Is hairpin formation in single-stranded polynucleotide diffusion- controlled?

Journal of Physical Chemistry B

Volumn 109, Issue 26, 2005, Pages 12982-12989

  Ansari, Anjum ^a,b   Kuznetsov, Serguei V ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^b University of Illinois at Chicago   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIZATION; HAIRPIN STRUCTURES; ISOSTABILITY; RELAXATION TIMES;

DIFFUSION; DNA; GLYCEROL; OLIGOMERS; REACTION KINETICS; RNA; VISCOSITY;

BIOPOLYMERS;

GLYCEROL; SINGLE STRANDED DNA; SOLVENT;

ARTICLE; CHEMISTRY; CONFORMATION; DIFFUSION; SPECTROSCOPY; TEMPERATURE;

DIFFUSION; DNA, SINGLE-STRANDED; GLYCEROL; NUCLEIC ACID CONFORMATION; SOLVENTS; SPECTRUM ANALYSIS; TEMPERATURE;

EID: 22344446165     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp044838a     Document Type: Article

References (69)

1. Dai, X.; Greizerstein, M. B.; Nadas-Chinni, K.; Rothman-Denes, L. B. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 2174.
2. Lilley, D. M. Nucleic Acids Res. 1981, 9, 1271.
3. Roth, D. B.; Menetski, J. P.; Nakajima, P. B.; Bosma, M. J.; Gellert, M. Cell 1992, 70, 983.
4. Tang, J. Y.; Temsamani, J.; Agrawal, S. Nucleic Acids Res. 1993, 21, 2729.
5. Bonnet, G.; Tyagi, S.; Libchaber, A.; Kramer, F. R. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 6171.
6. Varani, G. Annu. Rev. Biophys. Biomol. Struct. 1995, 24, 379.
7. Uhlenbeck, O. C. Nature 1990, 346, 613.
8. Marino, J. P.; Gregorian, R. S.; Csankovszki, G.; Crothers, D. M. Science 1995, 268, 1448.
9. Draper, D. E. J. Mol. Biol. 1999, 293, 255.
10. Rupert, P. B.; Massey, A. P.; Sigurdsson, S. T.; Ferre-D'Amare, A. R. Science 2002, 298, 1421.
11. Lilley, D. M. Trends Biochem. Sci. 2003, 28, 495.
12. Cech, T. R.; Zaug, A. J.; Grabowski, P. J. Cell 1981, 27, 487.
13. Thirumalai, D.; Woodson, S. A. Acc. Chem. Res. 1996, 29, 433.
14. Cantor, C. R.; Schimmel, P. R. The Behavior of Biological Macromolecules; W. H. Freeman and Company: New York, 1980.
15. Shen, Y.; Kuznetsov, S. V.; Ansari, A. J. Phys. Chem. B. 2001, 105, 12202.
16. Ansari, A.; Kuznetsov, S. V. Hairpin Formation in Polynucleotides: A Simple Folding Problem? In Biological Nanostructures and Applications of Nanostructures in Biology: Electrical, Mechanical and Optical Properties; Stroscio, M. A., Dutta, M., Eds.; Kluwer Academic Publishers: New York, 2004.
17. Gralla, J.; Crothers, D. M. J. Mol. Biol. 1973, 73, 497.
18. Porschke, D. Biophys. Chem. 1974, 1, 381.
19. Bonnet, G.; Krichevsky, O.; Libchaber, A. Proc. Natl Acad. Sci. U.S.A. 1998, 95, 8602.
20. Ansari, A.; Kuznetsov, S. V.; Shen, Y. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 7771.
21. Wang, J. C.; Davidson, N. J. Mol. Biol. 1966, 19, 469.
22. Wang, J. C.; Davidson, N. J. Mol. Biol. 1966, 15, 111.
23. Wang, J. C.; Davidson, N. Cold Spring Harbor Symp. Quant. Biol. 1968, 33, 409.
24. Wallace, M. I.; Ying, L.; Balasubramanian, S.; Klenerrnan, D. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5584.
25. Bonner, G.; Klibanov, A. M. Biotechnol. Bioeng.2000, 68, 339.
26. Jacob, M.; Schindler, T.; Balbach, J.; Schmid, F. X. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 5622.
27. Plaxco, K. W.; Baker, D. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 13591.
28. Qiu, L.; Hagen, S. J. J. Am. Chem. Soc. 2004, 126, 3398.
29. Ansari, A.; Shen, Y.; Kuznetsov, S. V. Phys. Rev. Lett. 2002, 88, 069801.
30. Newman, A. A. Glycerol; CRC Press: Cleveland, OH, 1968.
31. Chalikian, T. V.; Volker, J.; Plum, G. E.; Breslauer, K. J. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 7853.
