Recent Publications

Stephen H. Hughes

Leferovich, J.M., D.P. Lana, P. Sutrave, S.H. Hughes, and A.M. Kelly.  1995.  Regulation of c-ski transgene expression in developing and mature mice.  J. Neurol. Sci. 15:596-603.

Natsoulis, G., P. Seshaiah, M.F. Federspiel, A. Rein, S.H. Hughes, and J.D. Boeke.  1995.  Targeting of a nuclease to murine leukemia virus capsids inhibits viral multiplication.  Proc. Natl. Acad. Sci. USA 92:364-368.

Givol, I., P.L. Boyer, and S.H. Hughes.  1995.  Isolation and characterization of the chicken c-sno gene.  Gene 156:271-276.

Ghosh, M., K.J. Howard, C.E. Cameron, S.J. Benkovic, S.H. Hughes, and S.F.J. Le Grice.  1995.  Truncating  -helix E' of p66 human immunodeficiency virus reverse transcriptase modulates RNase H function and impairs DNA strand transfer.  J. Biol. Chem. 270:7068-7076, 1995.

Patel, P.H., A. Jacobo-Molina, J. Ding, C. Tantillo, A.D. Clark, Jr., R. Raag, R.G. Nanni, S.H. Hughes and E. Arnold.  1995.  Insights into DNA polymerization mechanisms from structure and function analysis of HIV-1 reverse transcriptase.  Biochemistry 34:5351-5363.

Ding, J., K. Das, C. Tantillo, W. Zhang, A.D. Clark, Jr., S. Jessen, X. Lu, Y. Hsiou, A. Jacobo-Molina, K. Andries, R. Pauwels, H. Moereels, L. Koymans, P.A.J. Janssen, R.H. Smith, Jr., M.K. Koepke, C.J. Michejda, S.H. Hughes, and E. Arnold.  1995.  Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor  -APA R 95845 at 2.8 Å resolution.  Structure 3:365-379.

Buckheit, Jr., R.W., V. Fliakas-Boltz, S. Yeagy-Bargo, O. Weislow, D. L. Mayers, P.L. Boyer, S.H. Hughes, B.-C. Pan, S.-H. Chu, and J.P. Bader.  1995.  Resistance to 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine derivatives is generated by mutations at multiple sites in the HIV-1 reverse transcriptase.  Virology 210:186-193.

Boyer, P.L., and S.H. Hughes.  1995.  Analysis of mutations at position 184 in reverse transcriptase of human immunodeficiency virus type 1.  Antimicrob. Agents Chemother. 39:1624-1628.

Pauly, G.T., S.H. Hughes, and R.C. Moschel.  1995.  Mutagenesis in Escherichia coli by three O⁶-substituted guanines in double-stranded or gapped plasmids.  Biochemistry 34:8924-8930.

Whitcomb, J.M., B.A. Ortiz-Conde, and S.H. Hughes.  1995.  Replication of avian leukosis viruses with mutations at the primer binding site:  Use of alternative tRNAs as primers.  J. Virol. 69:6228-6238.

Rulong, S., R. Zhou, I. Tsarfaty, S. Hughes, G. Vande Woude, and P. Pinto da Silva.  1995.  Immunogold labeling of oncogenic and tumor related proteins.  Microscopy Res. Tech. 31:159-173.

Ding, J., K. Das, H. Moereels, L. Koymans, K. Andries, P.A.J. Janssen, S.H. Hughes and E. Arnold.  1995.  Structure of HIV-1 RT/TIBO R 86183 complex reveals similarity in the binding of diverse nonnucleoside inhibitors.  Nature Structural Biology 2:407-415.

Kroeger Smith, M.B., C.A. Rouzer, L.A. Taneyhill, N.A. Smith, S.H. Hughes, P.L. Boyer, P.A.J. Janssen, H. Moereels, L. Koymans, E. Arnold, J. Ding. K. Das, W. Zhang, C.J. Michejda, and R.H. Smith, Jr.  1995.  Molecular modeling studies of HIV-1 reverse transcriptase nonnucleoside inhibitors:  Total energy of complexation as a predictor of drug placement and activity.  Protein Science 4:2203-2222.

Givol, I., D. Givol, S. Rulong, J. Resau, I. Tsarfaty and S.H. Hughes.  1995.  Overexpression of human p21^waf1/cip1 arrests the growth of chicken embryo fibroblasts transformed by individual oncogenes.  Oncogene 11:2609-2618.

