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Beilhartz, G.L., Wendeler, M., Baichoo, N., Rausch, J., Le Grice, S.F.J., and Götte, M. (2009) HIV-1 reverse transcriptase can simultaneously engage its DNA/RNA substrate at both the DNA polymerase and RNase H active sites: Implications for RNase H inhibition. J. Mol. Biol., in press. Wendeler, M., and Le Grice, S.F.J. (2009) HIV-1 reverse transcriptase. In Gotte, M., Cameron, C.E., and Raney, K. (eds.), Viral Genome Replication, Springer Publications Company, New York, NY. Wilkinson,
T.A., Januszyk, K., Phillips, M.L., Tekeste, S.S., Zhang, M., Miller, J.T., Le
Grice, S.F.J., Clubb, R.T., and Chow, S.A. (2009) Identifying
and characterizing a functional HIV-1 reverse transcriptase-binding site on integrase.
J. Biol. Chem. 284: 7931-7939. Rausch,
J.W., Chelico, L., Goodman, M.F., and Le Grice, S.F.J. (2009)
Dissecting APOBEC3G substrate specificity by nucleoside analog interference.
J. Biol. Chem. 284: 7047-7058. [Abstract] [Full-text
PDF
article - 986 K] Wendeler,
M., Beilhartz, G.L., Beutler, J.A., Götte, M., and Le Grice, S.F.J.
(2009) HIV ribonuclease H: Continuing the search for small molecule antagonists.
HIV Ther. 3: 39-53. Liu,
S., Abbondanzieri, E.A., Rausch, J.W., Le Grice, S.F.J., and Zhuang, X.
(2008) Slide into action: Dynamic shuttling of HIV reverse transcriptase
on nucleic acid substrates. Science 322: 1092-1097. [Abstract] [Full-text
PDF
article - 470 K] Dash,
C., Scarth, B.J., Badorrek, C., Götte, M., and Le Grice, S.F.J.
(2008) Examining the ribonuclease H primer grip of HIV-1 reverse transcriptase
by charge neutralization of RNA/DNA hybrids. Nucleic Acids Res. 36: 6363-6371.
Ehteshami, M., Scarth, B.J., Tchesnokov, E.P., Dash, C., Le Grice, S.F.J., Hallenberger, S., Jochmans, D., and Goette, M. (2008) Mutations M184V and Y115F in HIV-1 reverse transcriptase discriminate against "nucleotide-competing reverse transcriptase inhibitors." J. Biol. Chem. 283: 29904-29911. [Abstract] [Full-text PDF article - 451 K] Wendeler,
M., Lee, H.-F., Bermingham, A., Miller, J.T., Chertov, O., Bona, M.K., Baichoo,
N.S., Ehteshami, M., Beutler, J., O'Keefe, B.R., Götte, M., Kvaratskhelia, M.,
and Le Grice, S. (2008) Vinylogous ureas as a novel class of
inhibitors of reverse transcriptase-associated ribonuclease H activity.
ACS Chem. Biol. 3: 635-644. Bokesch, H.R., Wamiru, A., Le Grice, S.F.J., Beutler, J.A., McKee, T.C., and McMahon, J.B. (2008) HIV-1 ribonuclease H inhibitory phenolic glycosides from Eugenia hyemalis. J. Nat. Prod. 71: 1634-1636. [Abstract] [Full-text PDF article - 68 K] Legiewicz, M., Badorrek, C.S., Turner, K.B., Fabris, D., Hamm, T.E., Rekosh, D., Hammarskjold, M.-L., and Le Grice, S.F.J. (2008) Resistance to RevM10 inhibition reflects a conformational switch in the HIV-1 Rev response element. Proc. Natl. Acad. Sci. USA 105: 14365-14370. [Abstract] [Full-text PDF article - 958 K] Kvaratskhelia, M., and Le Grice, S.F.J. (2008) Structural analysis of protein-RNA interactions with mass spectrometry. In Lin, R.J. (ed.), RNA-Protein Interaction Protocols, Methods in Molecular Biology, Vol. 488, Humana Press, Totowa, NJ, pp. 213-220. Abbondanzieri,
E.A., Bokinsky, G., Rausch, J.W., Zhang, J., Le Grice, S.F.J., and Zhuang,
X. (2008) Dynamic binding orientations direct activity of HIV reverse
transcriptase. Nature 453: 184-189. [Abstract] [Full-text
PDF
article] Efroni, S., Duttagupta, R., Cheng, J., Deghnani, H., Hoeppner, D.J., Dash, C., Bazett-Jones, D.P., Le Grice, S.F.J., McKay, R.D.G., Buetow, K.H., Gingeras, T.R., Misteli, T., and Meshorer, E. (2008) Global transcription in pluripotent embryonic stem cells. Cell Stem Cell 2: 437-447. [Abstract] [Full-text PDF article] [Cell Stem Cell Previews Feature] Turner,
K.B., Brinson, R.G., Yi-Brunozzi, H.Y., Rausch, J.W., Miller, J.T., Le Grice,
S.F.J., Marino, J.P., and Fabris, D. (2008) Structural probing
of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands.
