Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson - Crick base pairs

Biochemistry

Volumn 37, Issue 42, 1998, Pages 14719-14735

  Xia, Tianbing ^a   SantaLucia Jr , John ^b   Burkard, Mark E ^a   Kierzek, Ryszard ^c   Schroeder, Susan J ^a   Jiao, Xiaoqi ^a   Cox, Christopher ^a   Turner, Douglas H ^a  

^a UNIVERSITY OF ROCHESTER   (United States)

^b WAYNE STATE UNIVERSITY   (United States)

^c INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA;

ARTICLE; BASE PAIRING; OPTICAL ROTATION; PHYSICAL MODEL; PRIORITY JOURNAL; PROTEIN PURIFICATION; RNA STRUCTURE; RNA SYNTHESIS; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

BASE PAIRING; BASE SEQUENCE; DATABASES, FACTUAL; HYDROGEN BONDING; LINEAR MODELS; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HETERODUPLEXES; RNA; THERMODYNAMICS;

EID: 0032552882     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi9809425     Document Type: Article

References (105)

1. Turner, D. H., Sugimoto, N., and Freier, S. M. (1988) Annu. Rev. Biophys. Biophys. Chem. 17, 167-192.
2. Michel, F., and Westhof, E. (1990) J. Mol. Biol. 216, 585-610.
3. Sugimoto, N., Kierzek, R., and Turner, D. H. (1988) Biochemistry 27, 6384-6392.
4. Bevilacqua, P. C., and Turner, D. H. (1991) Biochemistry 30, 10632-10640.
5. Pyle, A. M., and Cech, T. R. (1991) Nature 350, 628-631.
6. Li, Y., Bevilacqua, P. C., Mathews, D. H., and Turner, D. H. (1995) Biochemistry 34, 14394-14399.
7. Gluick, T. C., and Draper, D. (1994) J. Mol. Biol. 241, 246-262.
8. Borer, P. N., Dengler, B., Tinoco, I., Jr., and Uhlenbeck, O. C. (1974) J. Mol. Biol. 86, 843-853.
9. Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., and Turner, D. H. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 9373-9377.
10. Gray, D. (1997) Biopolymers 42, 783-793.
11. Gray, D. (1997) Biopolymers 42, 795-810.
12. Kierzek, R., Caruthers, M. H., Longfellow, C. E., Swinton, D., Turner, D. H., and Freier, S. M. (1986) Biochemistry 25, 7840-7846.
13. Goldstein, R., and Benight, A. (1992) Biopolymers 32, 1679-1693.
14. Gray, D., and Tinoco, I., Jr. (1970) Biopolymers 9, 223-244.
15. Allawi, H. T., and SantaLucia, J., Jr. (1997) Biochemistry 36, 10581-10594.
16. SantaLucia, J., Jr. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 1460-1465.
17. Sugimoto, N., Honda, K., and Sasaki, M. (1994) Nucleosides Nucleotides 13, 1311-1317.
18. Sugimoto, N., Nakano, S., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi, T., Yoneyama, M., and Sasaki, M. (1995) Biochemistry 34, 11211-11216.
19. Beaucage, S. L., and Caruthers, M H. (1981) Tetrahedron Lett. 22, 1859-1863.
20. McBride, L. J., and Caruthers, M. H. (1983) Tetrahedron Lett. 24, 245-249.
21. Usman, N., Ogilvie, K. K., Jiang, M.-V., and Cedergren, R. (1987) J. Am. Chem. Soc. 109, 7845-7854.
