The DeStefano Lab

Retroviral Recombination and Replication 

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Peer-reviewed Publications:

  1. DeStefano, J., Olmstead, E., Panniers, R., and Lucas-Lenard, J. (1990) The Al­pha Sub­unit of Eukaryotic Initiation Factor 2 is Phosphorylated in Mengovirus-In­fected Mouse L Cells. J. Virol. 64, 4445-4453.
  2. DeStefano, J. J., Buiser, R.G., Mallaber, L. M., Myers, T. W., Bambara, R. A., and Fay, P. J. (1991) Polymerization and RNase H Activities of the Reverse Transcr­iptases from Avian Myeloblastosis, Human Immunodeficiency, and Moloney Murine Leuke­mia Viruses Are Functionally Uncoupled. J. Biol. Chem. 266, 7423-7431.
  3. Buiser, R. G., DeStefano, J. J., Mallaber, L. M., Fay, P. J., and Bambara, R. A. (1991) Requirements for the Catalysis of Strand Transfer Synthesis by Retroviral DNA Polymerases. J. Biol. Chem. 266,13103-13109.
  4. DeStefano, J. J., Buiser, R. G., Mallaber, L. M., Bambara, R. A., and Fay, P. J. (1991) Human Immunodeficiency Virus Reverse Transcriptase Possesses a 3' to 5' Endonucle­ase Activity. J.Biol. Chem. 266, 24295-24301.
  5. DeStefano, J. J., Buiser, R. G., Mallaber, L. M., Fay, P. J., and Bambara, R. A. (1992) Parameters that Influence Processive Synthesis and Site Specific Termi­nation by Hu­man Immunodeficiency Virus Reverse Transcriptase on RNA and DNA Tem­ plates. Biochim. Biophys. Acta. 1131, 270-280.
  6. DeStefano, J. J., Mallaber, L. M., Rodriguez-Rodriguez, L., Fay, P. J., and Bambara, R. A. (1992) Requirments for Strand Transfer Between Internal Re­gions of Heteropolymer Templates by Human Immunodeficiency Virus Reverse Transcriptase. J. Virol. 66, 6370-6378.
  7. DeStefano, J. J., Bambara, R. A., and Fay, P. J. (1992) Parameters That Influence the Binding of Human Immunodeficiency Virus Reverse Transcriptase to Nucleic Acid Structures. Bio­chem­is­try 32, 6908-6915.
  8. DeStefano, J. J., Mallaber, L. M., Fay, P. J., and Bambara, R. A. (1993) Determi­nants of the RNase H Cleavage Specificity of Human Immunodeficiency Virus Reverse Transcrip­tase. Nuc. Acids Res. 21,4330-4338.
  9. DeStefano, J. J., Bambara, P. J., and Fay, P. J. (1994) The Mechanism of Human Im­munodeficiency Virus Reverse Transcriptase-catalyzed Strand Trans­fer Be­tween Inter­nal Regions of Heteropolymeric RNA Templates. J. Biol Chem. 269, 161-168.
  10. DeStefano, J. J. (1994) Kinetic Analysis of the Catalysis of Strand Transfer from Internal Regions of Heteropolymeric RNA Templates by Human Immunodeficiency Virus Reverse Transcriptae. J. Mol. Biol. 243, 558-567.
  11. DeStefano, J. J., Wu, W., Seehra, J., McCoy, J., Laston, D., Albone, E., Fay, P.J. and Bambara, R.A. (1994) Characterization of an RNaseH Deficient Mutant of Human Immunodeficiency Virus-1 Reverse Transcriptase Having an Aspartate to Asparagine Change at Position 498. Biochem. Biophys. Acta., 1219, 380-388.
  12. DeStefano, J. J., Mallaber, L. M., Fay, P. J., and Bambara, R. A. (1994) Quantitative Analysis of RNA Cleavage During RNA-Directed DNA Synthesis by Human Immunodeficiency and Avian Myeloblastosis Virus Reverse Transcriptases. Nuc. Acids. Res. 22, 3793-3800.
  13. DeStefano, J. J. (1995) The orientation of binding of human immunodeficiency virus reverse transcriptase on nucleic acid hybrids. Nuc. Acids Res. 23, 3901-3908.
  14. DeStefano, J. J. (1995) Human immunodeficiency virus nucleocapsid protein stimulates strand transfer from internal regions of heteropolymeric RNA. Arch. Virol. 140:1775-1789.
