RNA aggregation during sulfhydryl-agarose chromatography of mercurated RNA

Isolation of newly synthesized mercurated RNA transcripts by chromatography on sulfhydryl-agarose has recently been used to reduce contamination by endogenous RNA derived from the chromatin template. We show that substantial RNA aggregation occurs during standard isolation procedures, causing significant retention of endogenous (unmercurated) RNA on sulfhydryl-agarose. We describe methods to reduce substantially this problem and discuss the implications of our findings for interpretation of previous hybridization and transcription experiments.