22. Wincott, F., DiRenzo, A., Shaffer, C., Grimm, S., Tracz, D., Workman, C., Sweedler, D., Gonzalez, C., Scaringe, S., and Usman, N. (1995) Nucleic Acids Res. 23, 2677-2684.
23. Stawinski, J., Strömberg, R., Thelin, M., and Westman, E. (1988) Nucleosides Nucleotides 7, 779-782.
24. Chou, S.-H., Flynn, P., and Reid, B. (1989) Biochemistry 28, 2422-2435.
25. Borer, P. N. (1975) in Handbook of Biochemistry and Molecular Biology: Nucleic Acids (Fasman, G. D., Ed.) 3rd ed., Vol. I, p 589, CRC Press, Cleveland, OH.
26. Richards, E. G. (1975) in Handbook of Biochemistry and Molecular Biology: Nucleic Acids (Fasman, G. D., Ed.) 3rd ed., Vol. I, p 197, CRC Press, Cleveland, OH.
27. Peritz, A. E., Kierzek, R., Sugimoto, N., and Turner, D. H. (1991) Biochemistry 30, 6428-6436.
28. Albergo, D. D., Marky, L. A., Breslauer, K. J., and Turner, D. H. (1981) Biochemistry 20, 1409-1413.
29. Petersheim, M., and Turner, D H. (1983) Biochemistry 22, 256-263.
30. McDowell, J. A., and Turner, D. H. (1996) Biochemistry 35, 14077-14089.
31. Cantor, C. R., and Schimmel, P. R. (1980) Biophysical Chemistry, Part III, W. H. Freeman & Co., San Francisco, CA.
32. SantaLucia, J., Jr. (1991) Ph.D. Thesis, University of Rochester, New York.
33. SantaLucia, J., Jr., Kierzek, R., and Turner, D. H. (1991) J. Am. Chem. Soc. 113, 4313-4322.
34. Xia, T., McDowell, J. A., and Turner, D. H. (1997) Biochemistry 36, 12486-12497.
35. Bevington, P. R., and Robinson, D. K. (1992) Data Reduction and Error Analysis for the Physical Sciences, 2nd ed., McGraw-Hill, New York.
36. Meyer, S. L. (1975) Data Analysis for Scientists and Engineers, Wiley, New York.
37. Krug, R. R., Hunter, W. G., and Grieger, R. A. (1976) J. Phys. Chem. 80, 2335-2341.
38. Snedecor, G. W., and Cochran, W. G. (1982) in Statistical Methods, 7th ed., p 189, The Iowa State University Press, Ames, IA.
39. SantaLucia, J., Jr., and Turner, D. H. (1997) Biopolymers 44, 309-319.
40. Wilson, E. B., Jr. (1952) An Introduction to Scientific Research, McGraw-Hill, New York.
41. Pyle, A. M., Moran, S., Strobel, S. A., Chapman, T., Turner, D. H., and Cech, T. R. (1994) Biochemistry 33, 13856-13863.
42. Narlikar, G. J., Khosla, M., Usman, N., and Herschlag, D. (1997) Biochemistry 36, 2465-2477.
43. Gralla, J., and Crothers, D. M. (1973) J. Mol. Biol. 73, 497-511.
44. Cantor, C. R., and Tinoco, I., Jr. (1965) J. Mol. Biol. 13, 65-77.
45. Cantor, C. R., Jaskunas, S. R., and Tinoco, I., Jr. (1966) J. Mol. Biol. 20, 39-62.
46. Lewis, G. N., and Randall, M. (1961) Thermodynamics, 2nd ed., McGraw-Hill, New York.
47. Finkelstein, A. V., and Janin, J. (1989) Protein Eng. 3, 1-3.
48. Williams, D. H., Cox, J. P. L., Doig, A. J., Gardner, M., Gerhard, U., Kaye, P. T., Lal, A. R., Nicholls, I. A., Salter, C. J., and Mitchell, R. C. (1991) J. Am. Chem. Soc. 113, 7020-7030.
49. Bailey, W. F., and Monahan, A. S. (1978) J. Chem. Educ. 55, 489-493.
50. Seber, G. A. F. (1977) Linear Regression Analysis, John Wiley & Sons, Inc., New York.
