604 Nucleic Acids Research, 2006, Vol. 34, No. 2 21. Ganser,B.K., Li,S., Klishko,V.Y., Finch,J.T. and Sundquist,W.I. (1999) Assembly and analysis of conical models for the HIV-1 core. Science, 183, 80–83. 22. Briggs,J.A.G., Wilk,T., Welker,R., Kra¨usslich,H.-G. and Fuller,S.D. (2003) Structural organization of authentic, mature HIV-1 virions and cores. EMBO J., 22, 1707–1715. 23. Briggs,J.A., Simon,M.N., Gross,I., Krausslich,H.G., Fuller,S.D., Vogt,V.M. and Johnson,M.C. (2004) The stoichiometry of Gag protein in HIV-1. Nature Struct. Mol. Biol., 11, 672–675. 24. Roldan,A., Warren,O.U., Russell,R.S., Liang,C. and Wainberg,M.A. (2005) A HIV-1 minimal Gag protein is superior to nucleocapsid at in vitro annealing and exhibits multimerization-induced inhibition of reverse transcription. J. Biol. Chem., 280, 17488–17496. 25. Guo,J., Wu,T., Anderson,J., Kane,B.F., Johnson,D.G., Gorelick,R.J., Henderson,L.E. and Levin,J.G. (2000) Zinc finger structures in the human immunodeficiency virus type 1 nucleocapsid protein facilitate efficient minus- and plus-strand transfer. J. Virol., 74, 8980–8988. 26. Guo,J., Wu,T., Kane,B.F., Johnson,D.G., Henderson,L.E., Gorelick,R.J. and Levin,J.G. (2002) Subtle alterations of the native zinc finger structures have dramatic effects on the nucleic acid chaperone activity of human immunodeficiency virus type 1 nucleocapsid protein. J. Virol., 76, 4370–4378. 27. Carteau,S., Gorelick,R.J. and Bushman,F.D. (1999) Coupled integration of human immunodeficiency virus type 1 cDNA ends by purified integrase in vitro: stimulation by the viral nucleocapsid protein. J. Virol., 73, 6670–6679. 28. Gao,K., Gorelick,R.J., Johnson,D.G. and Bushman,F.D. (2003) Cofactors for human immunodeficiency virus type 1 cDNA integration in vitro. J. Virol., 77, 1598–1603. 29. Kelly,R.C., Jensen,D.E. and von Hippel,P.H. (1976) DNA ‘melting’ proteins. IV. Fluorescence measurements of binding parameters for bacteriophage T4 gene 32-protein to mono-, oligo-, and polynucleotides. J. Biol. Chem., 251, 7240–7250. 30. McGhee,J.D. and von Hippel,P.H. (1974) Theoretical aspects of DNA–protein interactions: cooperative and non-cooperative binding of large ligands to a one-dimensional homogeneous lattice. J. Mol. Biol., 86, 469–489. 31. Record,M.T.J., Lohman,T.M. and de Haseth,P.L. (1976) Ion effects on ligand–nucleic acid interactions. J. Mol. Biol., 107, 145–158. 32. Record,M.T.J., Zhang,W. and Anderson,C.F. (1998) Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. Adv. Protein Chem., 51, 281–353. 33. Perrin,F. (1926) Polarization de la luminiere de fluorescence. Vie moyenne de molecules dans l’etat excite. J. Phys. Radium, 7, 390–401. 34. Lakowicz,J.R. (1999) Principles of Fluorescence Spectroscopy. 2nd edn. Plenum Publishers, NY. 35. Williams,M.C., Rouzina,I., Wenner,J.R., Gorelick,R.J., Musier-Forsyth,K. and Bloomfield,V.A. (2001) Mechanism for nucleic acid chaperone activity of HIV-1 nucleocapsid protein revealed by single molecule stretching. Proc. Natl Acad. Sci. USA, 98, 6121–6126. 36. Williams,M.C., Gorelick,R.J. and Musier-Forsyth,K. (2002) Specific zinc finger architecture required for HIV-1 nucleocapsid protein’s nucleic acid chaperone function. Proc. Natl Acad. Sci. USA, 99, 8614–8619. 37. Lee,B.M., De Guzman,R.N., Turner,B.G., Tjandra,N. and Summers,M.F. (1998) Dynamical behavior of the HIV-1 nucleocapsid protein. J. Mol. Biol., 279, 633–649. 38. Martin,S.L., Cruceanu,M., Branciforte,D., Li,P.W.-l., Kwok,S.C., Hodges,R.S. and Williams,M.C. (2005) LINE-1 retrotransposition requires the nucleic acid chaperone activity of the ORF1 protein. J. Mol. Biol., 348, 549–561. 39. Priel,E., Aflalo,E., Seri,I., Henderson,L.E., Arthur,L.O., Aboud,M., Segal,S. and Blair,D.G. (1995) DNA binding properties of the zinc-bound and zinc-free HIV nucleocapsid protein: supercoiled DNA unwinding and DNA–protein cleavable complex formation. FEBS Lett., 362, 59–64. 40. Pant,K., Karpel,R.L., Rouzina,I. and Williams,M.C. (2004) Mechanical measurement of single molecule binding rates: kinetics of DNA helix-destabilization by T4 gene 32 protein. J. Mol. Biol., 336, 851–870. 41. Cantor,C.R. and Schimmel,P.R. (1980) Biophysical Chemistry. W. H. Freeman and Company, New York. 42. Rouzina,I. and Bloomfield,V.A. (2001) Force-induced melting of the DNA double helix-1. Thermodynamic analysis. Biophys. J., 80, 882–893. 