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Examining Ty3 Polypurine Tract Structure and Function by Nucleoside Analog Interference



Chandravanu Dash, John Marino, Stuart F. Le Grice


Although retroviral and LTR-retrotransposon PPTs differ significantly in both their length and sequence, they are accurately removed from (+) RNA and (+) DNA by their cognate RTs, suggesting common structural features of these RNA/DNA hybrids contribute to the sequestration and positioning of the viral polymerase such that its RNase H catalytic center is correctly located over the scissile bond at PPT/U3 junction. For the HIV-1 PPT, X-ray crystallography, chemical footprinting and nucleoside analog interference studies make a strong case for an interaction between the thumb subdomain of RT and a destabilized ( unzipped ) portion of the duplex 12 - 15 bp upstream of this junction. This region of the PPT has been implicated in an induced fit with HIV-1 RT as a potential mechanism of correctly locating its RNase H active site. In this study, whether a similar mechanism applies to PPT recognition by LTR-retrotransposon enzymes has been investigated using scanning mutagenesis of both the DNA and RNA strands. Our results suggests that both the 5' and 3' portions of the PPT are sensitive to nucleoside analog substitution, while the intervening region can be modified without altering cleavage specificity. These two regions likely correspond to portions of the PPT which make close contact with the Ty3 RT thumb subdomain and ribonuclease H (RNase H) catalytic center, respectively, and suggest a mechanism similar to HIV-1 for the RT processing in retrotransposons.
Journal of Biological Chemistry
No. 5


Dash, C. , Marino, J. and Le Grice, S. (2006), Examining Ty3 Polypurine Tract Structure and Function by Nucleoside Analog Interference, Journal of Biological Chemistry (Accessed March 3, 2024)
Created January 31, 2006, Updated October 12, 2021