51. Neter, J., Wasserman, W., and Kutner, M. H. (1985) Applied Statistical Models, 2nd ed., Richard D. Irwin, Inc., Homewood, IL.
52. Press, W. H., Teukolsky, S. A., Vetterling, W. T., and Flannery, B. P. (1992) Numerical Recipes in C, 2nd ed., Cambridge University Press, New York.
53. Wolfram, S. (1996) MATHEMATICA version 3.0, Wolfram Research, Inc.
54. SantaLucia, J., Jr., Allawi, H. T., and Seneviratne, P. A. (1996) Biochemistry 35, 3555-3562.
55. SAS Institute Inc. (1990) Cary, NC.
56. Freier, S. M., Burger, B. J., Alkema, D., Neilson, T., and Turner, D. H. (1983) Biochemistry 22, 6198-6206.
57. Freier, S. M., Alkema, D., Sinclair, A., Neilson, T., and Turner, D. H. (1985) Biochemistry 24, 4533-4539.
58. Hickey, D. R., and Turner, D. H. (1985) Biochemistry 24, 2086-2094.
59. Turner, D. H., and Bevilacqua, P. C. (1993) in The RNA World (Gesteland, R. F., and Atkins, J. F., Eds.) Cold Spring Harbor Laboratory Press, New York.
60. Turner, D. H. (1999) in Nucleic Acids: Structure, Properties, and Functions (Bloomfield, V. A., Crothers, D. M., and Tinoco, I., Jr., Eds.) University Science Books, Mill Valley, CA.
61. Doktycz, M. J., Morris, M. D., Dormady, S. J., Beattie, K. L., and Jacobson, K. B. (1995) J. Biol. Chem. 270, 8439-8445.
62. Wada, A., Yubuki, S., and Husimi, Y. (1980) Crit. Rev. Biochem. 9, 87-144.
63. Gotoh, O. (1983) Adv. Biophys. 16, 1-52.
64. Wartell, R. M., and Benight, A. S. (1985) Phys. Rep. 126, 67-107.
65. Schmitz, M., and Steger, G. (1992) Comput. Appl. Biosci. 8, 389-399.
66. Bloomfield, V. A., Crothers, D. M., and Tinoco, I., Jr. (1974) Physical Chemistry of Nucleic Acids, Harper and Row, New York.
67. Poland, D., and Scheraga, H. (1970) Theory of Helix-Coil Transitions in Biopolymers, Academic Press, New York.
68. Poland, D. (1978) Cooperative Equilibria in Physical Biochemistry, Clarendon Press, Oxford, U.K.
69. Steger, G. (1994) Nucleic Acids Res. 22, 2760-2768.
70. Watson, J. D., Hopkins, N. H., Roberts, J. W., Steitz, J. A., and Weiner, A. M. (1987) Molecular Biology of the Gene, Benjamin Cummings, Inc., Menlo Park, CA.
71. Lewin, B. (1997) Genes VI, Oxford University Press, Oxford, U.K.
72. Gesteland, R. F., and Atkins, J. F. (1993) The RNA World, Cold Spring Harbor Laboratory Press, New York.
73. Freier, S. M., Sugimoto, N., Sinclair, A., Alkema, D., Neilson, T., Kierzek, R., Caruthers, M. H., and Turner, D. H. (1986) Biochemistry 25, 3214-3219.
74. Turner, D. H., Sugimoto, N., Kierzek, R., and Dreiker, S. D. (1987) J. Am. Chem. Soc. 109, 3783-3785.
75. Martin, F. H., Castro, M. M., Aboul-ela, F., and Tinoco, I., Jr. (1985) Nucleic Acids Res. 13, 8927-8938.
76. Aboul-ela, F., Koh, D., Tinoco, I., Jr., and Martin, F. H. (1985) Nucleic Acids Res. 13, 4811-4824.
77. Kawase, Y., Iwai, S., Inoue, H., Miura, K., and Ohtsuka, E. (1986) Nucleic Acids Res. 14, 7727-7736.
