The DeStefano Lab

Retroviral Recombination and Replication 
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Peer-reviewed Publications:

  1. Rose KM, Alves Ferreira-Bravo I, Li M, Craigie R, Ditzler MA, Holliger P, DeStefano JJ. Selection of 2'-Deoxy-2'-Fluoroarabino Nucleic Acid (FANA) Aptamers That Bind HIV-1 Integrase with Picomolar Affinity. ACS Chem Biol. 2019 Oct 18;14(10):2166-2175. doi: 10.1021/acschembio.9b00237. Epub 2019 Oct 7. PubMed [citation] PMID: 31560515
  2. Das K, Martinez SE, DeStefano JJ, Arnold E. Structure of HIV-1 RT/dsRNA initiation complex prior to nucleotide incorporation. Proc Natl Acad Sci U S A. 2019 Apr 9;116(15):7308-7313. doi: 10.1073/pnas.1814170116. Epub 2019 Mar 22. PubMed [citation] PMID: 30902895, PMCID: PMC6462067
  3. DeStefano JJ. Non-nucleoside Reverse Transcriptase Inhibitors Inhibit Reverse Transcriptase through a Mutually Exclusive Interaction with Divalent Cation-dNTP Complexes. Biochemistry. 2019 Apr 23;58(16):2176-2187. doi: 10.1021/acs.biochem.9b00028. Epub 2019 Apr 5. PubMed [citation] PMID: 30900874, PMCID: PMC6629025
  4. DeStefano JJ, Alves Ferreira-Bravo I. A highly sensitive aptamer-based HIV reverse transcriptase detection assay. J Virol Methods. 2018 Jul;257:22-28. doi: 10.1016/j.jviromet.2018.04.005. Epub 2018 Apr 6. PubMed [citation] PMID: 29630943, PMCID: PMC5960635
  5. Fenstermacher KJ, Achuthan V, Schneider TD, DeStefano JJ. An Evolutionary/Biochemical Connection between Promoter- and Primer-Dependent Polymerases Revealed by Systematic Evolution of Ligands by Exponential Enrichment. J Bacteriol. 2018 Mar 12;200(7). pii: e00579-17. doi: 10.1128/JB.00579-17. Print 2018 Apr 1. PubMed [citation] PMID: 29339418, PMCID: PMC5847653
  6. Stevens AM, Smith AC, Marbach-Ad G, Balcom SA, Buchner J, Daniel SL, DeStefano JJ, El-Sayed NM, Frauwirth K, Lee VT, McIver KS, Melville SB, Mosser DM, Popham DL, Scharf BE, Schubot FD, Seyler RW Jr, Shields PA, Song W, Stein DC, Stewart RC, Thompson KV, et al. Using a Concept Inventory to Reveal Student Thinking Associated with Common Misconceptions about Antibiotic Resistance. J Microbiol Biol Educ. 2017 Apr 21;18(1). pii: 18.1.10. doi: 10.1128/jmbe.v18i1.1281. eCollection 2017 Apr. PubMed [citation] PMID: 28512513, PMCID: PMC5524436
  7. Achuthan V, Singh K, DeStefano JJ. Physiological Mg(2+) Conditions Significantly Alter the Inhibition of HIV-1 and HIV-2 Reverse Transcriptases by Nucleoside and Non-Nucleoside Inhibitors in Vitro. Biochemistry. 2017 Jan 10;56(1):33-46. doi: 10.1021/acs.biochem.6b00943. Epub 2016 Dec 27. PubMed [citation] PMID: 27936595, PMCID: PMC5453313
  8. Das K, Balzarini J, Miller MT, Maguire AR, DeStefano JJ, Arnold E. Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet. ACS Chem Biol. 2016 Aug 19;11(8):2158-64. doi: 10.1021/acschembio.6b00187. Epub 2016 Jun 6. Erratum in: ACS Chem Biol. 2016 Nov 18;11(11):3226. PubMed [citation] PMID: 27192549, PMCID: PMC4992415
  9. Achuthan V, DeStefano JJ. Mismatched Primer Extension Assays. Bio Protoc. 2015 Jun 20;5(12). pii: e1508. PubMed [citation] PMID: 27081667, PMCID: PMC4829118
  10. Chauhan J, Chen SE, Fenstermacher KJ, Naser-Tavakolian A, Reingewertz T, Salmo R, Lee C, Williams E, Raje M, Sundberg E, DeStefano JJ, Freire E, Fletcher S. Synthetic, structural mimetics of the ?-hairpin flap of HIV-1 protease inhibit enzyme function. Bioorg Med Chem. 2015 Nov 1;23(21):7095-109. doi: 10.1016/j.bmc.2015.09.002. Epub 2015 Sep 7. PubMed [citation] PMID: 26474665, PMCID: PMC4661106
