Enrichment of viroid small RNAs by hybridization selection using biotinylated RNA transcripts to analyze viroid induced RNA silencing

We have successfully applied a hybridization selection method using biotinylated-viroid transcripts and streptavidin-coupled magnetic beads, followed by re-amplification, restriction enzyme digestion and concatemerization, to clone viroid small RNAs. The cloning efficiency with the PSTVd-specific small RNAs increased more than 100-fold over that with random cloning of unselected small RNAs. The method can be used to analyze small RNA biogenesis, especially to find hotspots, in various host–pathogen interactions.