Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides: Implications for triplet expansion diseases

Proceedings of the National Academy of Sciences of the United States of America

Volumn 99, Issue 23, 2002, Pages 14700-14705

  Volker J ^a   Makube, N ^b   Plum, G E ^a,c   Klump, H H ^a,b   Breslauer, K J ^a  

^a RUTGERS UNIVERSITY   (United States)

^b UNIVERSITY OF CAPE TOWN   (South Africa)

^c IBET Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; REPETITIVE DNA;

ARTICLE; BASE PAIRING; DNA CONFORMATION; DNA SEQUENCE; ENERGY TRANSFER; ENTHALPY; ENTROPY; PRIORITY JOURNAL; THERMODYNAMICS;

BASE SEQUENCE; CALORIMETRY, DIFFERENTIAL SCANNING; DNA; GENETIC DISEASES, INBORN; HEAT; HUMANS; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HETERODUPLEXES; SPECTROPHOTOMETRY; THERMODYNAMICS; TRINUCLEOTIDE REPEATS;

EID: 0037069430     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.222519799     Document Type: Article

References (70)

1. Cummings, C. J. & Zoghbi, H. Y. (2000) Annu. Rev. Genomics Hum. Genet. 1, 281-328.
2. Ashley, C. T., Jr., & Warren, S. T. (1995) Annu. Rev. Genet. 29, 703-728.
3. Timchenko, L. T. & Caskey, C. T. (1999) Cell Mol. Life Sci. 55, 1432-1447.
4. Wells, R. D. (1996) J. Biol. Chem. 271, 2875-2878.
5. Mitas, M. (1997) Nucleic Acids Res. 25, 2245-2254.
6. McMurray, C. T. (1999) Proc. Natl. Acad. Sci. USA 96, 1823-1825.
7. Pearson, C. E. & Sinden, R. R. (1998) Curr. Opin. Struct. Biol. 8, 321-330.
8. Razin, S. V., Ioudinkova, E. S., Trifonov, E. N. & Scherrer, K. (2001) J. Mol. Biol. 307, 481-486.
9. Bowater, R. P., Rosche, W. A., Jaworski, A., Sinden, R. R. & Wells, R. D. (1996) J. Mol. Biol. 264, 82-96.
10. Ohshima, K., Montermini, L., Wells, R. D. & Pandolfo, M. (1998) J. Biol. Chem. 273, 14588-14595.
11. Ohshima, K. & Wells, R. D. (1997) J. Biol. Chem. 272, 16798-16806.
12. Ohshima, K., Kang, S., Larson, J. E. & Wells, R. D. (1996) J. Biol. Chem. 271, 16773-16783.
13. Ohshima, K., Kang, S. & Wells, R. D. (1996) J. Biol. Chem. 271, 1853-1856.
14. Pearson, C. E. & Sinden, R. R. (1996) Biochemistry 35, 5041-5053.
15. Gacy, A. M., Goellner, G., Juranic, N., Macura, S. & McMurray, C. T. (1995) Cell 81, 533-540.
16. Smith, G. K., Jie, J., Fox, G. E. & Gao, X. (1995) Nucleic Acids Res. 23, 4303-4311.
17. LeProust, E. M., Pearson, C. E., Sinden, R. R. & Gao, X. (2000) J. Mol. Biol. 302, 1063-1080.
18. Pearson, C. E., Wang, Y. H., Griffith, J. D. & Sinden, R. R. (1998) Nucleic Acids Res. 26, 816-823.
19. Mitas, M., Yu, A., Dill, J., Kamp, T. J., Chambers, E. J. & Haworth, I. S. (1995) Nucleic Acids Res. 23, 1050-1059.
