PAUSING OF REVERSE-TRANSCRIPTASE ON RETROVIRAL RNA TEMPLATES IS INFLUENCED BY SECONDARY STRUCTURES BOTH 5' AND 3' OF THE CATALYTIC SITE

In the most extensive examination to date of the relationship between the pausing of reverse transcriptase (RT) and RNA secondary structures , pause events were found to be correlated to inverted repeats both ah ead of, and behind the catalytic site in vitro, In addition pausing ev ents were strongly associated with polyadenosine sequences and to a le sser degree diadenosines and monoadenosine residues. Pausing was also inversely proportional to the potential bond strength between the nasc ent strand and the template at the point of termination, for both mono and dinucleotides. A run of five adenosine and four uridine residues caused most pausing on the HIV-1 template, a region which is the site of much sequence heterogeneity in HIV-1, We propose that homopolyadeno sine tracts can act as termination signals for RT in the context of in verted repeats as they do for certain RNA polymerases.