Ternary complexes of vaccinia virus RNA polymerase containing 3'-OMeGMP-arrested 
transcripts were purified by native gel electrophoresis. These complexes resumed 
elongation in situ when gel slices were incubated with magnesium and NTPs. 
Elongation occurred in the absence of pyrophosphate, suggesting that the 
blocking 3'-OMeGMP residue was removed via a novel pathway. We show that 
purified elongation complexes contain an intrinsic nuclease activity that 
shortens nascent RNA from the 3'-end. RNA cleavage was absolutely dependent on a 
divalent cation and was stimulated by CTP. The initial 5' cleavage product 
remained associated with the ternary complex and could be elongated in the 
presence of NTPs. Multiple stepwise cleavages generated progressively shorter 
chains. Purified ternary complexes containing 3'-OH-terminated RNAs also 
displayed nuclease activity. Involvement of the vaccinia RNA polymerase subunit 
rpo30 in the transcript-shortening reaction is suggested based on sequence 
similarity of rpo30 to mammalian protein SII (TFIIS), an extrinsic transcription 
factor required for nascent RNA cleavage by RNA polymerase II (Reines, D. (1991) 
J. Biol. Chem. 267, 3795-3800).