Thermodynamic analysis of conformational transitions in oligonucleotide complexes in presence of Na+ and Mg2+ ions, using "staggering zipper" model

Biopolymers

Volumn 86, Issue 1, 2007, Pages 32-41

  Blagoi, Yurii ^a   Zozulya, Victor ^a   Egupov, Sergey ^a   Onishchenko, Vladimir ^a   Gladchenko, Galina ^a  

^a B VERKIN INSTITUTE FOR LOW TEMPERATURE PHYSICS AND ENGINEERING   (Ukraine)

Author keywords

"staggering zipper" model; Conformational transitions; Metal ions; Nucleation parameter; Oligonucleotide

Indexed keywords

CONFORMATIONS; MELTING; METAL IONS; MOLECULAR DYNAMICS; NUCLEATION;

CONFORMATIONAL TRANSITIONS; MELTING CURVES; STAGGERING ZIPPER MODEL;

OLIGONUCLEOTIDES;

MAGNESIUM ION; OLIGOMER; OLIGONUCLEOTIDE; SODIUM ION;

ARTICLE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; MATHEMATICAL COMPUTING; MOLECULAR MODEL; THERMODYNAMICS; TRANSITION TEMPERATURE;

CATIONS; MAGNESIUM; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; SODIUM; TEMPERATURE; THERMODYNAMICS;

EID: 34248187479     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.20702     Document Type: Article

References (49)

1. Frank-Kamenetskii, M. D.; Mirkin, S. M. Annu Rev Biochem 1997, 64, 65-95.
2. Crooke, S. T. Med Res Rev 1996, 16, 319-344.
3. Goodchild, J. Bioconjugate Chem 1990, 1, 165-187.
4. Plum, G. E. Biopolymers 1998, 44, 241-256.
5. Roberts, R. W.; Crothers, D. M. Proc Natl Acad Sci USA 1996, 93, 4320-4325.
6. Pilch, D. S.; Levenson, C.; Shafer, R. H. Proc Natl Acad Sci USA 1990, 87, 1942-1946.
7. Craig, M. E.; Crothers, D. M.; Doty, P. J Mol Biol 1971, 62, 383-401.
8. Plum, G. E.; Park, Y.; Singleton, S. F.; Dervan, P. B.; Breslauer, K. J. Proc Natl Acad Sci USA 1990, 87, 9436-9440.
9. Hogget, J. G.; Maass, G. Ber Bunsenges Phys Chem 1971, 75, 45-54.
10. Plum, G. E.; Breslauer, K. J. J Mol Biol 1995, 248, 679-695.
11. Eigen, M.; Pörschke, D. J Mol Biol 1970, 53, 123-141.
12. Pörschke, D. Biopolymers 1971, 10, 1989-2013.
13. Pörschke, D.; Eigen, M. J Mol Biol 1971, 62, 361-381.
14. Hopkins, H. P.; Hamilton, D. D.; Wilson, D.; Zon, G. J Phys Chem 1993, 97, 6555-6563.
15. Kibler-Herzog, L.; Kell, B.; Zon, G.; Shinozuka, K.; Mizan, S.; Wilson, W. D. Nucleic Acids Res 1990, 18, 3545-3555.
16. Wilson, W. D.; Hopkins, H. P.; Mizan, S.; Zon, G. J Am Chem Soc 1994, 116, 3607-3608.
17. Applequist, J.; Damle V. J Chem Phys 1963, 39, 2719-3555.
18. Applequist, J.; Damle V. J Am Chem Soc 1965, 87,7, 1450-1458.
19. Zimm, B. H. J Chem Phys 1960, 33, 1349-1356.
20. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1987.
21. Blagoi, Y. P.; Zozulya, V. N.; Egupov, S. A.; Ryazanova, O. A.; Shcherbakova, A. S. Biophys Bull (Visnik Khar Univ) 2001, 2, 10-16.
22. Blagoi, Y. P.; Zozulya, V. N.; Egupov, S. A.; Ryazanova, O. A.; Shcherbakova, A. S. Biophys Bull (Visnik Khar Univ) 2002, 1, 5-10.
23. Blagoi, Y. P.; Zozulya, V. N.; Shcherbakova, A. S. Biophys Bull (Visnik Khar Univ) 1998, 1, 21-32.
24. Massoulie, J. Eur J Biochem 1968, 3, 428-438.
25. SantaLucia, J., Jr. Proc Natl Acad Sci USA 95: 1460-1465, 1998.
26. Stevens, C. L.; Felsenfeld, G. Biopolymers 1964, 2, 293-314.
27. Kankia, B. I. Biophys Chem 2003, 104, 643-654.
28. Chalikian, T. V.; Völker, J.; Plum, G. E.; Breslauer, K. J. Proc Natl Acad Sci USA 1999, 96, 7853-7858.
29. Riley, M.; Making, B.; Chamberlin, M. J Mol Biol 1966, 20, 359-389.
30. Klump, H. H. Can J Chem 1988, 66, 804-811.
31. Hopkins, H. P.; Hamilton, D. D.; Wilson, W. D.; Campbell, J.; Fumero, J. J Chem Thermodyn 1993, 25, 111-126.
32. Zozulya, V. N.; Nesterov, A. B.; Ryazanova, O. A.; Blagoi, Y. P. Int J Biol Macromol 2003, 33, 183-191.
33. Sugimoto, N.; Tanaka, A.; Shintani, Y.; Sasaki, M. Chem Lett 1991, 1, 9-12.
34. Nguyen, H.-K.; Fournier, O.; Asseline, U.; Dupret, D.; Thuong, N. T. Nucleic Acids Res 1999, 27, 1492-1498.
35. Seela, F.; Leonard, P. Helv Chim Acta 1997, 80, 1301-1315.
36. Pilch, D. S.; Brousseau, R.; Shafer, R. H. Nucleic Acids Res 1990, 18, 5743-5750.
37. Sugimoto, N.; Wu, P.; Hara, H.; Kawamoto, Y. Biochemistry 2001, 40, 9396-9405.
38. Blagoi, Y. P.; Sorokin, V. A.; Valeev, V. A.; Khomenko, S. A.; Gladchenko, G. O. Biopolymers 1978, 17, 1103-1118.
39. Tan, Z. J.; Chen, S. J. Biophys J 2006, 90, 1175-1190.
40. Pilch, D. S.; Kirolos, M. A.; Breslauer, K. J. Biochemistry 1995, 34, 16107-16124.
41. Sugimoto, N.; Nakano, S.; Yoneyama, M.; Honda, K. Nucleic Acids Res 1996, 24, 4501-4505.
42. Pörschke, D.; Uhlenbeck, O. C.; Martin, F. H. Biopolymers 1973, 12, 1313-1335.
43. Vesnaver, G.; Breslauer, K. J. Proc Natl Acad Sci USA 1991, 88, 3669-3573.
44. Kamiya, M.; Torigoe, H.; Shindo, H.; Sarai A. J Am Chem Soc 1996, 118, 4532-4538.
45. Cantor, C. R.; Schimmel, P. R. Biophysical Chemistry; W.H. Freeman and Company: San Francisco, 1980; Part III.
46. SantaLucia, J., Jr.; Allawi, H. T.; Ananta Senevirante, P. Biochemistry 1996, 35, 3555-3562.
47. Scheffler, I. E.; Elson, E. L.; Baldwin, R. L. J Mol Biol 1970, 48, 145-171.
48. Appleby, D. W.; Kallenbach, N. R. Biopolymers 1973, 12, 2093-2119.
49. Delisi, C.; Crothers, D. M. Proc Natl Acad Sci USA 1971, 68, 2682-2685.