  11. Alves Ferreira-Bravo I, Cozens C, Holliger P, DeStefano JJ. Selection of 2'-deoxy-2'-fluoroarabinonucleotide (FANA) aptamers that bind HIV-1 reverse transcriptase with picomolar affinity. Nucleic Acids Res. 2015 Nov 16;43(20):9587-99. doi: 10.1093/nar/gkv1057. Epub 2015 Oct 17. PubMed [citation] PMID: 26476448, PMCID: PMC4751925
  12. Miller MT, Tuske S, Das K, DeStefano JJ, Arnold E. Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer. Protein Sci. 2016 Jan;25(1):46-55. doi: 10.1002/pro.2776. Epub 2015 Sep 18. PubMed [citation] PMID: 26296781, PMCID: PMC4815302
  13. Achuthan V, DeStefano JJ. Primer Extension Reactions for the PCR- based ?- complementation Assay. Bio Protoc. 2015 Jun 20;5(12). pii: e1509. PubMed [citation] PMID: 27500187, PMCID: PMC4972330
  14. Achuthan V, DeStefano JJ. Alternative divalent cations (ZnČ?, CoČ?, and MnČ?) are not mutagenic at conditions optimal for HIV-1 reverse transcriptase activity. BMC Biochem. 2015 May 3;16:12. doi: 10.1186/s12858-015-0041-x. PubMed [citation] PMID: 25934642, PMCID: PMC4472245
  15. Achuthan V, Keith BJ, Connolly BA, DeStefano JJ. Human immunodeficiency virus reverse transcriptase displays dramatically higher fidelity under physiological magnesium conditions in vitro. J Virol. 2014 Aug;88(15):8514-27. doi: 10.1128/JVI.00752-14. Epub 2014 May 21. Erratum in: J Virol. 2015 Feb;89(3):1944. PubMed [citation] PMID: 24850729, PMCID: PMC4135932
  16. Lieberman OJ, DeStefano JJ, Lee VT. Detection of cyclic diguanylate G-octaplex assembly and interaction with proteins. PLoS One. 2013;8(1):e53689. doi: 10.1371/journal.pone.0053689. Epub 2013 Jan 7. Erratum in: PLoS One. 2013;8(6). doi:10.1371/annotation/1e2e5c25-79ad-4cf2-b619-f6972eafbadc. PubMed [citation] PMID: 23308275, PMCID: PMC3538687
  17. Nair GR, Dash C, Le Grice SF, DeStefano JJ. Viral reverse transcriptases show selective high affinity binding to DNA-DNA primer-templates that resemble the polypurine tract. PLoS One. 2012;7(7):e41712. doi: 10.1371/journal.pone.0041712. Epub 2012 Jul 27. PubMed [citation] PMID: 22848574, PMCID: PMC3407194
  18. Lai YT, DeStefano JJ. DNA aptamers to human immunodeficiency virus reverse transcriptase selected by a primer-free SELEX method: characterization and comparison with other aptamers. Nucleic Acid Ther. 2012 Jun;22(3):162-76. doi: 10.1089/nat.2011.0327. Epub 2012 May 3. PubMed [citation] PMID: 22554064, PMCID: PMC3423876
  19. Fenstermacher KJ, DeStefano JJ. 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. 2011 Nov 25;286(47):40433-42. doi: 10.1074/jbc.M111.289850. Epub 2011 Sep 26. PubMed [citation] PMID: 21953456, PMCID: PMC3220506
  20. Lai YT, DeStefano JJ. A primer-free method that selects high-affinity single-stranded DNA aptamers using thermostable RNA ligase. Anal Biochem. 2011 Jul 15;414(2):246-53. doi: 10.1016/j.ab.2011.03.018. Epub 2011 Mar 21. PubMed [citation] PMID: 21420926, PMCID: PMC3121183
  21. Gangaramani DR, Eden EL, Shah M, Destefano JJ. The twenty-nine amino acid C-terminal cytoplasmic domain of poliovirus 3AB is critical for nucleic acid chaperone activity. RNA Biol. 2010 Nov-Dec;7(6):820-9. Epub 2010 Nov 1. PubMed [citation] PMID: 21045553, PMCID: PMC3072266
