Thermodynamic characterization of human telomere quadruplex unfolding

Biopolymers

Volumn 99, Issue 12, 2013, Pages 1006-1018

  Buscaglia, R ^a   Gray, R D ^a   Chaires, J B ^a  

^a UNIVERSITY OF LOUISVILLE   (United States)

Author keywords

quadruplex; singular value decomposition; spectroscopy; telomere; unfolding

Indexed keywords

EUKARYOTIC CHROMOSOMES; HIGH-RESOLUTION TECHNIQUES; QUADRUPLEX; REPEATED DNA SEQUENCES; TELOMERES; THERMODYNAMIC CHARACTERIZATION; TRIPLE HELICAL STRUCTURES; UNFOLDING;

DNA; DYES; SINGULAR VALUE DECOMPOSITION; SPECTROSCOPY; TOPOLOGY;

CHROMOSOMES;

ACETONITRILE; SINGLE STRANDED DNA; DNA; GUANINE QUADRUPLEX;

ARTICLE; CHROMOSOME; CIRCULAR DICHROISM; DNA CONFORMATION; DNA DENATURATION; DNA FLANKING REGION; DNA SEQUENCE; HUMAN; TELOMERE; THERMODYNAMICS; THERMOSTABILITY; CHEMISTRY; CONFORMATION;

CIRCULAR DICHROISM; DNA; DNA, SINGLE-STRANDED; G-QUADRUPLEXES; HUMANS; NUCLEIC ACID CONFORMATION; TELOMERE; THERMODYNAMICS;

EID: 84884954839     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.22247     Document Type: Article

References (50)

