binding of strain-specific homologous oligonucleotides. The two PVY strai ns were thus differentiated. Applicability of this method to virus strain d ifferentiation in general is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.