20. Mitas, M., Yu, A., Dill, J. & Haworth, I. S. (1995) Biochemistry 34, 12803-12811.
21. Fry, M. & Loeb, L. A. (1994) Proc. Natl. Acad. Sci. USA 91, 4950-4954.
22. Kettani, A., Bouaziz, S., Skripkin, E., Majumdar, A., Wang, W., Jones, R. A. & Patel, D. J. (1999) Struct. Fold. Des. 7, 803-815.
23. Chen, X., Mariappan, S. V., Catasti, P., Ratliff, R., Moyzis, R. K., Laayoun, A., Smith, S. S., Bradbury, E. M. & Gupta, G. (1995) Proc. Natl. Acad. Sci. USA 92, 5199-5203.
24. Ohshima, K., Kang, S., Larson, J. E. & Wells, R. D. (1996) J. Biol. Chem. 271, 16784-16791.
25. Mariappan, S. V., Catasti, P., Silks, L. A., III, Bradbury, E. M. & Gupta, G. (1999) J. Mol. Biol. 285, 2035-2052.
26. Mariappan, S. V., Catasti, P., Chen, X., Ratliff, R., Moyzis, R. K., Bradbury, E. M. & Gupta, G. (1996) Nucleic Acids Res. 24, 784-792.
27. Mariappan, S. V., Silks, L. A., III, Bradbury, E. M. & Gupta, G. (1998) J. Mol. Biol. 283, 111-120.
28. Mariappan, S. V., Silks, L. A., III, Chen, X., Springer, P. A., Wu, R., Moyzis, R. K., Bradbury, E. M., Garcia, A. E. & Gupta, G. (1998) J. Biomol. Struct. Dyn. 15, 723-744.
29. Petruska, J., Arnheim, N. & Goodman, M. F. (1996) Nucleic Acids Res. 24, 1992-1998.
30. Petruska, J., Hartenstine, M. J. & Goodman, M. F. (1998) J. Biol. Chem. 273, 5204-5210.
31. Hartenstine, M. J., Goodman, M. F. & Petruska, J. (2000) J. Biol. Chem. 275, 18382-18390.
32. Gacy, A. M. & McMurray, C. T. (1998) Biochemistry 37, 9426-9434.
33. Yu, A., Barron, M. D., Romero, R. M., Christy, M., Gold, B., Dai, J., Gray, D. M., Haworth, I. S. & Mitas, M. (1997) Biochemistry 36, 3687-3699.
34. Harvey, S. C. (1997) Biochemistry 36, 3047-3049.
35. Völker, J., Klump, H. H. & Breslauer, K. J. (2001) Proc. Natl. Acad. Sci. USA 98, 7694-7699.
36. Gelfand, C. A., Plum, G. E., Mielewczyk, S., Remeta, D. P. & Breslauer, K. J. (1999) Proc. Natl. Acad. Sci. USA 96, 6113-6118.
37. Plum, G. E. (2000) in Current Protocols in Nucleic Acid Chemistry (Wiley, New York), pp. 7.3.1-7.3.17.
38. Snell, F. D. & Snell, C. T. (1972) Colorimetric Methods of Analysis, Including Some Turbidimetric and Nephelometric Methods (Krieger, Huntington, NY).
39. Breslauer, K. J. (1995) Methods Enzymol. 259, 221-242.
40. Breslauer, K. J. (1994) in Methods in Molecular Biology, ed. Agrawal, S. (Humana, Totowa, NJ), Vol. 26, pp. 347-372.
41. Marky, L. A. & Breslauer, K. J. (1987) Biopolymers 26, 1601-1620.
42. Cantor, C. R. & Schimmel, P. R. (1980) Techniques for the Study of Biological Structure and Function (Freeman, San Francisco).
43. Privalov, P. L. & Potekhin, S. A. (1986) Methods Enzymol. 131, 4-51.
44. Privalov, G. P. & Privalov. P. L. (2000) Methods Enzymol. 323, 31-62.