Nasioulas, G., S.H. Hughes, B.K. Felber, and J.W. Whitcomb.  1995.  Production of avian leukosis virus particles in mammalian cells can be mediated by the interaction of HIV-1 Rev and the Rev responsive element.  Proc. Natl. Acad. Sci. USA 92:11940-11944.

Engert, J.C., S. Servaes, P. Sutrave, S.H. Hughes, and N. Rosenthal.  1995.  Activation of a muscle-specific enhancer by the Ski proto-oncogene.  Nucl. Acids Res. 23:2988-2994.

Hsiou, Y., K. Das, J. Ding, C. Tantillo, P.L. Boyer, S.H. Hughes, and E. Arnold.  1995.  The role of nucleic acid in the resistance of HIV-1 reverse transcriptase to nucleoside and nonnucleoside inhibitors.  Méd. Biol. Environ. 23:209-215.

Lana, D.P., J.M. Leferovich, A.M. Kelly, and S.H. Hughes.  1996.  Selective expression of a ski transgene affects fast muscles and skeletal structure.  Devel. Dynamics 205:13-23.

Flavin, M.T., J.D. Rizzo, A. Khilevich, A. Kucherenko, A.K. Sheinkman, V. Vilaychak, L. Lin, W. Chen, E.M. Greenwood, T. Pengsupart, J.M. Pezzuto, S.H. Hughes, T.M. Flavin, M. Cibulski, W.A. Boulanger, R.L. Shone, and Z.-Q. Xu.  1996.  Synthesis, chromatographic resolution and anti-HIV activity of (±)-Calanolide A and its enantiomers.  J. Med. Chem. 39:1303-1313.       

Barsov, E.V., and S.H. Hughes.  1996.  Gene transfer into mammalian cells by a Rous sarcoma virus-based retroviral vector with the host range of the amphotropic murine leukemia virus.  J. Virol. 70:3922-3929.

Hughes, S.H., Z. Hostomsky, S.F.J. Le Grice, K. Lentz, and E. Arnold.  1996.  What is the

orientation of DNA polymerases on their templates?  J. Virol. 70:2679-2683.

Barsov, E.V., W.E. Huber, J. Marcotrigiano, P.K. Clark, A.D. Clark, E. Arnold, and S.H. Hughes.  1996.  Inhibition of human immunodeficiency virus type 1 integrase by the Fab fragment of a specific monoclonal antibody suggests that different multimerization states are required for different enzymatic functions.  J. Virol. 70:4484-4494.

Federspiel, M.J., D.A. Swing, B. Eagleson, S.W. Reid, and S.H. Hughes.  1996.  Expression of transduced genes in mice generated by infecting blastocysts with avian leukosis virus-based retroviral vectors.  Proc. Natl. Acad. Sci. 93:4931-4936.

Petropoulos, C.J., I. Givol, and S.H. Hughes.  1996.  Comparative analysis of the structure and function of the chicken c-myc and v-myc genes:  v-myc is a more potent inducer of cell proliferation and apoptosis than c-myc.  Oncogene 12:2611-2621.

Arnold, E., K. Das, J. Ding, P.N.S. Yadav, Y. Hsiou, P.L. Boyer, and S.H. Hughes.  1996.  Targeting HIV reverse transcriptase for anti-AIDS drug design:  Structural and biological considerations for chemotherapeutic strategies.  Drug Design and Discovery 13:29-47.

Boyer, P.L., and S.H. Hughes.  1996.  Nucleoside-analogue resistance involves the p66 subunit of HIV-1 RT.  Nature Struc. Biol. 3:579-580.

McGrew, M.J., N. Bogdanova, K. Hasegawa, S.H. Hughes, R.N. Kitsis, and N. Rosenthal.  1996.  Distinct gene expression patterns in skeletal and cardiac muscle are dependent on common regulatory sequences in the MLC1/3 locus.  Mol. Cell. Biol. 16:4524-4534.

Hsiou, Y., J. Ding, K. Das, A.D. Clark, Jr., S.H. Hughes, and E. Arnold.  1996.  Structure of unliganded human immunodeficiency virus type 1 reverse transcriptase at 2.7 Å resolution:  implications of conformational changes for polymerization and inhibition mechanisms.  Structure 4:853-860.