43. Williams,M.C., Rouzina,I. and Bloomfield,V.A. (2002) Thermodynamics of DNA interactions from single molecule stretching experiments. Acc. Chem. Res., 35, 159–166. 44. Leger,J.F., Romano,G., Sarkar,A., Robert,J., Bourdieu,L., Chatenay,D. and Marko,J.F. (1999) Structural transitions of a twisted and stretched DNA molecule. Phys. Rev. Lett., 83, 1066–1069. 45. Urbaneja,M.A., Kane,B.P., Johnson,D.G., Gorelick,R.J., Henderson,L.E. and Casas-Finet,J.R. (1999) Binding properties of the human immunodeficiency virus type 1 nucleocapsid protein p7 to a model RNA: elucidation of the structural determinants for function. J. Mol. Biol., 287, 59–75. 46. Bombarda,E., Ababou,A., Vuilleumier,C., Ge´rard,D., Roques,B.P., Pie´mont,E. and Me´ly,Y. (1999) Time-resolved fluorescence investigation of the human immunodeficiency virus type 1 nucleocapsid protein: influence of the binding of nucleic acids. Biophys. J., 76, 1561–1570. 47. Urbaneja,M.A., Wu,M., Casas-Finet,J.R. and Karpel,R.L. (2002) HIV-1 nucleocapsid protein as a nucleic acid chaperone: spectroscopic study of its helix-destabilizing properties, structural binding specificity, and annealing activity. J. Mol. Biol., 318, 749–764. 48. Fisher,R.J., Rein,A., Fivash,M., Urbaneja,M.A., Casas-Finet,J.R., Medaglia,M. and Henderson,L.E. (1998) Sequence-specific binding of human immunodeficiency virus type 1 nucleocapsid protein to short oligonucleotides. J. Virol., 72, 1902–1909. 49. Vuilleumier,C., Bombarda,E., Morellet,N., Gerard,D., Roques,B.P. and Mely,Y. (1999) Nucleic acid sequence discrimination by the HIV-1 nucleocapsid protein NCp7: a fluorescence study. Biochemistry, 38, 16816–16825. 50. Paoletti,A.C., Shubsda,M.F., Hudson,B.S. and Borer,P.N. (2002) Affinities of the nucleocapsid protein for variants of SL3 RNA in HIV-1. Biochemistry, 41, 15423–15428. 51. Cen,S., Huang,Y., Khorchid,A., Darlix,J.-L., Wainberg,M.A. and Kleiman,L. (1999) The role of Pr55(gag) in the annealing of tRNA3Lys to human immunodeficiency virus type 1 genomic RNA. J. Virol., 73, 4485–4488. 52. Crawford,S. and Goff,S.P. (1985) A deletion mutation in the 50 part of the pol gene of Moloney murine leukemia virus blocks proteolytic processing of the gag and pol polyproteins. J. Virol., 53, 899–907. 53. Feng,Y.-X., Campbell,S., Harvin,D., Ehresmann,B., Ehresmann,C. and Rein,A. (1999) The human immunodeficiency virus type 1 Gag polyprotein has nucleic acid chaperone activity: possible role in dimerization of genomic RNA and placement of tRNA on the primer binding site. J. Virol., 73, 4251–4256. 54. Hargittai,M.R.S., Gorelick,R.J., Rouzina,I. and Musier-Forsyth,K. (2004) Mechanistic insights into the kinetics of HIV-1 nucleocapsid protein-facilitated tRNA annealing to the primer binding site. J. Mol. Biol., 337, 951–968. 55. Guo,J.H., Henderson,L.E., Bess,J., Kane,B. and Levin,J.G. (1997) Human immunodeficiency virus type 1 nucleocapsid protein promotes efficient strand transfer and specific viral DNA synthesis by inhibiting TAR-dependent self-priming from minus-strand strong-stop DNA. J. Virol., 71, 5178–5188. 56. Golinelli,M.P. and Hughes,S.H. (2001) Self-priming of retroviral minus-strand strong-stop DNAs. Virology, 285, 278–290. 57. Heilman-Miller,S.L., Wu,T. and Levin,J.G. (2004) Alteration of nucleic acid structure and stability modulates the efficiency of minus-strand transfer mediated by the HIV-1 nucleocapsid protein. J. Biol. Chem., 279, 44154–44165. 58. Driscoll,M.D. and Hughes,S.H. (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 seqeunces. J. Virol., 74, 8785–8792. 59. Negroni,M. and Buc,H. (1999) Recombination during reverse transcription: an evaluation of the role of the nucleocapsid protein. J. Mol. Biol., 286, 15–31. 60. Negroni,M. and Buc,H. (2001) Mechanisms of retroviral recombination. Ann. Rev. Genet., 35, 275–302. 61. Chen,Y., Balakrishnan,M., Roques,B. and Bambara,R.A. (2003) Steps of the acceptor invasion mechanism for HIV-1 minus strand strong stop transfer. J. Biol. Chem., 278, 38368–38375. 62. Chen,Y., Balakrishnan,M., Roques,B., Fay,P.J. and Bambara,R.A. (2003) Mechanism of minus strand strong stop transfer in HIV-1 reverse transcription. J. Biol. Chem., 278, 8006–8017.