  22. Olimpo JT, DeStefano JJ. Duplex structural differences and not 2'-hydroxyls explain the more stable binding of HIV-reverse transcriptase to RNA-DNA versus DNA-DNA. Nucleic Acids Res. 2010 Jul;38(13):4426-35. doi: 10.1093/nar/gkq169. Epub 2010 Mar 24. PubMed [citation] PMID: 20338878, PMCID: PMC2910049
  23. DeStefano JJ. Effect of reaction conditions and 3AB on the mutation rate of poliovirus RNA-dependent RNA polymerase in a alpha-complementation assay. Virus Res. 2010 Jan;147(1):53-9. doi: 10.1016/j.virusres.2009.10.006. Epub 2009 Oct 20. PubMed [citation] PMID: 19850090, PMCID: PMC2791190
  24. DeStefano JJ, Nair GR. Novel aptamer inhibitors of human immunodeficiency virus reverse transcriptase. Oligonucleotides. 2008 Jun;18(2):133-44. doi: 10.1089/oli.2008.0103. PubMed [citation] PMID: 18637731, PMCID: PMC2966829
  25. Jacob DT, DeStefano JJ. A new role for HIV nucleocapsid protein in modulating the specificity of plus strand priming. Virology. 2008 Sep 1;378(2):385-96. doi: 10.1016/j.virol.2008.06.002. Epub 2008 Jul 15. PubMed [citation] PMID: 18632127, PMCID: PMC2607142
  26. Baird HA, Gao Y, Galetto R, Lalonde M, Anthony RM, Giacomoni V, Abreha M, Destefano JJ, Negroni M, Arts EJ. Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination. Retrovirology. 2006 Dec 12;3:91. PubMed [citation] PMID: 17164002, PMCID: PMC1764423
  27. Anthony RM, Destefano JJ. In vitro synthesis of long DNA products in reactions with HIV-RT and nucleocapsid protein. J Mol Biol. 2007 Jan 12;365(2):310-24. Epub 2006 Oct 6. PubMed [citation] PMID: 17070544, PMCID: PMC2493291
  28. Narayanan N, Gorelick RJ, DeStefano JJ. 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. 2006 Oct 17;45(41):12617-28. PubMed [citation] PMID: 17029416, PMCID: PMC4829079
  29. Bohlayer WP, DeStefano JJ. Tighter binding of HIV reverse transcriptase to RNA-DNA versus DNA-DNA results mostly from interactions in the polymerase domain and requires just a small stretch of RNA-DNA. Biochemistry. 2006 Jun 20;45(24):7628-38. PubMed [citation] PMID: 16768458, PMCID: PMC2519887
  30. DeStefano JJ, Titilope O. Poliovirus protein 3AB displays nucleic acid chaperone and helix-destabilizing activities. J Virol. 2006 Feb;80(4):1662-71. PubMed [citation] PMID: 16439523, PMCID: PMC1367131
  31. DeStefano JJ, Cristofaro JV. Selection of primer-template sequences that bind human immunodeficiency virus reverse transcriptase with high affinity. Nucleic Acids Res. 2006 Jan 5;34(1):130-9. Print 2006. PubMed [citation] PMID: 16397296, PMCID: PMC1325207
  32. Heath MJ, Destefano JJ. 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. 2005 Mar 15;44(10):3915-25. PubMed [citation] PMID: 15751967
  33. Derebail SS, DeStefano JJ. Mechanistic analysis of pause site-dependent and -independent recombinogenic strand transfer from structurally diverse regions of the HIV genome. J Biol Chem. 2004 Nov 12;279(46):47446-54. Epub 2004 Sep 1. PubMed [citation] PMID: 15342633
  34. Heath MJ, Derebail SS, Gorelick RJ, DeStefano JJ. Differing roles of the N- and C-terminal zinc fingers in human immunodeficiency virus nucleocapsid protein-enhanced nucleic acid annealing. J Biol Chem. 2003 Aug 15;278(33):30755-63. Epub 2003 Jun 3. PubMed [citation] PMID: 12783894
  35. Liesch GR, DeStefano JJ. Analysis of mutations made during active synthesis or extension of mismatched substrates further define the mechanism of HIV-RT mutagenesis. Biochemistry. 2003 May 20;42(19):5925-36. PubMed [citation] PMID: 12741851
