EFFECTS OF STAINING OF RNA WITH ETHIDIUM-BROMIDE BEFORE ELECTROPHORESIS ON PERFORMANCE OF NORTHERN BLOTS

Staining of RNA with ethidium bromide (EtdBr) prior to running agarose gels has been reported to afford certain advantages over staining gel s after electrophoresis We have examined prior staining of RNA with a wide range of EtdBr concentrations, particularly with respect to its e ffects on Northern blot hybridizations using antisense RNA probes. Pri or staining with EtdBr at concentrations of 100-1000 mug/ml caused sig nificant alterations in RNA mobilities and significantly decreased hyb ridization with antisense RIVA probes compared with unstained RNA. Pri or staining with EtdBr at 10-50 mug/ml resulted in the best combinatio n of staining sensitivity, absence of alterations in RNA mobility and efficiency of hybridization. Conventional staining of gels after elect rophoresis also resulted in decreased hybridization efficiency with RN A probes compared with unstained RNA.