Conformational Influence of the Ribose 2′-Hydroxyl Group: Crystal Structures of DNA-RNA Chimeric Duplexess

Biochemistry

Volumn 32, Issue 13, 1993, Pages 3221-3237

  Egli, Martin ^a   Usman, Nassim ^b   Rich, Alexander ^c  

^a ETH ZURICH   (Switzerland)

^b Sirna Therapeutics Inc   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HYDROXYL GROUP; RNA;

ARTICLE; CIRCULAR DICHROISM; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DNA CONFORMATION; DNA RNA HYBRIDIZATION; HYDROGEN BOND; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; RNA CONFORMATION;

NASA DISCIPLINE EXOBIOLOGY; NASA DISCIPLINE NUMBER 52-20; NASA PROGRAM EXOBIOLOGY; NON-NASA CENTER;

BASE SEQUENCE; CRYSTALLOGRAPHY; DEOXYRIBOSE; DNA; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RIBOSE; RNA; SUPPORT, NON-U.S. GOV'T; SUPPORT, U.S. GOV'T, NON-P.H.S.; SUPPORT, U.S. GOV'T, P.H.S.; X-RAYS;

EID: 0027299690     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi00064a004     Document Type: Article

References (84)

1. Arnold, E., Jacobo-Molina, A., Nanni, R. G., Williams, R. L., Lu, X., Ding, J., Clark, A. D., Jr., Zhang, A., Ferris, A. L., Clark, P., Hizi, A., & Hughes, S. H. (1992) Nature 357, 85- 89.
2. Arnott, S., Chandrasekaran, R., & Seising, E. (1975) in Structure and Conformation of Nucleic Acids and Protein-Nucleic Acid Interactions (Sundaralingam, M., & Rao, S. T., Eds.) pp 577- 596, University Park Press, Baltimore.
3. Arnott, S., Smith, P. J. C., & Chandrasekaran, R. (1976) in CRC Handbook of Biochemistry and Molecular Biology (Fasman, G. D., Ed.) 3rd ed., Vol. 2, pp 411-422, CRC Press, Cleveland, OH.
4. Arnott, S., Chandrasekaran, R., Millane, R. P., & Park, H.-S. (1986) J. Mol. Biol. 188, 631-640.
5. Benevides, J. M., & Thomas, G. J., Jr. (1988) Biochemistry 27, 3868-3873.
6. Benevides, J. M., Wang, A.H.-J., Rich, A., Kyogoku, Y., van der Marel, G. A., van Boom, J. H., & Thomas, G. J., Jr. (1986) Biochemistry 25, 41-50.
7. Chou, S.-H., Flynn, P., & Reid, B. (1989) Biochemistry 28,2435-2443.
8. Chou, S.-H., Flynn, P., Wang, A., & Reid, B. (1991) Biochemistry 30, 5248-5257.
9. Conner, B. N., Takano, T., Tanaka, S., Itakura, K., & Dickerson, R. E. (1982) Nature 295, 294-299.
10. Crouch, R. J., & Dirksen, M.-L. (1982) in Nuclease (Linn, S. M., & Roberts, R. J., Eds.) pp 211-241, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
11. Dickerson, R. E., et al. (1989) Nucleic Acids Res. 17, 1797— 1803.
12. Dobler, M. (1992) MoMo (color version 1.4), ETH Zürich.
13. Dock-Bregeon, A. C., Chevrier, B., Podjarny, A., Johnson, J. E., deBear, J. S., Gough, G. R., Gilham, P. T., & Moras, D. (1989) J. Mol. Biol. 209, 459-474.
14. Egli, M. (1992) in Structure Correlation (Dunitz, J. D., & Burgi, H.-B., Eds.) VCH Publishers, Weinheim (in press).
15. Egli, M., Usman, N., Zhang, S., & Rich, A. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 534-538.
16. Evans, D. B., Brawn, K., Deibel, M. R., Jr., Tarpley, W. G., & Sharma, S. K. (1991) J. Biol. Chem. 266, 20583-20585.
17. Frederick, C. A., Quigley, G. J., Teng, M.-K., Coll, M., van der Marel, G. A., van Boom, J. H., Rich, A., & Wang, A.H.-J. (1989) Eur. J. Biochem. 181, 295-307.
18. Fujii, S., Matsui, S., Tomita, K., Orita, M., Tanaka, T., & Uesugi, S. (1989) Nucleic Acids Symp. Ser. 21, 67-68.