Pengsuparp, T., M. Serit, S.H. Hughes, D.D. Soejarto, and J.M. Pezzuto.  1996.  Specific inhibition of human immunodeficiency virus type 1 reverse transcriptase mediated by soulattrolide, a coumarin isolated from the latex of Calophyllum teysmannii.  J. Nat. Prod. 59:839-842.   

Das, K., J. Ding, Y. Hsiou, A.D. Clark, Jr., H. Moereels, L. Koymans, K. Andries, R. Pauwels, P.A.J. Janssen, P.L. Boyer, P. Clark, R.H. Smith, Jr., M.B. Kroeger Smith, C.J. Michejda, S.H. Hughes, and E. Arnold.  1996.  Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant.  J. Mol. Biol. 264:1085-1100.

VanBrocklin, M., A.L. Ferris, S.H. Hughes, and M.J. Federspiel.  1997.  Expression of a murine leukemia virus gag-Escherichia coli RNase HI fusion polyprotein significantly inhibits virus spread.  J. Virol. 71:3312-3318.

Perach, M., T. Rubinek, S.H. Hughes, and A. Hizi.  1997.  Analysis of HIV-2 RT mutants provides evidence that resistance of HIV-1 RT and HIV-2 RT to nucleoside analogs involves a repositioning of the template-primer.  J. Mol. Biol. 268:648-654.

Loya, S., H.-Q. Gao, O. Avidan, P.L. Boyer, S.H. Hughes, and A. Hizi.  1997.  Subunit-specific mutagenesis of cysteine 280 residue of the reverse transcriptase of human immunodeficiency virus type 1:  Effects on sensitivity to a specific inhibitor of ribonuclease H activity.  J. Virol. 71:5668-5672.

Lauermann, V., S.H. Hughes, and K.W.C. Peden.  1997.  Maintenance of an unusual polypurine tract in HIV-2:  Stability to passage in culture.  Virology 236:208-212.

Fu, W., B.A. Ortiz-Conde, R.J. Gorelick, S.H. Hughes, and A. Rein.  1997.  Placement of tRNA primer on the primer-binding site requires pol gene expression in avian, but not murine retroviruses.  J. Virol. 71:6940-6946.

Ding, J., S.H. Hughes, and E. Arnold.  1997.  Protein-nucleic acid interactions and DNA conformation in a complex of human immunodeficiency virus type 1 reverse transcriptase with a double-stranded DNA template primer.  Nucl. Acid Sci. 44:125-138.

Roth, T., M.L. Morningstar, P.L. Boyer, S.H. Hughes, R.W. Buckheit, Jr., and C.J. Michejda.

1997.  Synthesis and biological activity of novel nonnucleoside inhibitors of HIV-1 reverse transcriptase.  2-Aryl-substituted benzimidazoles.  J. Med. Chem. 40:4199-4207.

Lin, Y.-M., H. Anderson, M.T. Flavin, Y.-H. S. Pai, E. Mata-Greenwood, T. Pengsuparp, J.M. Pezzutto, R.F. Schinazi, S.H. Hughes, and F.-C. Chen.  1997.  In vitro anti-HIV activity of biflavonoids isolated from Rhus succedanea and Garcinia multiflora.  J. Natl. Prod. 60:884-888.

Kroeger Smith, M.B., C.J. Michejda, S.H. Hughes, P.L. Boyer, P.A.J. Janssen, K. Andries,

R.W. Buckheit, Jr., and R.H. Smith, Jr.  1997.  Molecular modeling of HIV-1 reverse transcriptase drug-resistant mutant strains:  implications for the mechanism of polymerase action.  Protein Eng. 10:1379-1383.

Boyer, P.L., H.-Q. Gao, and S.H. Hughes.  1998.  A mutation at position 190 of human immunodeficiency virus type 1 reverse transcriptase interacts with mutations at positions 74 and 75 via the template-primer.  Antimicrob. Agents Chemother. 42:447-452.

Gao, H.-Q., P.L. Boyer, E. Arnold, and S.H. Hughes.  1998.  Effects of mutations in the polymerase domain on the polymerase, RNase H and strand transfer activities of human immunodeficiency virus type 1 reverse transcriptase.  J. Mol. Biol. 277:559-572.

