NMR structure of the chimeric hybrid duplex r(gcaguggc)·r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription

Journal of Biomolecular NMR

Volumn 13, Issue 4, 1999, Pages 343-355

  Szyperski, Thomas ^a,d   Götte, Matthias ^b,e   Billeter, Martin ^a,f   Perola, Emanuele ^c   Cellai, Luciano ^c   Heumann, Hermann ^b   Wüthrich, Kurt ^a  

^a ETH ZURICH   (Switzerland)

^b MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^c CNR   (Italy)

^d UNIVERSITY AT BUFFALO   (United States)

^e MCGILL UNIVERSITY   (Canada)

^f UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

AIDS; DYANA; HIV 1; NMR structure; Ribonuclease H; RNA DNA hybrid; Torsion angle dynamics

Indexed keywords

NUCLEIC ACID; RIBONUCLEASE H; RNA DIRECTED DNA POLYMERASE;

ARTICLE; CIRCULAR DICHROISM; DNA RNA HYBRIDIZATION; ENZYME ACTIVITY; ENZYME SPECIFICITY; HUMAN IMMUNODEFICIENCY VIRUS 1; HYBRID; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION; SIGNAL NOISE RATIO; STEREOSPECIFICITY; STRUCTURE ANALYSIS; TRANSCRIPTION INITIATION;

BASE SEQUENCE; COMPUTER SIMULATION; DNA, VIRAL; HIV-1 REVERSE TRANSCRIPTASE; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HETERODUPLEXES; OLIGODEOXYRIBONUCLEOTIDES; OLIGORIBONUCLEOTIDES; RIBONUCLEASE H, CALF THYMUS; RNA, TRANSFER; RNA, VIRAL; SOFTWARE;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0345379316     PISSN: 09252738     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008350604637     Document Type: Article

References (78)

