Mercurated pyrimidine nucleotides have been used to study RNA synthesis and processing in isolated nuclei from mouse L cells. 5-mercuridine triphosphete (5-Hg-UTP) or 5-Hg-CTP are accepted as substrates by the purified RNA polymerases (I+III) and (II) from mouse cells, respectively, as well as by the enzymes still bound to the nuclear chromatin. In nuclei, RNA synthesis in the presence of Hg-UTP is reduced to 60–70%of a control. 30–60%of RNA labeled in vitro with (3H)UTP in isolated nuclei is not retained on sulfhydryl sepharose columns. Sucrose gradient analysis reveals a size distribution of the non-bound RNA similar to non-mercurated control RNA. Hg–RNA is found in a single peak from 4–10S. Chase experiments indicate that this RNA is the original transcript. It is argued that Hg-nucleotides may cause premature chain termination. Methylation of RNA in vitro by S-adenosyl methionine ((3H)SAM) is reduced to 75%of controls in the presence of Hg–UTP. Only 6%of the methyl groups appear in Hg–RNA. Polyadenylation is reduced as well. 15%of poly(A) (+)RNA are found in control assays whereas only 1%of Hg–RNA carries a poly(A) end added in vitro. These results limit the use of mercurated nucleotides for studies of nuclear RNA synthesis a