Characterization of RNA products associated with or aborted by a viral RNA-dependent RNA polymerase.

Ternary RNA-dependent RNA polymerase complexes were arrested at various stages of synthesis in vitro by limiting one or more NTPs. The RNAs synthesized prior to/during the arrest of the complex were characterized and the ability of the arrested complexes to continue elongation of these nascent RNAs in the presence of all four NTPs was analyzed. Nascent RNAs of 10 nt and longer remained associated with the RdRp complex and could be extended into full-length RNAs while shorter nascent RNAs were released by the complex. These results establish that previously observed RdRp-synthesized oligoribonucleotides of 8 nt or less are abortive initiation products and confirms that RdRp undergoes a transition from initiation to elongation after the synthesis of 8 nt.