32. Rouzina, I.; Bloomfield, V. A. Biophys. J. 1999, 77, 3242.
33. Hofrichter, J. Laser Temperature-Jump Methods for Studying Folding Dynamics. In Protein Structure, Stability, and Folding; Murphy, K. P., Ed.; Methods in Molecular Biology 168; Humana Press: Totowa, NJ, 2001.
34. Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P. Science 1983, 220, 671.
35. Press, W. H.; Flannery, B. P.; Teukolsky, S. A. Numerical Recipes: The Art of Scientific Computing; Cambridge University Press: Cambridge, U. K., 1986.
36. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J. Chem. Phys. 1953, 21, 1087.
37. Kuznetsov, S. V.; Shen, Y.; Benight, A. S.; Ansari, A. Biophys. J. 2001, 81, 2864.
38. Vallone, P. M.; Paner, T. M.; Hilario, J.; Lane, M. J.; Faldasz, B. D.; Benight, A. S. Biopolymers 1999, 50, 425.
39. DeGennes, P. G. Scaling Concepts in Polymer Physics; Cornell University Press: Ithaca, NY, 1979.
40. Kramers, H. A. Physica 1940, 7, 284.
41. Hanggi, P.; Talkner, P.; Borkovec, M. Rev. Mod. Phys. 1990, 62, 251.
42. Schuler, B.; Lipman, E. A.; Eaton, W. A. Nature 2002, 419, 743.
43. Levinthal, C. How to Fold Graciously? In Mossbauer Spectroscopy in Biological Systems, Proceedings of a Meeting held at Allerton House, Monticello, IL; Debrunner, P., Tsibris, J. C. M., Münck, E., Eds.; University of Illinois Press; Urbana, IL, 1969.
44. Baldwin, R. L. Proc. Natl Acad. Sci. U.S.A. 1996, 93, 2627.
45. Zwanzig, R.; Szabo, A.; Bagchi, B. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 20.
46. Leopold, P. E.; Montai, M.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 8721.
47. Sali, A.; Shakhnovich, E.; Karplus, M. Nature 1994, 369, 248.
48. Onuchic, J. N.; Wolynes, P. G.; Luthey-Schulten, Z.; Socci, N. D. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 3626.
49. Zwanzig, R. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 2029.
50. Bryngelson, J. D.; Wolynes, P. G. J. Phys. Chem. 1989, 93, 6902.
51. Socci, N. D.; Onuchic, J. N.; Wolynes, P. G. J. Chem. Phys. 1996, 104, 5860.
52. Lapidus, L. J.; Eaton, W. A.; Hofrichter, J. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 7220.
53. Bustamante, C.; Smith, S. B.; Liphardt, J.; Smith, D. Curr. Opin. Struct. Biol. 2000, 10, 279.
54. Maier, B.; Bensimon, D.; Croquette, V. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 12002.
55. Wuite, G. J.; Smith, S. B.; Young, M.; Keller, D.; Bustamante, C. Nature 2000, 404, 103.
56. Gerland, U.; Bundschuh, R.; Hwa, T. Biophys. J. 2001, 81, 1324.
57. Montanari, A.; Mezard, M. Phys. Rev. Lett. 2001, 86, 2178.
58. Zhang, Y.; Zhou, H.; Ou-Yang, Z. C. Biophys. J. 2001, 81, 1133.
59. Cocco, S.; Marko, J. F.; Monasson, R.; Sarkar, A.; Yan, J. Eur. Phys. J. E 2003, 10, 249.
60. Mathews, D. H.; Sabina, J.; Zuker, M.; Turner, D. H. J. Mol. Biol. 1999, 288, 911.
61. Vallone, P. M.; Benight, A. S. Nucleic Acids Res. 1999, 27, 3589.
62. Sorin, E. J.; Rhee, Y. M.; Nakatani, B. J.; Pande, V. S. Biophys. J. 2003, 85, 790.
63. Wang, X.; Nau, W. M. J. Am. Chem. Soc. 2004, 126, 808.
64. Mills, J. B.; Vacano, E.; Hagerman, P. J. J. Mol. Biol. 1999, 285, 245.
65. Tinland, B.; Pluen, A.; Sturm, J.; Weill, G. Macromolecules 1997, 30, 5763.
66. Smith, S. B.; Cui, Y.; Bustamante, C. Science 1996, 271, 795.
67. Cocco, S.; Marko, J. F.; Monasson, R. Eur. Phys. J. E 2003, 10, 153.
68. Liphardt, J.; Onoa, B.; Smith, S. B.; Tinoco, I. J.; Bustamante, C. Science 2001, 292, 733.
69. Pabit, S. A.; Roder, H.; Hagen, S. J. Biochemistry 2004, 43, 12532.