Pauly, G.T., S.H. Hughes, and R.C. Moschel.  1998.  Comparison of mutagenesis by O⁶-methyl- and O⁶-ethylguanine and O⁴-methylthymine in Escherichia coli using double-stranded and gapped plasmids.  Carcinogenesis 19:457-461.

Givol, I., D. Givol, and S.H. Hughes.  1998.  Overexpression of p21^waf1/cip1 arrests the growth of chicken embryo fibroblasts that overexpress E2F1.  Oncogene 16:3115-3122.

Smith, Jr., R.H., C.J. Michejda, S.H. Hughes, E. Arnold, P.A.J. Janssen, and M.B. Kroeger Smith.  1998.  Structure and mechanism of action of nonnucleoside inhibitors of HIV-1 reverse transcriptase:  strategies to combat drug resistance.  Theochem. 423:67-77.

Schaefer-Klein, J., I. Givol, E.V. Barsov, J.M. Whitcomb, M. VanBrocklin, D.N. Foster, M.J. Federspiel, and S.H. Hughes.  1998.  The EV-O derived cell line DF-1 supports the efficient replication of avian leukosis-sarcoma viruses and vectors.  Virology 248:305-311.

Nissley, D.V., P.L. Boyer, D.J. Garfinkel, S.H. Hughes, and J.N. Strathern.  1998.  Hybrid Ty/HIV-1 elements used to detect inhibitors and monitor the activity of HIV-1 reverse transcriptase.  Proc. Natl. Acad. Sci. U.S.A. 95:13905-13910.

Hsiou, Y., K. Das, J. Ding, A.D. Clark, Jr., J.-P. Kleim, M. Rösner, I. Winkler, G. Riess, S.H. Hughes, and E. Arnold.  1998.  Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097:  Inhibitor flexibility is a useful design feature for reducing drug resistance.  J. Mol. Biol. 284:313-323.

Ding, J., K. Das, Y. Hsiou, S.G. Sarafianos, A.D. Clark, Jr., A. Jacobo-Molina, C. Tantillo, S.H. Hughes, and E. Arnold.  1998.  Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8   resolution.  J. Mol. Biol. 284:1095‑1111.

Boyer, P.L., J. Lisziewicz, F. Lori, and S.H. Hughes. 1999.  Analysis of amino insertion mutations in the fingers subdomain of HIV-1 reverse transcriptase.  J. Mol. Biol. 286:995-1008.

Zheng, X.H., and S.H. Hughes.  1999.  An avian sarcoma/leukosis virus-based gene trap vector for mammalian cells.  J. Virol. 73:6946-6952.

Ortiz-Conde, B.A., and S.H. Hughes.  1999.  Studies of the genomic RNA of leukosis viruses:  Implications for RNA dimerization.  J. Virol. 73:7165-7174.

Ceccarelli, E., M. J. McGrew., T. Nguyen, U. Grieshammer, D. Horgan, S. H. Hughes, and N. Rosenthal.  1999. An E box comprises a positional sensor for regional differences in skeletal muscle gene expression and methylation.  Dev. Biol. 213:217-229.

Sarafianos, S.G., K. Das, A.D. Clark, Jr., J. Ding, P.L. Boyer, S.H. Hughes, and E. Arnold.  1999.  3TC (Lamivudine) resistance in HIV-1 reverse transcriptase involves steric hindrance with  -branched amino acids.  Proc. Natl. Acad. Sci. U.S.A. 96:10027-10032.

Holmen, S.L., D.W. Salter, W.S. Payne, J.B. Dodgson, S.H. Hughes, and M.J. Federspiel.  1999.  Soluble forms of the subgroup A avian leukosis virus [ALV(A)] receptor Tva significantly inhibit ALV(A) infection in vitro and in vivo.  J. Virol. 73:10051-10060.

Gao, H.-Q., S.G. Sarafianos, E. Arnold, and S.H. Hughes.  1999.  Similarities and differences in the RNase H activities of human immunodeficiency virus type 1 reverse transcriptase and Moloney murine leukemia virus reverse transcriptase.  J. Mol. Biol. 294:1097-1113.

Sutrave, P., J.M. Leferovich, A.M. Kelly, and S.H. Hughes.  2000.  The induction of skeletal muscle hypertrophy by a ski transgene is promoter-dependent.  Gene 241:107-116. 