19. Goff, S. (1990) J. Acquired Immune Defic. Syndr. 3, 817-831.
20. Gupta, G., Sarma, M. H., & Sarma, R. H. (1985) J. Mol. Biol. 186, 463-469.
21. Hansen, J., Schulze, T., Mellert, W., & Moelling, K. (1988) EMBO J. 7, 239-243.
22. Happ, C. S., Happ, E., Clore, G. M., & Gronenborn, A. M. (1988) FEBS Lett. 236, 62-70.
23. Haran, T. E., Shakked, Z., Wang, A.H.-J., & Rich, A. (1987) J. Biomol. Struct. Dyn. 5, 199-217.
24. Heinemann, U., Lauble, H., Frank, R., & Blöcker, H. (1987) Nucleic Acids Res. 15, 9531-9550.
25. Hendrickson, W. A., & Konnert, J. H. (1981) in Biomolecular Structure, Conformation, Function and Evolution (Srinivasan, R., Ed.) pp 43-57, Pergamon, Oxford.
26. Hirshfeld, F. L. (1968) Acta Crystallogr. A24, 301-311.
27. Hu, W.-S., & Temin, H. M. (1990) Science 250, 1227-1233.
28. Huber, H. E., & Richardson, C. C. (1990) J. Biol. Chem. 265, 10565-10573.
29. Inoue, H., Hayase, Y., Iwai, S., & Ohtsuka, E. (1987) FEBS Lett. 215, 327-330.
30. Jain, S., & Sundaralingam, M. (1989) J. Biol. Chem. 264,12780— 12784.
31. Jain, S., Zon, G., & Sundaralingam, M. (1989) Biochemistry 28, 2360-2364.
32. Jeffrey, G. A., Maluszynska, H., & Mitra, J. (1985) Int. J. Biol. Macromol. 7, 336-348.
33. Johnson, M. S., McCure, M. A., Feng, D. F., Gray, J., & Doolittle, R. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 7648-7652.
34. Jones, T. A. (1978) J. Appl. Crystallogr. 11, 268-272.
35. Kabsch, W. (1978) Acta Crystallogr. A34, 827-828.
36. Katahira, M., Lee, S. J., Kobayashi, Y., Sugeta, H., Kyogoku, Y., Iwai, S., Ohtsuka, E., Benevides, J. M., & Thomas, G. J., Jr. (1990) J. Am. Chem. Soc. 112, 4508-4512.
37. Kohlstaedt, L. A., Wang, J., Friedman, J. M., Rice, P. A., & Steitz, T. A. (1992) Science 256, 1783-1790.
38. Kornberg, A. (1974) DNA Synthesis, p 367, Freeman, San Francisco.
39. Lauble, H., Frank, R., Blöcker, H., & Heinemann, U. (1988) Nucleic Acids Res. 16, 7799-7816.
40. McCall, M., Brown, T., & Kennard, O. (1985) J. Mol. Biol. 183, 385-396.
41. McCall, M., Brown, T., Hunter, W. N., & Kennard, O. (1986) Nature 322, 661-664.
42. Mellema, J.-R., Haasnoot, C. A. G., van der Marel, G. A., Wille, G., van Boeckel, C. A. A., van Boom, J. H., & Altona, C. (1983) Nucleic Acids Res. 11, 5717-5738.
43. Milman, G., Langridge, R., & Chamberlin, M. J. (1967) Proc. Natl. Acad. Sci. U.S.A. 57, 1804-1810.
44. Mitsuya, H., & Broder, S. (1987) Nature 325, 773-778.
45. Musier-Forsyth, K., & Schimmel, P. R. (1992) Nature 357,513-515.
46. Nakamura, H., Oda, Y., Iwai, S., Inoue, H., Ohtsuka, E., Kanaya, S., Kimura, S., Katsuda, C., Katayanagi, K., Morikawa, K., Miyashiro, H., & Ikehara, M. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 11535-11539.
47. North, A. C. T., Phillips, D., & Matthews, F. S. (1968) Acta Crystallogr. A24, 351-359.
48. Ogawa, T., & Okazaki, T. A. (1980) Annu. Rev. Biochem. 49, 421-457.
49. Okazaki, R., Okazaki, T., Sakabe, K., & Sugimoto, K. (1967) Jpn. J. Med. Sci. Biol. 20, 255-260.
50. Okazaki, R., Okazaki, T., Sakabe, K., Sugimoto, K., & Sugino, A. (1968) Proc. Natl. Acad. Sci. U.S.A. 59, 598-605.
51. Omer, C. A., & Faras, A. J. (1982) Cell 30, 797-805.
52. Panganiban, A. T., & Fiore, D. (1988) Science 241,1064-1069.