78. Gaffney, B. L., Marky, L. A., and Jones, R. A. (1984) Tetrahedron 40, 3-13.
79. Serra, M., Barnes, T., Betschart, K., Gutierrez, M. J., Sprouse, K. J., Riley, C. K., Stewart, L., and Temel, R. E. (1997) Biochemistry 36, 4844-4851.
80. Wu, M., McDowell, J. A., and Turner, D. H. (1995) Biochemistry 34, 3204-3211.
81. SantaLucia, J., Jr., and Turner, D. H. (1993) Biochemistry 32, 12612-12623.
82. Wu, M., and Turner, D. H. (1996) Biochemistry 35, 9677-9689.
83. Wu, M., SantaLucia, J., Jr., and Turner, D. H. (1997) Biochemistry 36, 4449-4460.
84. McDowell, J. A., He, L., Chen, X., and Turner, D. H. (1997) Biochemistry 36, 8030-8038.
85. Wang, S., and Kool, E. T. (1995) Biochemistry 34, 4125-4132.
86. Vologodskii, A. V., Amirikyan, B. R., Lyubchenko, Y. L., and Frank-Kamenetskii, M. D. (1984) J. Biomol. Struct. Dyn. 2, 131-148.
87. Sugimoto, N., Kierzek, R., and Turner, D. H. (1987) Biochemistry 26, 4554-4558.
88. Burkard, M. E., Turner, D. H., and Tinoco, I., Jr. (1998) in The RNA World II (Cech, T. R., Gesteland, R. F., and Atkins, J. F., Eds.) Cold Spring Harbor Laboratory Press, New York (in press).
89. Williams, A. P., Longfellow, C. E., Freier, S. M., Kierzek, R., and Turner, D. H. (1989) Biochemistry 28, 4283-4291.
90. Manning, G. (1978) Q. Rev. Biophvs. 11, 179-246.
91. Olmsted, M. C., Anderson, C. F., and Record, M. T., Jr. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 7766-7770.
92. Walter, A. E., Turner, D. H., Kim, J., Lyttle, M. H., Müller, P., Mathews, D. H., and Zuker, M. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 9218-9222.
93. Serra, M., and Turner, D. H. (1995) Methods Enzymol. 259, 242-261.
94. Mathews, D. H., Andre, T. C., Kim, J., Turner, D. H., and Zuker, M. (1998) in Molecular Modeling of Nucleic Acids (Leontis, N. B., SantaLucia, J., Eds.) ACS Symposium Series 682, American Chemical Society, Washington, D.C., pp 246-257.
95. Walter, A. E., and Turner, D. H. (1994) Biochemists 33, 12715-12719.
96. Zuker, M., and Stiegler, P. (1981) Nucleic Acids Res. 9, 133-148.
97. Zuker, M. (1989) Science 244, 48-52.
98. Freier, S. M., Sinclair, A., Neilson, T., and Turner, D. H. (1985) J. Mol. Biol. 185, 645-647.
99. Hall, K., and McLaughlin, L. W. (1991) Biochemistry 30, 10606-10613.
100. He, L., Kierzek, R., SantaLucia, J., Jr., Walter, A. E., and Turner, D. H. (1991) Biochemistry 30, 11124-11132.
101. Longfellow, C. E., Kierzek, R., and Turner, D. H. (1990) Biochemistry 29, 278-285.
102. Sugimoto, N., Kierzek, R., Freier, S. M., and Turner, D. H. (1986) Biochemistry 25, 5755-5759.
103. Nelson, J. W., Martin, F. H., and Tinoco, I., Jr. (1981) Biopolymers 20, 2509-2531.
104. Freier, S. M., Petersheim, M., Hickey, D. R., and Turner, D. H. (1984) J. Biomol. Struct. Dyn. 1, 1229-1242.
105. Walter, A. E., Wu, M., and Turner, D. H. (1994) Biochemistry 33, 11349-11354.