Boyer, P.L., S.G. Sarafianos, E. Arnold, and S.H. Hughes.  2000.  Analysis of mutations at positions 115 and 116 in the dNTP binding site of HIV-1 reverse transcriptase.  Proc. Natl. Acad. Sci. USA 97:3056-3061.

Gao, H.-Q., P.L. Boyer, S.G. Sarafianos, E. Arnold and S.H. Hughes.  2000.  The role of steric hindrance in 3TC resistance of human immunodeficiency virus type-1 reverse transcriptase. 

J. Mol. Biol. 300:403-418, 2000.

Boyer, P.L. and S.H. Hughes.  2000.  Effects of amino acid substitutions at position 115 on the fidelity of human immunodeficiency virus type-1 reverse transcriptase.  J. Virol. 74:6494-6500.

Pinto, V.B., S. Prasad, J. Yewdell, J. Bennink and S.H. Hughes.  2000.  Restricting expression prolongs the expression of foreign genes introduced into animals by retroviruses.  J. Virol. 74:10202-10206.

Driscoll, M.D. and S.H. Hughes.  2000.  Human immunodeficiency virus type 1 nucleocapsid protein can prevent self-priming of minus strand strong stop DNA by promoting the annealing of short oligonucleotides to hairpin sequences.  J. Virol. 74:8785-8792.

Driscoll, M.D., M.-P. Golinelli, and S.H. Hughes.  2001.  In vitro analysis of human immunodeficiency virus type 1 minus-strand strong-stop DNA synthesis and genomic RNA processing.  J. Virol. 75:672-686.

Sarafianos, S.G., K. Das, C. Tantillo, A.D. Clark, Jr., J. Ding, J.M. Whitcomb, P.L. Boyer, S.H. Hughes, and E. Arnold.  2001.  Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.  EMBO J. 20:1449-1461.

Boyer, P.L., H.-Q. Gao, P. Frank, P.K. Clark, and S.H. Hughes.  2001.  The basic loop of the RNase H domain of MLV RT is important both for RNase H and polymerase activity.  Virology 282:206-213.

Boyer, P.L., S.G. Sarafianos, E. Arnold, and S.H. Hughes.  2001.  Selective excision of AZT by drug-resistant human immunodeficiency virus reverse transcriptase.  J. Virol. 75:4832-4842.

Barsov, E.V., W.S. Payne, and S.H. Hughes.  2001.  Adaptation of chimeric retroviruses in vitro and in vivo:  Isolation of avian retroviral vectors with extended host range.  J. Virol. 75:4973-4983.

Hsiou, Y., J. Ding, K. Das, A.D. Clark, Jr., P.L. Boyer, P. Lewi, P.A.J. Janssen, J.P. Kleim, M. Rösner, S.H. Hughes, and E. Arnold.  2001.  The Lys103Asn mutation of HIV-1 RT:  A novel mechanism of drug resistance.  J. Mol. Biol. 309:437-445.

Boyer, P.L., H.-Q. Gao, P.K. Clark, S.G. Sarafianos, E. Arnold and S.H. Hughes.  2001.  The YADD mutants of human immunodeficiency virus type 1 and Moloney Murine Leukemia Virus reverse transcriptase are resistant to 3TCTP in vitro.  J. Virol. 75:6321-6328.

Julias, J.G., A. L. Ferris, P. L. Boyer, and S.H. Hughes.  2001.  Replication of phenotypically mixed HIV-1 virions containing catalytically active and catalytically inactive reverse transcriptase.  J. Virol. 75:6537-6546.

Golinelli, M.-P. and S.H. Hughes.  2001.  Self-priming of retroviral minus-strand strong-stop DNAs.  Virology 285:278-290.

Peletskaya, E.N., P.L. Boyer, A.A. Kogon, P. Clark, H. Kroth, J.M. Sayer, D.M. Jerina, and S.H. Hughes.  2001.  Crosslinking of the fingers subdomain of HIV-1 RT to template-primer.  J. Virol. 75:9435-9445.

Sevilya, Z., S. Loya, S.H. Hughes, and A. Hizi.  2001.  The ribonuclease H activity of the reverse transcriptases of human immunodeficiency viruses type 1 and type 2 is affected by the thumb subdomain of the small protein subunits.  J. Mol. Biol. 311:957-971.

