Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides

Russian Chemical Bulletin

Volumn 51, Issue 7, 2002, Pages 1145-1155

  Pyshnyi, D V ^a   Ivanova, E M ^a  

^a INSTITUTE OF CHEMICAL BIOLOGY AND FUNDAMENTAL MEDICINE   (Russian Federation)

Author keywords

Coaxial stacking; Continuous stacking hybridization; Cooperative interaction; DNA duplexes; Thermal stability

Indexed keywords

DINUCLEOTIDE; OLIGODEOXYRIBONUCLEOTIDE;

ARTICLE; BASE PAIRING; DNA DENATURATION; DNA DETERMINATION; DNA HYBRIDIZATION; DNA STRUCTURE; DNA TEMPLATE; ENERGY; MOLECULAR INTERACTION; THERMAL ANALYSIS; THERMODYNAMICS;

EID: 0141833644     PISSN: 10665285     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1020954307319     Document Type: Article

References (44)

1. S. Parinov, V. Barsky, G. Yershov, E. Kirillov, E. Timofeev, A. Belgovskiy, and A. Mirzabekov, Nucleic Acids Res., 1996, 24, 2998.
2. R. Maldonado-Rodriguez, M. Espinosa-Lara, P. Loyola-Abitia, W. G. Beattie, and K. L. Beattie, Molecular Biotechnology, 1999, 11, 13.
3. I. V. Kutyavin, M. A. Podyminogin, Yu. N. Bazhina, O. S. Fedorova, D. G. Knorre, A. S. Levina, S. V. Mamayev, and V. F. Zarytova, FEBS Lett., 1988, 238, 35.
4. D. V. Pyshnyi, S. G. Lokhov, E. M. Ivanova, and V. F. Zarytova, Bioorg. Khim., 1998, 24, 201 [Russ. J. Bioorg. Chem., 1998, 24 (Engl. Transl.)].
5. A. Adina-zada and O. S. Fedorova, Bioorg. Khim., 1995, 21, 703 [Russ. J. Bioorg. Chem., 1995, 21 (Engl. Transl.)].
6. M. I. Dobrikov, S. A. Gaidamakov, A. A. Koshkin, and V. V. Vlassov, Dokl. Akad. Nauk, 1996, 351, 687 [Dokl. Chem., 1996 (Engl. Transl.)].
7. Z. A. Sergeeva, A. G. Venyaminova, and V. F. Zarytova, Nucleosides Nucleotides, 1998, 17, 2153.
8. J. Kieleczawa, J. J. Dunn, and F. W. Studier, Science, 1992, 258, 1787.
9. D. G. Knorre, D. V. Pyshnyi, E. M. Ivanova, A. A. Bondar', I. V. Morozov, N. P. Mertvetsov, and V. F. Zarytova, Dokl. Akad. Nauk, 1996, 350, 119 [Dokl. Chem., 1996 (Engl. Transl.)].
10. M. J. Engler and C. C. Richardson, in The Enzymes, Ed. P. D. Boyer, Academic Press, New York, 1982, 15, 3.
11. D. V. Pyshnyi, A. A. Krivenko, S. G. Lokhov, E. M. Ivanova, G. M. Dymshits, and V. F. Zarytova, Bioorg. Khim., 1998, 24, 25 [Russ. J. Bioorg. Chem., 1998, 24 (Engl. Transl.)].
12. J. Brams, A. M. Michelson, and K. E. van Hold, J. Mol. Biol, 1966, 15, 467.
13. E. R. Kandimalla, A. Manning, C. Lathan, R. A. Byrn, and S. Agrawal, Nucleic Acids Res., 1995, 23, 3578.
14. T. V. Abramova, V. V. Gorn, I. V. Kutyavin, A. V. Lebedev, S. G. Lokhov, and M. A. Podyminogin, Dokl. Akad. Nauk, 1990, 315, 1485 [Dokl. Chem., 1990 (Engl. Transl.)].
15. D. V. Pyshnyi, I. A. Pyshnaya, S. G. Lokhov, E. M. Ivanova, and V. F. Zarytova, Bioorg. Khim., 1995, 21, 709 [Russ. J. Bioorg. Chem., 1995, 21 (Engl. Transl.)].
16. M. J. Lane, T. Paner, I. Kashin, B. D. Faldasz, B. Li, F. J. Gallo, and A. S. Benight, Nucleic Acids Res., 1997, 25, 611.
17. D. H. Mathews, J. Sabina, M. Zuker, and D. H. Turner, J. Mol. Biol., 1999, 288, 911.