1. Anil Kumar, Ernst, R.R. and Wüthrich, K. (1980) Biochem. Biophys. Res. Commun., 95, 1-6.
2. Arnott, S., Chandrasekaran, R., Millane, R.P. and Park, H.-S. (1986) J. Mol. Biol., 188, 631-640.
3. Babcock, M.S., Pednault, E.P.D. and Olson, W.K. (1994) J. Mol. Biol., 237, 125-156.
4. Bachelin, M., Hessler, G., Kurz, G., Hacia, J.G., Dervan, P.B. and Kessler, H. (1998) Nat. Struct. Biol., 5, 271-275.
5. Baltimore, D. (1970) Nature, 226, 1209-1211.
6. Ban, C., Ramakrishnan, B. and Sundaralingam, M. (1992) Curr. Opin. Struct. Biol, 5, 282-295.
7. Bartels, C., Xia, T., Billeter, M., Güntert, P. and Wüthrich, K. (1995) J. Biomol. NMR, 6, 1-10.
8. Bebenek, K., Beard, W. A., Darden, T. A., Li, L., Prasard, R., Luton, B.A., Gorenstein, D.A., Wilson, S.H. and Kunkel, T.A. (1997) Nat. Struct. Biol., 4, 194-197.
9. Blain, S.W. and Goff, S.P. (1993) J. Biol Chem., 268, 23585-23592.
10. Cheatham, T.E. and Kollman, P.A. (1996) J. Am. Chem. Soc., 119, 4805-4825.
11. Chuprina, V.P., Fedoroff, O.Y. and Reid, B.R. (1991a) Biochemistry, 30, 561-568.
12. Chuprina, V.P., Lipanov, A.A., Fedoroff, O.Y, Kim, S.-G., Kintanar, A. and Reid, B.R. (1991b) Proc. Natl. Acad. Sci. USA, 88, 9087-9091.
13. Davies, J.F., Hostomska, Z., Hostomsky, Z., Jordan, S.R. and Matthews, D.A. (1991) Science, 252, 88-95.
14. DeMesmaeker, A., Altmann, K.-H., Waldner, A. and Wendeborn, S. (1995) Curr. Opin. Struct. Biol., 5, 343-355.
15. Dickerson, R.E. (1992) Methods Enzymol., 211, 67-111.
16. Ding, J., Jacobo-Molina, A., Tantillo, C., Lu, X., Nanni, R.C. and Arnold, E. (1994) J. Mol. Recogn., 7, 157-161.
17. Dock-Bregeon, A.C., Chevrier, B., Podjarny, A., Johnson, J., de-Bear, J.S., Gough, G.R., Gilham, P.T. and Moras, D. (1989) J. Mol. Biol., 209, 459-474.
18. Egli, M., Usman, N., Zhang, S. and Rich, A. (1992) Proc. Natl. Acad. Sci. USA, 89, 534-538.
19. Egli, M., Usman, N. and Rich, A. (1993) Biochemistry, 32, 3221-3273.
20. Egli, M., Portmann, S. and Usman, N. (1996) Biochemistry, 35, 8489-8494.
21. Fedoroff, O.Y., Salazar, M. and Reid, B.R. (1993) J. Mol. Biol., 233, 509-523.
22. Fedoroff, O.Y, Salazar, M. and Reid, B.R. (1996) Biochemistry, 35, 11070-11080.
23. Fedoroff, O.Y., Ge, Y. and Reid, B.R. (1997) J. Mol. Biol., 269, 225-239.
24. Fernández, C., Szyperski, T., Bruyére, T., Ramage, P., Mösinger, E. and Wüthrich, K. (1997) J. Mol. Biol., 266, 576-593.
25. Furfine, E.S. and Reardon, J.E. (1991) Biochemistry, 30, 7041-7046.
26. Gonzalez, C., Stec, W., Kobylanska, A., Hogrefe, R.I., Reynolds, M. and James, T.L. (1994) Biochemistry, 33, 11062-11072.
27. Gorenstein, D.G., Schroeder, S.A., Fu, J.M., Metz, J.T., Roongta, V. and Jones, C.R. (1988) Biochemistry, 27, 7223-7237.
28. Götte, M., Fackler, S., Hermann, T., Perola, E., Cellai, L., Gross, H.J., Le Grice, S.F.J. and Heumann, H. (1995) EMBO J., 14, 833-841.
29. Griesinger, C., Sørensen, O. and Ernst, R.R. (1985) J. Am. Chem. Soc., 107, 6394-6396.
30. Griesinger, C., Otting, G., Wüthrich, K. and Ernst, R.R. (1988) J. Am. Chem. Soc., 110, 7870-7872.
31. Guéron, M. and Leroy, J.L. (1995) Methods Enzymol., 261, 383-413.
32. Güntert, P., Braun, W. and Wüthrich, K. (1991) J. Mol. Biol., 217, 517-530.
33. Güntert, P., Dötsch, V., Wider, G. and Wüthrich, K. (1992) J. Biomol. NMR, 2, 619-629.
34. Güntert, P., Mumenthaler, C. and Wüthrich, K. (1997) J. Mol. Biol., 273, 283-298.
35. Güntert, P., Billeter, M., Ohlenschläger, O., Brown, L.R. and Wüthrich, K. (1998) J. Biomol. NMR, 12, 543-548.
36. Han, G.W., Kopka, M.L., Cascio, D., Grzeskowiak, K. and Dickerson, R.E. (1997) J. Mol. Biol., 269, 811-826.
37. Hartmann, B. and Lavery, R. (1996) Q. Rev. Biophys., 29, 309-368.
38. Horton, N.C. and Finzel, B.C. (1996) J. Mol. Biol., 264, 521-533.
39. Hostomsky, Z., Hughes, S.H., Goff, S.P. and Le Grice, S.F.J. (1994) J. Virol., 68, 1970-1971.
40. Isel, C., Landry, J.M., LeGrice, S.F., Ehresmann, C., Ehresmann, B. and Marquet, R. (1996) EMBO J., 15, 917-924.
