Nucleic Acids Research, Vol 26, Issue 14 3433-3442, Copyright © 1998 by Oxford University Press
GP Harrison, MS Mayo, E Hunter and AM Lever
In the most extensive examination to date of the relationship between the
pausing of reverse transcrip-tase (RT) and RNA secondary structures, pause
events were found to be correlated to inverted repeats both ahead of, and
behind the catalytic site in vitro. In addition pausing events were
strongly associated with polyadenosine sequences and to a lesser degree
diadenosines and monoadenosine residues. Pausing was also inversely
proportional to the potential bond strength between the nascent 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 homopolyadenosine tracts can act as
termination signals for RT in the context of inverted repeats as they do
for certain RNA polymerases.
ARTICLES
Pausing of reverse transcriptase on retroviral RNA templates is influenced by secondary structures both 5' and 3' of the catalytic site
Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL 35294, USA.
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