  15. DeStefano, J. J. (1996) Interactions of human immunodeficiency virus nucleocapsid protein with a structure mimicking a replication intermediate. J. Biol. Chem. 271, 16350-16356.
  16. Diaz, L., and DeStefano, J. J. (1996) Strand transfer is enhanced by mismatched nucleotides at the 3' primer terminus: A possible link between HIV-RT fidelity and recombination. Nuc. Acids Res. 24, 3086-3092.
  17. DeStefano, J. J., Roberts, B., and Shriner, D. (1997) The mechanism of retroviral recombination: the role of sequences proximal to the point of strand transfer. Arch. Virol. 142, 1797-1812.
  18. DeStefano, J., Ghosh, J., Prasad, B., and Raja, A. (1998) High fidelity of internal strand transfer catalyzed by human immunodeficiency virus reverse transcriptase. J. Biol Chem. 273, 1483-1489.
  19. Raja, A., and DeStefano, J. J. (1999) Kinetic analysis of the effect of HIV nucleocapsid protein (NCp) on retroviral strand transfer reactions. Biochemistry 38, 5178-5184.
  20. Diaz, L., Cristofaro, J. V., and DeStefano, J. J. (2000) Human immunodeficiency virus resverse transcriptase base misincorporations can promote strand transfer. Arch. Virol. 145, 1117-1131.
  21. DeStefano, J. J. Raja, A., and Crisotfaro, J. V. (2000) In vitro strand transfer from broken RNAs results in mismatch but not frameshift mutations. Virology 276, 7-15.
  22. Rodriguez-Wells, V., Plotch, S. J., and DeStefano, J. J. (2001) Determination of the mutation rate of poliovirus RNA-dependent RNA polymerase. Virus Res. 74, 119-1132.
  23. Rodriguez-Wells, V., Plotch, S. J., and DeStefano, J. J. (2001) Primer-dependent synthesis by poliovirus RNA-dependent RNA polymerase (3Dpol). Nucleic Acids Res. 29, 2715-2724.
  24. DeStefano, J. J., Critofaro, J. V., Derebail, S., Bohlayer, W. P., and Fitzgerald-Health, M. J. (2001) Physical mapping of HIV-RT to the 5' end of RNA primers. J. Biol. Chem. 276, 32515-32521.
  25. Cristofaro J. V., Rausch, J. W., Le Grice, S. F. J., and DeStefano, J. J. (2002) Mutations in the RNase H active site of HIV-RT reveal a role for this site in stabilizing enzyme-primer-template binding. Biochemistry 41, 10968-10975.
  26. Raja, A., and DeStefano, J. J. (2003) Interaction of HIV reverse transcriptase with structures mimicking recombination intermediates. J. Biol. Chem. 278, 10102-10111.
  27. Liesch, G. R., and DeStefano, J. J. (2003) Analysis of mutations made during active synthesis or extension of mismatched substrates further define the mechanism of HIV-RT mutagenesis. Biochemistry 42, 5925-5936.
  28. Derebail, S. S., Heath, M. J., and DeStefano, J. J. (2003) Evidence for the differential effects of nucleocapsid protein on strand transfer in various regions of the HIV genome. J. Biol. Chem. 278, 15702-15712.
  29. Heath, M. J., Derebail, S. S., Gorelick, R. J., and DeStefano, J. J. (2003) Differing roles of the N-terminal and C-terminal zinc fingers in HIV-1 nucleocapsid protein enhanced nucleic acid annealing. J. Biol. Chem. 278, 30755-30763.
  30. Derebail S. S., and DeStefano J. J. (2004) Mechanistic analysis of pause site-dependent and -independent recombinogenic strand transfer from structurally diverse regions of the HIV genome. J. Biol. Chem. 279, 47446-47454.
  31. Heath, M. J., and DeStefano, J. J. (2005) A complementary single stranded docking site is required for enhancement of strand exchange by human immunodeficiency virus nucleocapsid protein on substrates that model viral recombination. Biochemistry, 44, 3915-3925.
