Hybrid oligomer duplexes formed with phosphorothioate DNAs: CD spectra and melting temperatures of S-DNA·RNA hybrids are sequence-dependent but consistent with similar heteronomous conformations

Biochemistry

Volumn 37, Issue 1, 1998, Pages 61-72

  Hashem, Gihan M ^a   Pham, Lanhuong ^a   Vaughan, Marilyn R ^a   Gray, Donald M ^a  

^a UNIVERSITY OF TEXAS AT DALLAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; OLIGODEOXYNUCLEOTIDE PHOSPHOROTHIOATE; RNA;

ARTICLE; BASE PAIRING; CIRCULAR DICHROISM; DNA CONFORMATION; DNA DETERMINATION; DNA RNA HYBRIDIZATION; NUCLEAR OVERHAUSER EFFECT; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA ANALYSIS; RNA CONFORMATION; TEMPERATURE DEPENDENCE;

BASE COMPOSITION; CIRCULAR DICHROISM; DEOXYRIBONUCLEOTIDES; DNA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HETERODUPLEXES; RNA; TEMPERATURE; THERMODYNAMICS; THIONUCLEOTIDES;

EID: 0032488601     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi9713557     Document Type: Article

References (67)

1. Agrawal, S., Mayrand, S. H., Zamecnik, P. C., & Pederson, T. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 1401-1405.
2. Allawi, H. T., & SantaLucia, J., Jr. (1997) Biochemistry 36, 10581-10594.
3. Arnott, S., Chandrasekaran, R., Milane, R. P., & Park, H.-S. (1986) J. Mol. Biol. 188, 631-640.
4. Baum, R. (1994) Chem. Eng. News 72, 21-22.
5. Benevides, J. M., Wang, A. H., Rich, A., Kyogoku, Y., van der Marel, G. A., van Boom, J. H., & Thomas, G. J., Jr. (1986) Biochemistry 25, 41-50.
6. Breslauer, K. J., Frank, R., Blöcker, H., & Marky, L. A. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750.
7. Brown, D. A., Kang, S.-H., Gryaznov, S. M., DeDionisio, L., Heidenreich, O., Sullivan, S., Xu, X., & Nerenberg, M. I. (1994) J. Biol. Chem. 269, 26801-26805.
8. Callahan, D. E., Trapane, T. L., Miller, P. S., Ts'o, P. O. P., & Kan, L.-S. (1991) Biochemistry 30, 1650-1655.
9. Clark, C. L., Cecil, P. K., Singh, D., & Gray, D. M. (1997) Nucl. Acids Res 25, 4098-4105.
10. Cohen, J. S., & Hogan, M. E. (1994) Sci. Am. 271, 76-82.
11. Crooke, R. M., Graham, M. J., Cooke, M. E., & Crooke, S. T. (1995) J. Pharmacol. Exp. Ther. 275, 462-473.
12. Dean, N., McKay, R., Miraglia, L., Howard, R., Cooper, S., Giddings, J., Nicklin, P., Meister, L., Ziel, R., Geiger, T., Muller, M., & Fabbro, D. (1996) Cancer Res. 56, 3499-3507.
13. Ding, D., Gryaznov, S. M., Lloyd, D. H., Chandrasekaran, S., Yao, S., Ratmeyer, L., Pan, Y., & Wilson, W. D. (1996) Nucl. Acids Res. 24, 354-360.
14. Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., & Turner, D. H. (1986) Proc. Natl. Acad. Sci. 83, 9373-9377.
15. González, C., Stec, W., Kobylanska, A., Hogrefe, R. I., Reynolds, M., & James, T. L. (1994) Biochemistry 33, 11062-11072.
16. González, C., Stec, W., Kobylanska, Reynolds, M., & James, T. L. (1995) Biochemistry 34, 4969-4982.
17. Gray, D. M. (1997) Biopolymers, in press.
18. Gray, D. M., Liu, J. J., Ratliff, R. L., & Allen, F. S. (1981) Bioploymers 20, 1337-1382.
19. Gray, D. M., Hung, S. H., & Johnson, K. H. (1995) Methods Enzymol. 246, 19-34.
20. Gray, D. M., & Tinoco, I., Jr. (1970) Biopolymers 9, 223-244.
21. Gray, D. M., & Ratliff, R. L., (1975) Bioploymers 14, 487-498.
22. Gray, G. D., Basu, S., & Wickstrom, E. (1997) Biochem. Pharmacol. 53, 1465-1476.
23. Gupta, R. K., & Yushok, W. D. (1980) Proc. Natl. Acad. Sci. U.S.A. 77, 2487-2491.
24. Gura, T. (1995) Science 270, 575-577.
25. Gutierrez, A. J., Matteucci, M. D., Grant, D., Matsumura, S., Wagner, R. W., & Froehler, B. C. (1997) Biochemistry 36, 743-748.
26. Gyi, J. I., Conn, G. L., Lane, A. N., & Brown, T. (1996) Biochemistry 35, 12538-12548.
27. Hall, K. B., & McLaughlin, L. W. (1991) Biochemistry 30, 10606-10613.
28. Henry, E. R., & Hofrichter, J. (1992) Methods Enzymol. 210, 129-192.