Gao, H.-Q., S.G. Sarafianos, E. Arnold, and S.H. Hughes.  2001.  RNase H cleavage of the 5' end of the HIV-1 genome.  J. Virol.75:11874-11880.

Oh, J., J.G. Julias, A.L. Ferris, and S.H. Hughes.  2002.  Construction and characterization of a replication competent retroviral shuttle vector plasmid.  J. Virol. 76:1762-1768.

Boyer, P.L., S.G. Sarafianos, E. Arnold, and S.H. Hughes.  2002.  The M184V mutation reduces the selective excision of zidovudine 5'-monophosphate (AZTMP) by the reverse transcriptase of human immunodeficiency virus type 1.  J. Virol. 76:3248-3256.

Golinelli, M.-P. and S.H. Hughes.  2002.  Nontemplated base addition by HIV-1 RT can induce nonspecific strand transfer in vitro.  Virology 294:122-134.

Tam, W., S.H. Hughes, W.S. Hayward, and P. Besmer.  2002.  Avian bic, a gene isolated from a common retroviral site in avian leukosis virus-induced lymphomas that encodes a noncoding RNA, cooperates with c-myc in lymphomagenesis and erythroleukemogenesis.  J. Virol. 76:4275-4286.

Rausch, J.W.,  D. Lener, J.T. Miller, J.G. Julias, S.H. Hughes, and S.F.J. Le Grice.  2002.  Altering the RNase H primer grip of human immunodeficiency virus reverse transcriptase modifies cleavage specificity.  Biochemistry 41:4856-4865.

Golinelli, M.-P. and S.H. Hughes.  2002.  Nontemplated nucleotide addition by HIV-1 reverse transcriptase.  Biochemistry 41:5894-5906.

Rinke, C.S., P.L. Boyer, M.D. Sullivan, S.H. Hughes, and M.L. Linial.  2002.  Mutation of the catalytic domain of the foamy virus reverse transcriptase leads to loss of processivity and infectivity.  J. Virol. 76:7560-7570.

Julias, J.G., M.J. McWilliams, S.G. Sarafianos, E. Arnold, and S.H. Hughes.  2002.  Human immunodeficiency virus type 1 reverse transcriptase RNase H primer grip mutations affect the specificity of RNase H cleavage in vivo.  Proc. Natl. Acad. Sci. USA 99:9515-9520.

Sarafianos, S.G., A.D. Clark, Jr., K. Das, S. Tuske, J.J. Birktoft, P. Ilankumaran, A.R. Ramesha, J.M. Sayer, D.M. Jerina, P.L. Boyer, S.H. Hughes, and E. Arnold.  2002.  Structures of HIV-1 reverse transcriptase with pre- and post-translocation AZTMP-terminated DNA.  EMBO J. 21:6614-6624.

Boyer, P.L., S.G. Sarafianos, E. Arnold, and S.H. Hughes.  2002.  Nucleoside analog resistance caused by insertions in the fingers of HIV-1 RT involves ATP-mediated excision.  J. Virol. 76:9143-9151.

Skillman, A.G., K.W. Maurer, D.C. Roe, M.J. Stauber, D. Eargle, T.J.A. Ewing, A. Muscate, E. Davioud-Charvet, M.V. Medaglia, R.J. Fisher, E. Arnold, H.-Q. Gao, R. Buckheit, P.L. Boyer, S.H. Hughes, I.D. Kuntz, and G.L. Kenyon.  2002.  A novel mechanism for inhibition of HIV-1 reverse transcriptase.  Bioorganic Chem. 30:443-458.

Kroeger Smith, M.B., B.M. Hose, A. Hawkins, J. Lipchock, D.W. Farnsworth, R.C. Rizzo, J. Tirado-Rives, E. Arnold, W. Zhang, S.H. Hughes, William L. Jorgensen, C.J. Michejda, and R.H. Smith, Jr.  2003.  Molecular modeling calculations of HIV-1 RT nonnucleoside inhibitors:  Correlation of binding energy with biological activity for novel 2-Aryl-substituted benzimidazole analogues.  J. Med. Chem. 46:1940-1947.

Golinelli, M.-P., and S.H. Hughes.  Secondary structure in the nucleic acid affects the rate of

HIV-1 nucleocapsid-mediated strand annealing.  Biochemistry 42:8153-8162, 2003.