  32. DeStefano, J. J. and Cristofaro, J. V. (2006) Selection of primer-template sequences that bind human immunodeficiency virus reverse transcriptase with high affinity. Nucleic Acids Res. 34:130-139.
  33. DeStefano, J. J. and Odeyebo, T. (2006) Poliovirus protein 3AB displays nucleic acid chaperone and helix-destabilizing activities. J. Virol. 80(4):1662-71.
  34. Bohlayer W. P. and DeStefano J. J. (2006) Tighter binding of HIV reverse transcriptase to RNA-DNA vs. DNA-DNA results mostly from interactions in the polymerase domain and requires just a small stretch of RNA-DNA. Biochemistry 45(24):7628-38.
  35. Narayanan, N, Gorelick, R. J., and DeStefano, J. J. (2006) Structure/function mapping of amino acids in the N-terminal zinc finger of the human immunodeficiency virus type 1 nucleocapsid protein: residues responsible for nucleic acid helix destabilizing activity. Biochemistry 45(41):12617-28.
  36. Baird HA, Gao Y, Galetto R, Lalonde M, Anthony RM, Giacomoni V, Abreha M, Destefano JJ, Negroni M, Arts EJ. (2006) Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination. Retrovirology 3:91.
  37. Anthony, R. M. and DeStefano J. J. (2007) In vitro synthesis of long DNA products in reactions with HIV-RT and nucleocapsid protein. J. Mol. Biol. 365(2):310-324.
  38. DeStefano, J. J. and Nair, G. R. (2008) Novel aptamer inhibitors of human immunodeficiency virus reverse transcriptase. Oligonucleotides 18(2):133-143.
  39. Jacob, D. T. and DeStefano J. J. (2008) A new role for HIV nucleocapsid protein in modulating the specificity of plus strand priming. Virology 378(2):385-396.
  40. DeStefano J. J. (2010) Effect of reaction conditions and 3AB on the mutation rate of poliovirus RNA-dependent RNA polymerase in a alpha-complementation assay.  Virus Res. 47(1):53-59.
  41. Olimpo, J. T. and DeStefano, J. J. (2010) Duplex structural differences and not 2’-hydroxyls explain the more stable binding of HIV-RT to RNA-DNA vs. DNA-DNA.  Nucleic Acids Res. 38(10):4426-4435.
  42. Gangaramani, D. R., Eden, E. L., Shah, M., and DeStefano, J. J. (2010) The twenty-nine amino acid C-terminal cytoplasmic domain of poliovirus 3AB is critical for nucleic acid chaperone activity.  RNA Biology 7(6):8820-8829.
  43. Lai, Y. T., DeStefano J. J. (2011) A primer-free method that selects high-affinity single-stranded DNA aptamers using thermostable RNA ligase.  Anal. Biochem. 414(2):246-253.
  44. Fenstermacher, K. J., and DeStefano, J. J. (2011) Mechanism of HIV reverse transcriptase inhibition by zinc: formation of a highly stable enzyme-(primer-template) complex with profoundly diminished catalytic activity.  J. Biol. Chem. 286(47): 40433-40442.
  45. Lai, Y. T. and DeStefano, J. J. (2012) DNA aptamers to human immunodeficiency virus reverse transcriptase selected by a primer-free SELEX method: characterization and comparison to other aptamers. Nucleic Acids Therapeutics: 22(3):162-176.
  46. Nair, G.R., Dash, C., Le Grice, S.F. and DeStefano, J.J. (2012) Viral reverse transcriptases show selective high affinity binding to DNA-DNA primer-templates that resemble the polypurine tract. PloS One, 7, e41712.
  47. Lieberman O.J., DeStefano J.J. and Lee V.T. (2013) Detection of Cyclic Diguanylate G-Octaplex Assembly and Interaction with Proteins. PLoS ONE 8(1): e53689. doi:10.1371/journal.pone.0053689.

 


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