41. Jacobo-Molina, A., Ding, J., Nanni, R.G., Clark, A.D., Lu, X., Tantillo, C., Williams, R.L., Kamer, G., Ferris, A.L., Clark, P., Hizi, A., Hughes, S.H. and Arnold, E. (1993) Proc. Natl. Acad. Sci. USA, 90, 6320-6324.
42. Kanaya, E. and Kanaya, S. (1995) Eur. J. Biochem., 231, 557-562.
43. Kennard, O. and Hunter, W.N. (1991) Angew. Chem. Int. Ed. Engl., 30, 1254-1277.
44. Kiefer, J.R., Mao, C., Braman, J.C. and Beese, L.S. (1998) Nature, 391, 304-307.
45. Kim, S.-G., Lin, L.-J. and Reid, B.R. (1992) Biochemistry, 31, 3564-3574.
46. Klinck, R., Sprules, T. and Gehring, K. (1997) Nucleic Acid Res., 25, 2120-2137.
47. Koradi, R., Billeter, M. and Wüthrich, K. (1996) J. Mol. Graph., 14, 51-55.
48. Lanchy, J.-M., Ehresmann, C., Le Grice, S.F.J., Ehresmann, B. and Marquet, R. (1996) EMBO J., 15, 7178-7187.
49. Lane, A.N., Ebel, S. and Brown, T. (1993) Eur. J. Biochem., 215, 297-306.
50. Liepinsh, E., Otting, G. and Wüthrich, K. (1992) Nucleic Acid Res., 20, 6549-6553.
51. Luginbühl, P., Güntert, P., Billeter, M. and Wüthrich, K. (1996) J. Biomol. NMR, 8, 136-146.
52. Mak, J. and Kleiman, L. (1997) J. Virol., 71, 8087-8095.
53. Mandel, A.M., Akke, M. and Palmer III, A.G. (1995) J. Mol. Biol., 246, 144-162.
54. Marino, J.P., Schwalbe, H., Glaser, S.J. and Griesinger, C. (1996) J. Am. Chem. Soc., 118, 4388-4395.
55. Marquet, R., Isel, C., Ehresmann, C. and Ehresmann, B. (1995) Biochimie, 77, 113-124.
56. Müller, U., Maier, G., Onori, A.M., Cellai, L., Heumann, H. and Heinemann, U. (1998) Biochemistry, 37, 12005-12011.
57. Nakamura, H., Oda, Y., Iwai, S., Inoue, H., Ohtsuka, E., Kanaya, S., Kimura, S., Katsuda, C., Katayanagi, K., Morikawa, K., Miyashiro, H. and Ikehara, M. (1991) Proc. Natl. Acad. Sci. USA, 88, 11535-11539.
58. Nelson, H.C.M., Finch, J.T., Bonaventura, F.L. and Klug, A. (1986) Nature, 330, 221-226.
59. Nishizaki, T., Iwai, S., Ohkubo, T., Kojima, C., Nakamura, H., Kyogoku, Y. and Ohtsuka, E. (1995) Biochemistry, 34, 4016-4025.
60. Otting, G., Orbons, L.P.M. and Wüthrich, K. (1990) J. Magn. Reson., 89, 423-430.
61. Piotto, M., Saudek, V. and Sklenář, V. (1992) J. Biomol. NMR, 2, 661-665.
62. Rance, M., Sørensen, O.W., Bodenhausen, G., Wagner, G., Ernst, R.R. and Wüthrich, K. (1983) Biochem. Biophys. Res. Commun., 117, 479-485.
63. Ravishankar, G., Swaminathan, S., Beveridge, D.L., Lavery, R. and Sklenar, H. (1988) J. Biomol. Struct. Dyn., 6, 669-699.
64. Salazar, M., Fedoroff, O.Y., Zhu, L. and Reid, B.R. (1994) J. Mol. Biol., 241, 440-455.
65. Salazar, M., Fedoroff, O.Y. and Reid, B.R. (1996) Biochemistry, 35, 8126-8135.
66. Sklénař, V. and Bax, A. (1987) J. Magn. Reson., 74, 469-474.
67. Smith, J.S. and Roth, M.J. (1992) J. Biol. Chem., 267, 15071-15079.
68. Szyperski, T., Güntert, P., Otting, G. and Wüthrich, K. (1992) J. Magn. Reson., 99, 552-560.
69. Szyperski, T., Fernández, C., Ono, A., Kainosho, M. and Wüthrich, K. (1998) J. Am. Chem. Soc., 120, 821-822.
70. Telesnitsky, A. and Goff, S.P. (1997) Retroviruses (Eds, Coffin, J.M., Hughes, S.H. and Varmus, H.E.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, U.S.A., pp. 21-160.
71. Temin, H.M. and Mizutani, S. (1970) Nature, 226, 1211-1213.
72. Varani, G. and Tinoco Jr., I. (1991) Q. Rev. Biophys., 24, 479-532.
73. Wahl, M.C. and Sundaralingam, M. (1995) Curr. Opin. Struct. Biol., 5, 282-295.
74. Wang, A.C., Kim, S.G., Flynn, P.F., Chou, S.-H., Orba, J. and Reid, B.R. (1992) Biochemistry, 31, 3940-3946.
75. Weiner, S.J., Kollman, P.A., Nguyen, D.T. and Case, D.A. (1986) J. Comput. Chem., 7, 230-252.
76. Wijmenga, S.S., Mooren, M.M.W. and Hilbers, C. (1993) In NMR of Macromolecules. A Practical Approach (Ed., Roberts, G.C.K.), Oxford University Press, Oxford, U.K., pp. 217-283.
77. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York, NY, U.S.A.
78. Zhu, L., Salazar, M. and Reid, B.R. (1995) Biochemistry, 34, 2372-2380.