  36. Derebail SS, Heath MJ, DeStefano JJ. Evidence for the differential effects of nucleocapsid protein on strand transfer in various regions of the HIV genome. J Biol Chem. 2003 May 2;278(18):15702-12. Epub 2003 Feb 20. PubMed [citation] PMID: 12595541
  37. Raja A, DeStefano JJ. Interaction of HIV reverse transcriptase with structures mimicking recombination intermediates. J Biol Chem. 2003 Mar 21;278(12):10102-11. Epub 2003 Jan 16. PubMed [citation] PMID: 12533519
  38. Cristofaro JV, Rausch JW, Le Grice SF, DeStefano JJ. Mutations in the ribonuclease H active site of HIV-RT reveal a role for this site in stabilizing enzyme-primer-template binding. Biochemistry. 2002 Sep 10;41(36):10968-75. PubMed [citation] PMID: 12206668
  39. DeStefano JJ, Cristofaro JV, Derebail S, Bohlayer WP, Fitzgerald-Heath MJ. Physical mapping of HIV reverse transcriptase to the 5' end of RNA primers. J Biol Chem. 2001 Aug 31;276(35):32515-21. Epub 2001 Jul 5. PubMed [citation] PMID: 11441011
  40. Rodriguez-Wells V, Plotch SJ, DeStefano JJ. Primer-dependent synthesis by poliovirus RNA-dependent RNA polymerase (3D(pol)). Nucleic Acids Res. 2001 Jul 1;29(13):2715-24. PubMed [citation] PMID: 11433016, PMCID: PMC55776
  41. Wells VR, Plotch SJ, DeStefano JJ. Determination of the mutation rate of poliovirus RNA-dependent RNA polymerase. Virus Res. 2001 Apr;74(1-2):119-32. PubMed [citation] PMID: 11226580
  42. DeStefano JJ, Raja A, Cristofaro JV. In vitro strand transfer from broken RNAs results in mismatch but not frameshift mutations. Virology. 2000 Oct 10;276(1):7-15. PubMed [citation] PMID: 11021989
  43. Diaz L, Cristofaro JV, DeStefano JJ. Human immunodeficiency virus reverse transcriptase base misincorporations can promote strand transfer. Arch Virol. 2000;145(6):1117-31. Erratum in: Arch Virol. 2009;154(12):1973. PubMed [citation] PMID: 10948986
  44. Raja A, DeStefano JJ. Kinetic analysis of the effect of HIV nucleocapsid protein (NCp) on internal strand transfer reactions. Biochemistry. 1999 Apr 20;38(16):5178-84. PubMed [citation] PMID: 10213624
  45. DeStefano J, Ghosh J, Prasad B, Raja A. High fidelity of internal strand transfer catalyzed by human immunodeficiency virus reverse transcriptase. J Biol Chem. 1998 Jan 16;273(3):1483-9. PubMed [citation] PMID: 9430686
  46. DeStefano JJ, Roberts B, Shriner D. The mechanism of retroviral recombination: the role of sequences proximal to the point of strand transfer. Arch Virol. 1997;142(9):1797-812. PubMed [citation] PMID: 9672638
  47. Diaz L, DeStefano JJ. Strand transfer is enhanced by mismatched nucleotides at the 3' primer terminus: a possible link between HIV reverse transcriptase fidelity and recombination. Nucleic Acids Res. 1996 Aug 1;24(15):3086-92. PubMed [citation] PMID: 8760898, PMCID: PMC146025
  48. DeStefano JJ. Interaction of human immunodeficiency virus nucleocapsid protein with a structure mimicking a replication intermediate. Effects on stability, reverse transcriptase binding, and strand transfer. J Biol Chem. 1996 Jul 5;271(27):16350-6. PubMed [citation] PMID: 8663119
  49. DeStefano JJ. The orientation of binding of human immunodeficiency virus reverse transcriptase on nucleic acid hybrids. Nucleic Acids Res. 1995 Oct 11;23(19):3901-8. PubMed [citation] PMID: 7479034, PMCID: PMC307308
