Abstract

Structural features of the polypurine tract primer of (+) strand DNA synthesis mediating its recognition by the RNase H domain of HIV-1RT have been examined. Such studies have indicated that template nucleobases can be removed without loss of cleavage specificity at the scissile -1/+1 phosphodiester bond, while equivalent lesions in the RNA primer were inhibitory. Subsequent studies identified individual bases of the PPT primer that are critical to its function. The use of purine analogs has also allowed us to determine the role of the exocyclic groups of the purine ring at these critical positions. Finally, using a combination of analog-substituted substrates and mutants of HIV-1 RT, nucleoside analogs have been used to understand how the single stranded template interacts with residues of the fingers subdomain prior to accessing the DNA polymerase active site of HIV-1 RT.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
Division of Basic Sciences - NCI (NCI)
Type
Intramural Research (Z01)
Project #
1Z01BC010492-04
Application #
7338609
Study Section
(RML)
Project Start
Project End
Budget Start
Budget End
Support Year
4
Fiscal Year
2006
Total Cost
Indirect Cost

  Institution

Name
Basic Sciences
Department
Type
DUNS #
City
State
Country
United States
Zip Code

  Publications

Mandal, Dibyakanti; Dash, Chandravanu; Le Grice, Stuart F J et al. (2006) Analysis of HIV-1 replication block due to substitutions at F61 residue of reverse transcriptase reveals additional defects involving the RNase H function. Nucleic Acids Res 34:2853-63
Dash, Chandravanu; Fisher, Timothy S; Prasad, Vinayaka R et al. (2006) Examining interactions of HIV-1 reverse transcriptase with single-stranded template nucleotides by nucleoside analog interference. J Biol Chem 281:27873-81
Yi-Brunozzi, Hye Young; Brabazon, Danielle M; Lener, Daniela et al. (2005) A ribose sugar conformational switch in the LTR-retrotransposon Ty3 polypurine tract-containing RNA/DNA hybrid. J Am Chem Soc 127:16344-5
Ignatov, Michael E; Berdis, Anthony J; Le Grice, Stuart F J et al. (2005) Attenuation of DNA replication by HIV-1 reverse transcriptase near the central termination sequence. Biochemistry 44:5346-56
Bibillo, Arkadiusz; Lener, Daniela; Tewari, Alok et al. (2005) Interaction of the Ty3 reverse transcriptase thumb subdomain with template-primer. J Biol Chem 280:30282-90
Bibillo, Arkadiusz; Lener, Daniela; Klarmann, George J et al. (2005) Functional roles of carboxylate residues comprising the DNA polymerase active site triad of Ty3 reverse transcriptase. Nucleic Acids Res 33:171-81
Yi-Brunozzi, Hye Young; Le Grice, Stuart F J (2005) Investigating HIV-1 polypurine tract geometry via targeted insertion of abasic lesions in the (-)-DNA template and (+)-RNA primer. J Biol Chem 280:20154-62
Rausch, Jason W; Le Grice, Stuart F J (2004) 'Binding, bending and bonding': polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus. Int J Biochem Cell Biol 36:1752-66
Dash, Chandravanu; Yi-Brunozzi, Hye-Young; Le Grice, Stuart F J (2004) Two modes of HIV-1 polypurine tract cleavage are affected by introducing locked nucleic acid analogs into the (-) DNA template. J Biol Chem 279:37095-102
Dash, Chandravanu; Rausch, Jason W; Le Grice, Stuart F J (2004) Using pyrrolo-deoxycytosine to probe RNA/DNA hybrids containing the human immunodeficiency virus type-1 3' polypurine tract. Nucleic Acids Res 32:1539-47

Showing the most recent 10 out of 12 publications