45. Olmsted, M. C., Anderson, C. F. & Record, M. T., Jr. (1991) Biopolymers 31, 1593-1604.
46. Olmsted, M. C. (1996) J. Biomol. Struct. Dyn. 13, 885-902.
47. Senior, M. M., Jones, R. A. & Breslauer, K. J. (1988) Proc. Natl. Acad. Sci. USA 85, 6242-6246.
48. Mills, J. B., Vacano, E. & Hagerman, P. J. (1999) J. Mol. Biol. 285, 245-257.
49. Ferrari, M. E. & Lohman, T. M. (1994) Biochemistry 33, 12896-12910.
50. Goddard, N. L., Bonnet, G., Krichevsky, O. & Libchaber, A. (2000) Phys. Rev. Lett. 85, 2400-2403.
51. Ansari, A., Kuznetsov, S. V. & Shen, Y. (2001) Proc. Natl. Acad. Sci. USA 98, 7771-7776.
52. Ansari, A., Shen, Y. & Kuznetsov, S. V. (2002) Phys. Rev. Lett. 88, 069801.
53. Kuznetsov, S. V., Shen, Y., Benight, A. S. & Ansari, A. (2001) Biophys. J. 81, 2864-2875.
54. Bonnet, G., Krichevsky, O. & Libchaber, A. (1998) Proc. Natl. Acad. Sci. USA 95, 8602-8606.
55. Klump, H. H. (1988) in Biochemical Thermodynamics: Studies in Modern Thermodynamics, ed. Jones, M. N. (Elsevier, Amsterdam), Vol. 8, pp. xi, 403.
56. Breslauer, K. J., Frank, R., Blocker, H. & Marky, L. A. (1986) Proc. Natl. Acad. Sci. USA 83, 3746-3750.
57. Chalikian, T. V., Völker, J., Plum, G. E. & Breslauer, K. J. (1999) Proc. Natl. Acad. Sci. USA 96, 7853-7858.
58. Rouzina, I. & Bloomfield, V. A. (1999) Biophys. J. 77, 3242-3251.
59. Rouzina, I. & Bloomfield, V. A. (1999) Biophys. J. 77, 3252-3255.
60. Marino, J. P., Gregorian, R. S., Jr., Csankovszki, G. & Crothers, D. M. (1995) Science 268, 1448-1454.
61. Barbault, F., Huynh Dinh, T., Paoletti, J. & Lanceloti, G. (2002) J. Biomol. Struct. Dyn. 19, 649-658.
62. Tinoco, I., Jr. (1997) Nucleic Acids Symp. Ser. 36, 49-51.
63. Kim, C. H. & Tinoco, I., Jr. (2000) Proc. Natl. Acad. Sci. USA 97, 9396-9401.
64. Theilleux-Delalande, V., Girard, F., Huynh-Dinh, T., Lancelot, G. & Paoletti, J. (2000) Eur. J. Biochem. 267, 2711-2719.
65. Bush, C. A. (1974) in Basic Principles in Nucleic Acid Chemistry, ed. T'so, P. O. P. (Academic, New York), Vol. 2, pp. 91-169.
66. Plum, G. E., Grollman, A. P., Johnson, F. & Breslauer, K. J. (1995) Biochemistry 34, 16148-16160.
67. Kang, S., Ohshima, K., Shimizu, M., Amirhaeri, S. & Wells, R. D. (1995) J. Biol. Chem. 270, 27014-27021.
68. Kang, S., Jaworski, A., Ohshima, K. & Wells, R. D. (1995) Nat. Genet. 10, 213-218.
69. Jaworski, A., Rosche, W. A., Gellibolian, R., Kang, S., Shimizu, M., Bowater, R. P., Sinden, R. R. & Wells, R. D. (1995) Proc. Natl. Acad. Sci. USA 92, 11019-11023.
70. Moore, H., Greenwell, P. W., Liu, C. P., Arnheim, N. & Petes, T. D. (1999) Proc. Natl. Acad. Sci. USA 96, 1504-1509.