53. Perreault, J.-P., Labuda, D., Usman, N., Yang, J.-H., & Cedergren, R. J. (1991) Biochemistry 30, 4020-4025.
54. Quigley, G. J., Wang, A.H.-J., Seeman, N. C., Suddath, F. L., Rich, A., Sussman, J. L., & Kim, S. H. (1975) Proc. Natl. Acad. Sci. U.S.A. 72, 4866-4870.
55. Quigley, G. J., Teeter, M. M., & Rich, A. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 64-68.
56. Rabinovich, D., & Shakked, Z. (1984) Acta Crystallogr. A40, 195-200.
57. Rabinovich, D., Haran, T., Eisenstein, M., & Shakked, Z. (1988) J. Mol. Biol. 200, 151-161.
58. Rich, A. (1960) Proc. Natl. Acad. Sci. U.S.A. 46, 1044-1053.
59. Rich, A., & RajBhandary, U. L. (1976) Annu. Rev. Biochem. 45, 805-860.
60. Rosenberg, J. M., Seeman, N. C., Day, R. O., & Rich, A. (1976) J. Mol. Biol. 104, 145-167.
61. Saenger, W. (1984) Principles of Nucleic Acid Structure, 1st ed., pp 64-68, Springer-Verlag, New York.
62. Sawai, Y., & Tsukada, K. (1983) Biochem. Biophys. Res. Commun. 110, 470-476.
63. Schatz, O., Cromme, F., Gruninger-Leitch, R., & LeGrice, S. F. J. (1989) FEBS Lett. 257, 311-314.
64. Seeman, N. C., Rosenberg, J. M., Suddath, F. L., Kim, J. J. P., & Rich, A. (1976) J. Mol. Biol. 104, 109-144.
65. Selsing, E., Wells, R. D., Early, T. A., & Kearns, D. R. (1978) Nature 275, 249-250.
66. Seising, E., Wells, R. D., Alden, C. J., & Arnott, S. (1979) J. Biol. Chem. 254, 5417-5422.
67. Shakked, Z.,& Kennard, O. (1985) in Biological Macromolecules and Assemblies: Volume 2—Nucleic Acids and Interactive Proteins (Jurnak, F. A., & McPherson, A., Eds.) pp 1-36, Wiley, New York.
68. Shakked, Z., Rabinovich, D., Cruse, W. B. T., Egert, E., Kennard, O., Sala, G., Salisbury, S. A., & Viswamitra, M. A. (1981) Proc. R. Soc. London B213, 479-487.
69. Shakked, Z., Rabinovich, D., Kennard, O., Cruse, W. B. T., Salisbury, S. A., & Viswamitra, M. A. (1983) J. Mol. Biol. 166, 183-201.
70. Shakked, Z., Guerstein-Guzikevich, G., Eisenstein, M., Frolow, F., & Rabinovich, D. (1989) Nature 342, 456-459.
71. Shindo, H., & Matsumoto, U. (1984) J. Biol. Chem. 259, 8682- 8684.
72. Takusagawa, F. (1990) J. Biomol. Struct. Dyn. 7, 795-809.
73. Tisdale, M., Erl, P., Larder, B. A., Purifoy, D. J. M., Darby, G., & Powell, K. L. (1988) J. Virol. 62, 3662-3667.
74. Usman, N., Egli, M., & Rich, A. (1992) Nucleic Acids Res. 20, 6695-6699.
75. Verdaguer, N., Aymami, J., Fernández-Forner, D., Fita, I., Coll, M., Huynh-Dinh, T., Igolen, J., & Subirana, J. A. (1991) J. Mol. Biol. 221, 623-635.
76. Wang, A.H.-J., Fujii, S., van Boom, J. H., van der Marel, G. A., van Boeckel, S. A. A., & Rich, A. (1982a) Nature 299, 601-604.
77. Wang, A.H.-J., Fujii, S., van Boom, J. H., & Rich, A. (1982b) Proc. Natl. Acad. Sci. U.S.A. 79, 3968-3972.
78. Westhof, E. (1987) Int. J. Biol. Macromol. 9, 186-192.
79. Westhof, E., Dumas, P., & Moras, D. (1988) Biochimie 70, 145— 165.
80. Wyatt, J. R., & Walker, G. T. (1989) Nucleic Acids Res. 17, 7833-7842.
81. Yanagi, K., Prive, G. G., & Dickerson, R. E. (1990) J. Mol. Biol. 217, 201-214.
82. Yang, J.-H., Usman, N., Chartrand, P., & Cedergren, R. J. (1992) Biochemistry 31, 5005-5009.
83. Yang, W., Hendrickson, W. A., Crouch, R. J., & Satow, Y. (1990) Science 249, 1398-1405.
84. Zimmerman, S. B., & Pheiffer, B. H. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 78-82.