1. Lipps, H. J.,;, Rhodes, D., Trends Cell Biol 2009, 19, 414.
2. Bochman, M. L.,;, Paeschke, K.,;, Zakian, V. A., Nat Rev Genet 2012, 13, 770.
3. Sarkies, P.,;, Murat, P.,;, Phillips, L. G.,;, Patel, K. J.,;, Balasubramanian, S.,;, Sale, J. E., Nucleic Acids Res 2012, 40, 1485.
4. Sanders, C. M., Biochem J 2010, 430, 119.
5. Sarkies, P.,;, Reams, C.,;, Simpson, L. J.,;, Sale, J. E., Mol Cell 2010, 40, 703.
6. Hwang, H.,;, Buncher, N.,;, Opresko, P. L.,;, Myong, S., Structure 2012, 20, 1872.
7. Brooks, T. A.,;, Kendrick, S.,;, Hurley, L., FEBS J 2010, 277, 3459.
8. Bugaut, A.,;, Balasubramanian, S., Nucleic Acids Res 2012, 40, 4727.
9. Yang, D.,;, Okamoto, K., Future Med Chem 2010, 2, 619.
10. Webba da Silva, M., Chemistry 2007, 13, 9738.
11. Moyzis, R. K.,;, Buckingham, J. M.,;, Cram, L. S.,;, Dani, M.,;, Deaven, L. L.,;, Jones, M. D.,;, Meyne, J.,;, Ratliff, R. L.,;, Wu, J. R., Proc Natl Acad Sci USA 1988, 85, 6622.
12. Phan, A. T., FEBS J 2010, 277, 1107.
13. Wang, Y.,;, Patel, D., J. Structure 1993, 1, 263.
14. Parkinson, G. N.,;, Lee, M. P.,;, Neidle, S., Nature 2002, 417, 876.
15. Li, J.,;, Correia, J. J.,;, Wang, L.,;, Trent, J. O.,;, Chaires, J. B., Nucleic Acids Res 2005, 33, 4649.
16. Ambrus, A.,;, Chen, D.,;, Dai, J.,;, Bialis, T.,;, Jones, R. A.,;, Yang, D., Nucleic Acids Res 2006, 34, 2723.
17. Dai, J.,;, Punchihewa, C.,;, Ambrus, A.,;, Chen, D.,;, Jones, R. A.,;, Yang, D., Nucleic Acids Res 2007, 35, 2440.
18. Luu, K. N.,;, Phan, A. T.,;, Kuryavyi, V.,;, Lacroix, L.,;, Patel, D. J., J Am Chem Soc 2006, 128, 9963.
19. Dai, J.,;, Carver, M.,;, Punchihewa, C.,;, Jones, R. A.,;, Yang, D., Nucleic Acids Res 2007, 35, 4927.
20. Phan, A. T.,;, Kuryavyi, V.,;, Luu, K. N.,;, Patel, D. J., Nucleic Acids Res 2007, 35, 6517.
21. Lim, K. W.,;, Amrane, S.,;, Bouaziz, S.,;, Xu, W.,;, Mu, Y.,;, Patel, D. J.,;, Luu, K. N.,;, Phan, A. T., J Am Chem Soc 2009, 131, 4301.
22. Zhang, Z.,;, Dai, J.,;, Veliath, E.,;, Jones, R. A.,;, Yang, D., Nucleic Acids Res 2010, 38, 1009.
23. Miller, M. C.,;, Buscaglia, R.,;, Chaires, J. B.,;, Lane, A. N.,;, Trent, J. O., J Am Chem Soc 2010, 132, 17105.
24. Miyoshi, D.,;, Fujimoto, T.,;, Sugimoto, N., Top Curr Chem 2012, 330, 87.
25. Heddi, B.,;, Phan, A. T., J Am Chem Soc 2011, 133, 9824.
26. Knowles, D. B.,;, LaCroix, A. S.,;, Deines, N. F.,;, Shkel, I.,;, Record, M. T., Jr., Proc Natl Acad Sci USA 2011, 108, 12699.
27. Le, H. T.,;, Buscaglia, R.,;, Dean, W. L.,;, Chaires, J. B.,;, Trent, J. O., Top Curr Chem 2012, 330, 179.
28. Mashimo, T.,;, Yagi, H.,;, Sannohe, Y.,;, Rajendran, A.,;, Sugiyama, H., J Am Chem Soc 2010, 132, 14910.
29. Gray, R. D.,;, Buscaglia, R.,;, Chaires, J. B., J Am Chem Soc 2012, 134, 16834.
30. Boncina, M.,;, Lah, J.,;, Prislan, I.,;, Vesnaver, G., J Am Chem Soc 2012, 134, 9657.
31. Payet, L.,;, Huppert, J. L., Biochemistry 2012, 51, 3154.
32. Stegle, O.,;, Payet, L.,;, Mergny, J. L.,;, MacKay, D. J.,;, Leon, J. H., Bioinformatics 2009, 25, i374.
33. Gray, R. D.,;, Petraccone, L.,;, Trent, J. O.,;, Chaires, J. B., Biochemistry 2010, 49, 179.
34. Cantor, C. R.,;, Warshaw, M. M.,;, Shapiro, H., Biopolymers 1970, 9, 1059.
35. Li, J.,;, Center, T. U. o. M. M., Biophysical Studies of Human Telomeric DNA; University of Mississippi Medical Center, 2006.
36. Gray, R. D.,;, Chaires, J. B., Biophys Chem 2011, 159, 205.
37. Abu-Ghazalah, R. M.,;, Rutledge, S.,;, Lau, L. W.,;, Dubins, D. N.,;, Macgregor, R. B., Jr.,;, Helmy, A. S., Biochemistry 2012, 51, 7357.
38. Gray, R. D.,;, Chaires, J. B., In Current Protocols in Nucleic Acid Chemistry;, Beaucage, S. L., et al., Eds.; 2011; Chapter 17, Unit 17 4.
39. Hendler, R. W.,;, Shrager, R. I., J Biochem Biophys Methods 1994, 28, 1.
40. Petraccone, L.,;, Malafronte, A.,;, Amato, J.,;, Giancola, C., J Phys Chem B 2012, 116, 2294.
41. Saroff, H. A., Anal Biochem 1989, 176, 161.
42. Wallimann, P.,;, Kennedy, R. J.,;, Miller, J. S.,;, Shalongo, W.,;, Kemp, D. S., J Am Chem Soc 2003, 125, 1203.
43. Randazzo, A.,;, Spada, G. P.,;, Silva, M. W., Top Curr Chem 2012, 330, 67.
44. Koirala, D.,;, Mashimo, T.,;, Sannohe, Y.,;, Yu, Z.,;, Mao, H.,;, Sugiyama, H., Chem Commun (Camb) 2012, 48, 2006.
45. Motulsky, H. C., A Fitting Models to Biological Data Using Linear and Nonlinear Regression; GraphPad Software Inc.: San Diego, CA, 2003.
46. Lumry, R.,;, Biltonen, R., Biopolymers 1966, 4, 917.
47. Haq, I.,;, Chowdhry, B. Z.,;, Chaires, J. B., Eur Biophys J: EBJ 1997, 26, 419.
48. Phan, A. T.,;, Patel, D., J. J Am Chem Soc 2003, 125, 15021.
49. Limongelli, V.,;, De Tito, S.,;, Cerofolini, L.,;, Fragai, M.,;, Pagano, B.,;, Trotta, R.,;, Cosconati, S.,;, Marinelli, L.,;, Novellino, E.,;, Bertini, I.,;, Randazzo, A.,;, Luchinat, C.,;, Parrinello, M., Angew Chem Int Ed Engl 2013, 52, 2269.
50. Ren, J.,;, Qu, X.,;, Trent, J. O.,;, Chaires, J. B., Nucleic Acids Res 2002, 30, 2307.