Researchers interested in studying RNA structure and function or RNA-protein interactions are increasingly using site-specifically modified RNAs to probe sites of interest (1 ). In addition to expanding the repertoire of functional groups beyond the very limited set available through standard mutagenesis, current synthesis techniques allow for inclusion of radioactive labels and/or various crosslinking reagents at single internal sites in RNA. The latter probes are particularly useful for determining what proteins or other RNAs interact with a site of interest on the test RNA. This chapter deals mainly with recently developed methodology for introducing such modifications into long RNAs.