Nucleic Acids Res. 36: 2799-2810. Yi-Brunozzi,
H.Y., Brinson, R.G., Brabazon, D.M., Lener, D., Le Grice, S.F.J., and Marino,
J.P. (2008) High-resolution NMR analysis of the conformations of native
and base analog substituted retroviral and LTR-retrotransposon PPT primers.
Chem. Biol. 15: 254-262. Marchand, C., Beutler, J.A., Wamiru, A., Budihas, S., Moellmann, U., Heinisch, L., Mellors, J.W., Le Grice, S.F.J., and Pommier, Y. (2008) Madurahydroxylactone derivatives as dual inhibitors of human immunodeficiency virus type 1 integrase and RNase H. Antimicrob. Agents Chemother. 52: 361-364. [Abstract] [Full-text PDF article] Takada, K., Bermingham, A., O'Keefe, B., Wamiru, A., Beutler, J.A., Le Grice, S.F.J., Lloyd, J., Gustafson, K.R., and McMahon, J.B. (2007) An HIV RNase H inhibitory 1,3,4,5-tetragalloylapiitol from the African plant Hylodendron gabunensis. J. Nat. Prod. 70: 1647-1649. [Abstract] [Full-text PDF article] Dat,
N.T., Bae, K., Wamiru, A., McMahon, J.B., Le Grice, S.F.J., Bona, M.K.,
Beutler, J.A., and Kim, Y.H. (2007) A dimeric lactone from Ardisia
japonica with inhibitory activity for HIV-1 and HIV- 2 ribonuclease H.
J. Nat. Prod. 70: 839-841. Klarmann, G.K., Eisenhauer, B.M., Zhang, Y., Gotte, M., Pata, J.D., Chatterjee, D.K., Hecht, S.M., and Le Grice, S.F.J. (2007) Investigating the "steric gate" of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase by targeted insertion of unnatural amino acids. Biochemistry 46: 2118-2126. [Abstract] [Full-text PDF article] Rausch, J.R., and Le Grice, S.F.J. (2007) Exploiting structurally diverse nucleoside analogs as probes of reverse transcription complexes. Curr. HIV Res. 5: 11-22. [Abstract] Rausch, J.W., and Le Grice, S.F.J. (2007) Purine analog substitution of the HIV-1 polypurine tract primer defines regions controlling initiation of plus-strand DNA synthesis. Nucleic Acids Res. 35: 256-268. [Abstract] [Full-text PDF article] Dash,
C., Fisher, T.S., Prasad, V.R., and Le Grice, S.F.J. (2006)
Examining interactions of HIV-1 reverse transcriptase with single-stranded template
nucleotides by nucleoside analog interference. J. Biol. Chem. 281: 27873-27881.
Mandal,
D., Dash, C., Le Grice, S.F.J., and Prasad, V.R. (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: 2853-2863. Bampi, C., Bibillo, B., Wendeler, M., Divita, G., Gorelick, R.J., Le Grice, S.F.J., and Darlix, J.-L. (2006) Nucleotide excision repair and template-independent addition by HIV-1 reverse transcriptase in the presence of nucleocapsid protein. J. Biol. Chem. 281: 11736-11743. [Abstract] [Full-text PDF article] Dash,
C., Marino, J.P., and Le Grice, S.F.J. (2006) Examining Ty3
polypurine tract structure and function by nucleoside analog interference.