Choi, Y., C. George, M.J. Comin, J.J. Barchi, Jr., H.S. Kim, K.A. Jacobson, J. Balzarini, H. Mitsuya, P.L. Boyer, S.H. Hughes, and V.E. Marquez.  2003.  A conformationally locked analogue of the anti-HIV agent stavudine.  An important correlation between pseudorotation and maximum amplitude.  J. Med. Chem. 46:3292-3299.

Sarafianos, S.G., A.D. Clark, Jr., S. Tuske, C.H. Squire, K. Das, D. Sheng, P. Ilankumaran, A.R. Ramesha, H. Kroth, J.M. Sayer, D.M. Jerina, P.L. Boyer, S.H. Hughes, and E. Arnold.  (2003).   Trapping HIV-1 reverse transcriptase before and after translocation on DNA.  J. Biol. Chem. 278:16280-16288.

Julias, J.G., M.J. McWilliams, S. Sarafianos, E. Arnold, and S.H. Hughes.  2003.  Mutation of amino acids in the connection domain of human immunodeficiency virus type 1 reverse transcriptase that contact the template-primer affects RNase H activity.  J. Virol. 77:8548-8554.

McWilliams, M.J., J.G. Julias, S.G. Sarafianos, W. Gregory Alvord, E. Arnold, and S.G. Sarafianos.  2003.  Mutations in the 5' end of the HIV-1 polypurine affect RNase H cleavage specificity and virus titer.  J. Virol. 77:11150-11157.

Princler, G.L., J.G. Julias, S.H. Hughes, and D. Derse.  2003.  Roles of viral and cellular proteins in the expression of alternatively spliced HTLV-1 pX mRNAs.  Virology 317:136-145.

Julias, J.G., P.L. Boyer, M.J. McWilliams, W.G. Alvord, and S.H. Hughes.  2004.  Mutations at position 184 of human immunodeficiency virus type-1 reverse transcriptase affect virus titer and viral DNA synthesis.  Virology 322:13-21.

Peletskaya, E.N., A.A. Kogon, Stephen Tuske, Edward Arnold, and S.H. Hughes.  2004.  Nonnucleoside inhibitor binding affects the interactions of the fingers subdomain of human immunodeficiency virus type-1 reverse transcriptase with DNA.  J. Virol. 78:3387-3397.

Sismour, A.M., S. Lutz, J.-H. Park, M.J. Lutz, P.L. Boyer, S.H. Hughes, and S.A. Benner.  2004.  PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from human immunodeficiency virus-1.  Nucl. Acids Res. 32:728-735.

Tuske, S., S.G. Sarafianos, A.D. Clark, Jr., J. Ding, L.K. Naeger, K.L. White, M.D. Miller, C.S. Gibbs, P.L. Boyer, P. Clark, G. Wang, B.L. Gaffney, R.A. Jones, D.M. Jerina, S.H. Hughes, and E. Arnold.  2003.  Structures of HIV-1 RT-DNA complexes before and after incorporation of  the anti-AIDS drug tenofovir.  Nature Structural & Molecular Biology 11:469-474 .

Kroeger Smith, M. B., S. Ruby, S. Horouzhenko, B. Buckingham, J. Richardson, I. Puleri, E. Potts, W.L. Jorgensen, E. Arnold, W. Zhang, S.H. Hughes, C.J. Michejda, and R.H. Smith, Jr.  2003.  HIV-1 reverse transcriptase variantsMolecular modeling of Y181C, V106A, L100I, and K103N mutations with nonnucleoside inhibitors using Monte Carlo simulations in combination with a linear response method.  Drug Design and Discovery 18:151-163.

Das, K., A.D. Clark, Jr., P.J. Lewi, J. Heeres, M.R. de Jonge, L.M.H. Koymans, H. Maarten Vinkers, F. Daeyaert, D.W. Ludovici, M.J. Kukla, B. De Corte, R.W. Kavash, C.Y. Ho, H. Ye, M.A. Lichtenstein, K. Andries, R. Pauwels, M.-P. de Béthune, P.L. Boyer, P. Clark., S.H. Hughes, P.A.J. Janssen, and E. Arnold.  2004.  Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (Etravirine) and related nonnucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants.  J. Med. Chem. 47:2550-2560.

Boyer, P.L., C.R. Stenbak, P.K. Clark, M.L. Linial, and S.H. Hughes.  2004.  Characterization of the polymerase and RNase H activities of human foamy virus reverse transcriptase.  J. Virol. 78:6112-6121.