29. Hung, S.-H., Yu, Q., Gray, D. M., and Ratliff, R. L. (1994) Nucl. Acids Res. 22, 4326-4334.
30. Iversen, P. L., Zhu, S., Meyer, A., & Zon, G. (1992) Antisense Res. Dev. 2, 211-222.
31. Johnson, W. C, Jr. (1992) Methods Enzymol. 210, 426-447.
32. Johnson, W. C., Jr. (1994) in Circular Dichroism Principles & Applications (Nakaniski, K., Berova, N., & Woody, R. W., Eds.) pp 523-540, VCH Publishers, Inc., New York.
33. Khaled, Z., Benimetskaya, L., Zeltser, R., Khan, T., Sharima, H. W., Narayanan, R., & Stein, C. A. (1996) Nucl. Acids Res. 24, 737-745.
34. Lesnik, E. A., & Freier, S. M. (1995) Biochemistry 34, 10807-10815.
35. Lima, W. F., & Crooke, S. T. (1997) Biochemistry 36, 390-398.
36. Maltese, J. Y., Sharma, H. W., Vassilen, L., & Narayanan, R. (1995) Nucl. Acids. Res. 23, 1146-1151.
37. Marky, L. A., & Breslauer, K. J. (1987) Biopolymers 26, 1601-1620.
38. Matteucci, M. D, & Wagner, R. W. (1996) Nature 384, 20-22.
39. Monia, B. P., Lesnik, E. A., Gonzalez, C., Lima, W. F., McGee, D., Guinosso, C. J., Kawasaki, A. M., Cook, P. D., & Freier, S. M. (1993) J. Biol. Chem. 268, 14514-14522.
40. Nishizaki, T., Iwai, S., Ohkubo, T., Kojima, C., Nakamura, H., Kyogoku, Y., & Ohtsuka, E. (1996) Biochemistry 35, 4016-4025.
41. Oda, Y., Iwai, S., Ohtsuka, E., Ishikawa, M., Ikehara, M., & Nakamura, H. (1993) Nucl. Acids Res. 21, 4690-4695.
42. Ornstein, R. L., & Fresco, J. R. (1983a) Biopolymers 22, 1979-2000.
43. Ornstein, R. L., & Fresco, J. R. (1983b) Biopolymers 22, 2001-2016.
44. Perez, J. R., Li, Y., Stein, C. A., Majumder, S., Oorschat, A. V., & Narayanan, R. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 5957-5961.
45. Politz, J. C., Taneja, K. L., & Singer, R. H. (1995) Nucl. Acids Res. 23, 4946-4953.
46. Press, W. H., Teukolsky, S. A., Vetterling, W. T., & Flannery, B. P. (1992) Numerical Recipes in C; The Art of Scientific Computing, 2nd Ed., pp 59-70, Cambridge University Press, Cambridge, England.
47. Ratmeyer, L., Vinayak, R., Zhong, Y. Y., Zon, G., & Wilson, W. D. (1994) Biochemistry 33, 5298-5304.
48. Rice, J. S., & Gao, X. (1997) Biochemistry 36, 399-411.
49. Roberts, R. W., & Crothers, D. M. (1992) Science 258, 1463-1466.
50. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York, NY, pp 220-236.
51. Salazar, M., Fedoroff, O. Y., & Reid, B. R. (1996) Biochemistry 35, 8126-8135.
52. SantaLucia, J., Jr., Allawi, H. T., & Seneviratne, P. A. (1996) Biochemistry 35, 3555-3562.
53. Savitzky, A., & Golay, M. J. E. (1964) Anal. Chem. 36, 1627-1639.
54. Steely, H. T., Jr., Gray, D. M., & Ratliff, R. L. (1986) Nucl. Acids Res. 14, 10071-10090.
55. Stein, C. A. (1995) Nat. Med. 1, 1119-1121.
56. Stein, C. A., Subasinghe, C., Shinozuka, K., & Cohen, J. S. (1988) Nucl. Acids Res. 16, 3209-3221.
57. Stein, C. A., & Cheng, Y. C. (1993) Science 261, 1004-1012.
58. Stephenson, M. L., & Zamecnik, P. C. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 285-288.
59. Stull, R. A., Taylor, L. A., & Szoka, F. C., Jr. (1992) Nucl. Acids Res. 20, 3501-3508.
60. Sugimoto, N., Nakano, S., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi, T., Yoneyama, M., & Sasaki, M. (1995) Biochemistry 34, 11211-11216.
61. Sugimoto, N., Nakano, S., Yoneyama, M., & Honda, K. (1996) Nucl. Acids Res. 24, 4501-4505.
62. Temsamani, J., Kubert, M., Tang, J. Y. Padmapriya, A., & Agrawal, S. (1994) Antisense Res. Dev. 4, 35-42.
63. Thierry, A. R., & Dritschilo, A. (1992) Nucl. Acids Res. 20, 5691-5698.
64. Vologodskii, A. V., Amirikyan, B. R., Lyubchenko, Y. L., & Frank-Kamenetskii, M. D. (1984) J. Biomol. Struct. Dyn. 2, 131-148.
65. Wagner, R. W. (1994) Nature 372, 333-335.
66. Zamecnik, P. C., & Stephenson, M. L. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 280-284.
67. Zimmerman, S. B., & Pheiffer, B. H. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 78-82.