18. A. E. Walter, D. H. Turner, J. Kim, M. H. Lyttle, P. Muller, D. H. Mathews, and M. Zuker, Proc. Natl. Acad. Sci. USA, 1994, 91, 9218.
19. A. E. Walter and D. H. Turner, Biochemistry, 1994, 33, 12715.
20. L. A. Marky and K. J. Breslauer, Biopolymers, 1987, 26, 1601.
21. M. Zhong and N. R. Kallenbach, J. Mol. Biol., 1993, 230, 766.
22. S. G. Lokhov, A. A. Koshkin, I. V. Kutyavin, M. P. Mityakin, M. A. Podyminogin, and A. V. Lebedev, Bioorg. Khim., 1995, 21, 197 [Russ. J. Bioorg. Chem., 1995, 21 (Engl. Transl.)].
23. V. V. Koval, N. A. Lokteva, S. L. Karnaukhova, and O. S. Fedorova, J. Biomol. Struct. Dyn., 1999, 17, 259.
24. P. V. Riccelli, F. Merante, K. T. Leung, S. Bortolin, R. L. Zastawny, R. Janeczko, and A. S. Benight, Nucleic Acids Res., 2001, 29, 996.
25. V. A. Vasiliskov, D. V. Prokopenko, and A. D. Mirzabekov, Nucleic Acids Res., 2001, 29, 2303.
26. D. V. Pyshnyi, I. A. Pyshnaya, A. S. Levina, E. L. Goldberg, V. F. Zarytova, D. G. Knorre, and E. M. Ivanova, J. Biomol. Struct. Dyn., 2001, 19.
27. Handbook of Biochemistry and Molecular Biology: Nucleic Acids, Ed. G. D. Fasman, CRC Press, Cleveland, 1975, 1, 589.
28. D. V. Pyshnyi, S. G. Lokhov, V. N. Sil'nikov, G. V. Shishkin, E. M. Ivanova, and V. F. Zarytova, Bioorg. Khim., 1999, 25, 40 [Russ. J. Bioorg. Chem., 1999, 25 (Engl. Transl.)].
29. S. G. Lokhov and D. V. Pyshnyi, FEBS Lett., 1997, 420, 134.
30. M. Petersheim and D. H. Turner, Biochemistry, 1983, 22, 256.
31. J. Norberg and L. Nilsson, Biophysical J., 1995, 69, 2277.
32. I. Hirao, G. Kawai, S. Yoshizawa, Y. Nishimura, H. Ishido, K. Watanabe, and K. Miura, Nucleic Acids Res., 1994, 22, 576.
33. A. V. Fotin, A. L. Drobyshev, D. Y. Proudnikov, A. N. Perov, and A. D. Mirzabekov, Nucleic Acids Res., 1998, 26, 1515.
34. T. Xia, J. SantaLucia, Jr., M. E. Burkard, R. Kierzek, S. J. Schroeder, X. Jiao, C. Cox, and D. H. Turner, Biochemistry, 1998, 37, 14719.
35. K. J. Breslauer, R. Frank, H. Blocker, and L. A. Marky, Proc. Natl. Acad. Sci. USA, 1986, 83, 3746.
36. J. Santa Lucia, Proc. Natl. Acad. Sci. USA, 1998, 95, 1460.
37. D. J. Patel and C. W. Hilbers, Biochemistry, 1975, 14, 2651.
38. A. Yu. Denisov, T. V. Maltseva, A. Sandstrom, D. V. Pyshnyi, E. M. Ivanova, V. F. Zarytova, and J. Chattopadhyaya, J. Biomol. Struct. Dyn., 1997, 14, 809.
39. K. M. Guckian, B. A. Schweitzer, R. X. -F. Ren, C. J. Sheils, D. C. Tahmassebi, and E. T. Kool, J. Am. Chem. Soc., 2000, 122, 2213.
40. W. Saenger, Principles of Nucleic Acid Structure, Springer-Verlag, New York - Berlin - Heidelberg - Tokyo, 1984.
41. A. Aymami, M. Coll, G. A. van der Marel, J. H. van Boom, A. H.-J. Wang, and A. Rich, Proc. Natl. Acad. Sci. USA, 1990, 87, 2526.
42. J. M. Pieters, R. M. Mans, H. van der Elst, G. A. van der Marel, J. H. van Boom, and C. Altona, Nucleic Acids Res., 1989, 17, 4551.
43. C. Roll, C. Ketterle, V. Faibis, G. V. Fazakerley, and Y. Boulard, Biochemistry, 1998, 37, 4059.
44. S. Bommarito, N. Peyret, and J. SantaLucia, Jr., Nucleic Acids Res., 2000, 28, 1929.