Boyer, P.L., T. Imamichi, S.G. Sarafianos, E. Arnold, and S.H. Hughes.  2004.  The effects of the Δ67 complex of mutations in human immunodeficiency virus type 1 reverse transcriptase on nucleotide analog excision.  J. Virol. 78:9987-9997.

Siddiqui, M.A., S.H. Hughes, P.L. Boyer, H. Mitsuya,  Q.N. Van, C. George, S.G. Sarafianos, and V.E. Marquez.  2004.  A 4'-C-ethynyl-2',3'-dideoxynucleoside analogue highlights the role of the 3'-OH in anti-HIV active 4'-C-ethynyl-2'-deoxy nucleosides.  J. Med. Chem. 47:5041-5048.

Kvaratskhelia, M., P.K. Clark, S. Hess, D.C. Melder, M.J. Federspiel, and S.H. Hughes.  2004.  Identification of glycosylation sites in the SU component of the avian sarcoma/leukosis virus envelope glycoprotein (Subgroup A) by mass spectrometry.  Virology 326:171-181.

Sarafianos, S.G., S.H. Hughes, and E. Arnold.  2004.  Designing anti-AIDS drugs targeting the major mechanism of HIV-1 RT resistance to nucleoside analog drugs.  Int. J. Biochem. 36:1706-1715.

Das, K., P.J. Lewi, S.H. Hughes, and E. Arnold.  2004.  Crystallography and the design of anti-AIDS drugs:  conformational flexibility and positional adaptability are important in the design of non-nucleoside HIV-1 reverse transcriptase inhibitors.  Prog. Biophys. & Mol. Biol. 88:209-231.

Ambrose, Z., V. Boltz, S. Palmer, J.M. Coffin, S.H. Hughes, and V.N. KewalRamani.  2004.  In Vitro characterization of an SIV/HIV chimeric virus expressing HIV-1 reverse transcriptase (RT-SHIV) to study antiviral resistance in pigtail macaques.  J. Virol. 78:13553-13561.

Julias, J.G., M.J. McWilliams, S.G. Sarafianos, W.G. Alvord, E. Arnold, and S.H. Hughes.  2004.  Effects of mutations in the G-tract of the HIV-1 polypurine tract on virus replication and RNase H cleavage.  J. Virol. 78:13315-13324.

Boyer, P.L., J.G. Julias, V.E. Marquez, and S.H. Hughes.  2005.  Fixed conformation nucleoside analogs effectively inhibit excision-proficient HIV-1 reverse transcriptases.  J. Mol. Biol. 345:441-450.

Chang, K.W., E.V. Barsov, A.L. Ferris, and S.H. Hughes.  2005.  Mutations of a residue within the polypurine-rich region of env alter the replication rate and level of cytopathic effects in chimeric avian retroviral vectors.  J. Virol., in press.

Das, K., A.D. Clark, Jr., P.J. Lewi, S.H. Hughes, and E. Arnold.  2005.  Detection of non-nucleoside inhibitor binding to HIV-1 reverse transcriptase by dynamic light scattering.  Biophys. J., submitted.

Himmel, D.M., K. Das, A.D. Clark, Jr., S.H. Hughes, A. Benjahad, S. Oumouch, J. Guillemont, S. Coupa, A. Poncelet, I. Csoka, C. Meyer, K. Andries, C.H. Nguyen, D.S. Grierson, and E. Arnold.  2005.  Crystal structures for HIV-1 reverse transcriptase in complexes with three pyridinone derivatives:  A new class of non-nucleoside inhibitors effective against a broad range of drug-resistant strains.  J. Med. Chem., submitted.

McWilliams, M.J., J.G. Julias, S.G. Sarafianos, W.G. Alvord, E. Arnold, and S.H. Hughes.  2005.  Combining mutations in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase with mutations in the HIV-1 polypurine tract (PPT) affects RNase H cleavages involved in PPT utilization.  Virology, submitted.

Chang, K.W., J.G. Julias, W. Gregory Alvord, J. Oh, and S.H. Hughes.  2005.  Alternate polypurine tracts affect the Rous Sarcoma Virus RNase H cleavage specificity and reveal a preferential cleavage following a GA dinucleotide sequence at the PPT/U3 junction.  J. Virol., submitted.