J. Biol. Chem. 281: 2773-2783. El Omari, K., Ren, J., Bird, L.E., Bona, M.K., Klarmann, G., Le Grice, S.F.J., and Stammers, D.K. (2006) Molecular architecture and ligand recognition determinants for T4 RNA ligase. J. Biol. Chem. 281: 1573-1579. [Abstract] [Full-text PDF article] Yi-Brunozzi,
H.Y., Brabazon, D.M., Lener, D., Le Grice, S.F.J., and Marino, J.P.
(2005) A ribose sugar conformational switch in the LTR-retrotransposon Ty3
polypurine tract-containing RNA/DNA hybrid. J. Am. Chem. Soc. 127: 16344-16345. Bibillo,
A., Lener, D., Tewari, A., and Le Grice, S.F.J. (2005) Interaction
of the Ty3 reverse transcriptase thumb subdomain with template-primer. J.
Biol. Chem. 280: 30282-30290. Yi-Brunozzi, H.-Y., and Le Grice, S.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. [Abstract] [Full-text PDF article] Ignatov, M.E., Berdis, A.J., Le Grice, S.F.J., and Barkley, M.D. (2005) Attenuation of DNA replication by HIV-1 reverse transcriptase near the central termination sequence. Biochemistry 44: 5346-5356. [Abstract] [Full-text PDF article] Budihas, S.R., Gorshkova, I., Gaidamakov, S., Wamiru, A., Bona, M.K., Parniak, M.A., Crouch, R.J., McMahon, J.B., Beutler, J.A. and Le Grice, S.F.J. (2005) Selective inhibition of HIV-1 reverse transcriptase-associated ribonuclease H activity by hydroxylated tropolones. Nucleic Acids Res. 33: 1249-1256. [Abstract] [Full-text PDF article] Bibillo,
A., Lener, D., Klarmann, G.J., and Le Grice, S.F.J. (2005)
Functional roles of carboxylate residues comprising the DNA polymerase active
site triad of Ty3 reverse transcriptase. Nucleic Acids Res. 33: 171-181.
Williams,
K.L., Zhang, Y., Shkriabai, N., Karki, R.G., Nicklaus, M.C., Kotrikadze, N., Hess,
S., Le Grice, S.F.J., Craigie, R., Pathak, V.K., and Kvaratskhelia, M.
(2005) Mass spectrometric analysis of the HIV-1 integrase:pyridoxal-5'-phosphate
complex reveals a new binding site for a nucleotide inhibitor. J. Biol.
Chem. 280: 7949-7955. Miller, J.T., Khvorova, A., Scaringe, S.A., and Le Grice, S.F.J. (2004) Synthetic tRNALys,3 as the replication primer for the HIV-1HXB2 and HIV-1Mal genomes. Nucleic Acids Res. 32: 4687-4695. [Abstract] [Full-text PDF article] Klarmann,
G.J., Eisenhauer, B.M., Zhang, Y., Sitaraman, K., Chatterjee, D.K., Hecht, S.M.,
and Le Grice, S.F.J. (2004) Site- and subunit-specific incorporation
of unnatural amino acids into HIV-1 reverse transcriptase. Protein Expr.
Purif. 38: 37-44. Dash, C.V., Yi-Brunozzi, H.-Y., and Le Grice, S.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: 37095-37102. [Abstract] [Full-text PDF article] Rausch, J.W., and Le Grice, S.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: 1752-1766. [Abstract] [Full-text PDF article] Chan,
K.C., Budihas, S.R., Le Grice, S.F.J., Parniak, M.A., Crouch, R.J., Gaidamakov,
S.A., Isaaq, H.J., Wamiru, A., McMahon, J.B., and Beutler, J.A. (2004)
A capillary electrophoretic assay for ribonuclease H activity. Anal. Biochem.
331: 296-302. Shkriabai, N., Patil, S.S., Hess, S., Budihas, S.R., Craigie, R., Burke, T.R., Jr., Le Grice, S.F.J., and Kvaratskhelia, M. (2004) Identification of an inhibitor-binding site to HIV-1 integrase with affinity acetylation and mass spectrometry. Proc. Natl. Acad. Sci. USA 101: 6894-6899. [Abstract] [Full-text PDF article] Sitaraman,
K., Esposito, D., Klarmann, G., Le Grice, S.F.J., Hartley, J.H., and Chatterjee,
D.K. (2004) A novel cell-free protein synthesizing system. J.
