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A more recent version of this article appeared on May 3, 2002
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M109914200v1
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Papers In Press, published online ahead of print March 1, 2002
J. Biol. Chem, 10.1074/jbc.M109914200
Submitted on October 12, 2001
Revised on February 28, 2002
Accepted on February 28, 2002

Pre-existing distortions in nucleic acid structure aid polypurine tract selection by HIV-1 reverse transcriptase

Mamuka Kvaratskhelia, Scott R. Budihas, and Stuart F.J. Le Grice

HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702

Corresponding Author: mamukak{at}ncifcrf.gov

Precise cleavage at the PPT/U3 junction by HIV-1 reverse transcriptase RNaseH is critical for generating a correct viral DNA end for subsequent integration. Using potassium permanganate (KMnO4) modification, we have identified a significant distortion in the nucleic acid structure at the HIV-1 PPT/U3 junction in the absence of trans-acting factors. Unusually high reactivity of template thymine +1 is detected when the PPT primer is extended by DNA or RNA at its' 3' terminus. Chemical footprinting suggests that the extent of base unstacking in the wild type species is comparable when the +1 A:T base pair is replaced by a C:T mismatch. However, reactivity of this template base is diminished following alterations to upstream (rA)4:(dT)4 or (rG)6:(dC)6 tracts. Importantly, there is a correlation between the structural deformation at base pair +1 and precise cleavage at the PPT/U3 junction by HIV-1 reverse transcriptase/RNaseH. KMnO4 modification also revealed unusually high reactivity for one of two (dT)4:(rA)4 duplexes upstream of the PPT/U3 junction, suggesting a significant structural distortion within the PPT itself in the absence of the retroviral polymerase. Structural abnormalities in this region are not only essential for resistance of the PPT to hydrolysis but also significantly impact the conformation of the PPT/U3 junction. Our data collectively suggest the entire PPT sequence contributes to the structural distortion at the PPT/U3 junction, potentially providing a mechanism for its selective processing.


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