  50. DeStefano JJ. Human immunodeficiency virus nucleocapsid protein stimulates strand transfer from internal regions of heteropolymeric RNA templates. Arch Virol. 1995;140(10):1775-89. PubMed [citation] PMID: 7503678
  51. DeStefano JJ. Kinetic analysis of the catalysis of strand transfer from internal regions of heteropolymeric RNA templates by human immunodeficiency virus reverse transcriptase. J Mol Biol. 1994 Nov 4;243(4):558-67. PubMed [citation] PMID: 7525968
  52. DeStefano JJ, Wu W, Seehra J, McCoy J, Laston D, Albone E, Fay PJ, Bambara RA. Characterization of an RNase H deficient mutant of human immunodeficiency virus-1 reverse transcriptase having an aspartate to asparagine change at position 498. Biochim Biophys Acta. 1994 Oct 18;1219(2):380-8. PubMed [citation] PMID: 7522572
  53. DeStefano JJ, Mallaber LM, Fay PJ, Bambara RA. Quantitative analysis of RNA cleavage during RNA-directed DNA synthesis by human immunodeficiency and avian myeloblastosis virus reverse transcriptases. Nucleic Acids Res. 1994 Sep 11;22(18):3793-800. PubMed [citation] PMID: 7524028, PMCID: PMC308364
  54. DeStefano JJ, Bambara RA, Fay PJ. The mechanism of human immunodeficiency virus reverse transcriptase-catalyzed strand transfer from internal regions of heteropolymeric RNA templates. J Biol Chem. 1994 Jan 7;269(1):161-8. PubMed [citation] PMID: 7506252
  55. DeStefano JJ, Mallaber LM, Fay PJ, Bambara RA. Determinants of the RNase H cleavage specificity of human immunodeficiency virus reverse transcriptase. Nucleic Acids Res. 1993 Sep 11;21(18):4330-8. PubMed [citation] PMID: 7692401, PMCID: PMC310068
  56. DeStefano JJ, Bambara RA, Fay PJ. Parameters that influence the binding of human immunodeficiency virus reverse transcriptase to nucleic acid structures. Biochemistry. 1993 Jul 13;32(27):6908-15. PubMed [citation] PMID: 7687463
  57. DeStefano JJ, Mallaber LM, Rodriguez-Rodriguez L, Fay PJ, Bambara RA. Requirements for strand transfer between internal regions of heteropolymer templates by human immunodeficiency virus reverse transcriptase. J Virol. 1992 Nov;66(11):6370-8. PubMed [citation] PMID: 1383563, PMCID: PMC240129
  58. DeStefano JJ, Buiser RG, Mallaber LM, Fay PJ, Bambara RA. Parameters that influence processive synthesis and site-specific termination by human immunodeficiency virus reverse transcriptase on RNA and DNA templates. Biochim Biophys Acta. 1992 Jul 15;1131(3):270-80. PubMed [citation] PMID: 1378301
  59. DeStefano JJ, Buiser RG, Mallaber LM, Bambara RA, Fay PJ. Human immunodeficiency virus reverse transcriptase displays a partially processive 3' to 5' endonuclease activity. J Biol Chem. 1991 Dec 25;266(36):24295-301. PubMed [citation] PMID: 1722202
  60. Buiser RG, DeStefano JJ, Mallaber LM, Fay PJ, Bambara RA. Requirements for the catalysis of strand transfer synthesis by retroviral DNA polymerases. J Biol Chem. 1991 Jul 15;266(20):13103-9. PubMed [citation] PMID: 1712774
  61. DeStefano JJ, Buiser RG, Mallaber LM, Myers TW, Bambara RA, Fay PJ. 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. 1991 Apr 25;266(12):7423-31. PubMed [citation] PMID: 1708386
  62. DeStefano J, Olmsted E, Panniers R, Lucas-Lenard J. The alpha subunit of eucaryotic initiation factor 2 is phosphorylated in mengovirus-infected mouse L cells. J Virol. 1990 Sep;64(9):4445-53. PubMed [citation] PMID: 2166823, PMCID: PMC247914

 
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