Biotechnology 110: 257-263. Dash,
C.V., Rausch, J.W., and Le Grice, S.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: 1539-1547.
Le Grice, S.F.J. (2003) "In the beginning": Initiation of minus
strand DNA synthesis in retroviruses and LTR-containing retrotransposons.
Biochemistry 42: 14349-14355.
Parniak, M.A., Min, K.-L., Budihas, S.R., Le Grice, S.F.J., and Beutler,
J.A. (2003) A fluorescence-based high-throughput screening assay for
inhibitors of human immunodeficiency virus-1 reverse transcriptase-associated
ribonuclease H activity. Anal. Biochem. 322: 33-39. Rausch,
J.W., Qu, J., Yi-Brunozzi, H.Y., Kool, E.T., and Le Grice, S.F.J.
(2003) Hydrolysis of RNA/DNA hybrids containing nonpolar pyrimidine isosteres
defines regions essential for HIV type 1 polypurine tract selection. Proc.
Natl. Acad. Sci. USA 100: 11279-11284. Roda, R.H., Balakrishnan, M., Hanson, M.N., Wohrl, B.M., Le Grice, S.F.J., Roques, B.P., Gorelick, R.J., and Bambara, R.A. (2003) Role of the reverse transcriptase, nucleocapsid protein, and template structure in the two-step transfer mechanism in retroviral recombination. J. Biol. Chem. 278: 31536-31546. [Abstract] [Full-text PDF article] Lener,
D., Kvaratskhelia, M., and Le Grice, S.F.J. (2003) Nonpolar
thymine isosteres in the Ty3 polypurine tract DNA template modulate processing
and provide a model for its recognition by Ty3 reverse transcriptase. J.
Biol. Chem. 278: 26526-26532. Post, K., Guo, J., Howard, K.J., Powell, M.D., Miller, J.T., Hizi, A., Le Grice, S.F.J., and Levin, J.G. (2003) Human immunodeficiency virus type 2 reverse transcriptase activity in model systems that mimic steps in reverse transcription. J. Virol. 77: 7623-7634. [Abstract] [Full-text PDF article] Rigourd, M., Bec, G., Benas, P., Le Grice, S.F.J., Ehresmann, B., Ehresmann, C., and Marquet, R. (2003) Effects of tRNA3Lys aminoacylation on the initiation of HIV-1 reverse transcription. Biochimie 85: 521-525. [Abstract] [Full-text PDF article] Klarmann,
G.J., Hawkins, M.E., and Le Grice, S.F.J. (2002) Uncovering
the complexities of retroviral ribonuclease H reveals its potential as a therapeutic
target. AIDS Rev. 4: 183-194. Kvaratskhelia, M., Miller, J.T., Budihas, S.R., Pannel, L.K., and Le Grice, S.F.J. (2002) Identification of specific HIV-1 reverse transcriptase contacts to the viral RNA:tRNA complex by mass spectrometry and a primary amine selective reagent. Proc. Natl. Acad. Sci. USA 99: 15988-15993. [Abstract] [Full-text PDF article] Lener, D., Budihas, S., and Le Grice, S.F.J. (2002) Mutating conserved residues in the ribonuclease H domain of Ty3 reverse transcriptase affects specialized cleavage events. J. Biol. Chem. 273: 26486-26495. [Abstract] [Full-text PDF article] Moscardini,
M., Pistello, M., Bendinelli, M., Ficheux, D., Miller, J.T., Gabus, C., Le
Grice, S.F.J., Surewicz, W.K., and Darlix, J.-L. (2002) Functional
interactions of nucleocapsid protein of feline immunodeficiency virus and cellular
prion protein with the viral RNA. J. Mol. Biol. 318: 149-159. Kvaratskhelia, M., Budihas, S.R., and Le Grice, S.F.J. (2002) Pre-existing distortions in nucleic acid structure aid polypurine tract selection by HIV-1 reverse transcriptase. J. Biol. Chem. 277: 16689-16696. [Abstract] [Full-text PDF article] Rausch,
J.W., Lener, D., Miller J.T., Julias, J.G., Hughes, S.H., and Le Grice, S.F.
(2002) Altering the RNase H primer grip of human immunodeficiency virus
reverse transcriptase modifies cleavage specificity. Biochemistry 41: 4856-4865.
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