Single-molecule conformational analysis of G-quadruplex formation in the promoter DNA duplex of the proto-oncogene C-kit

Journal of the American Chemical Society

Volumn 129, Issue 24, 2007, Pages 7484-7485

  Shirude, Pravin S ^a   Okumus, Burak ^b   Ying, Liming ^c   Ha, Taekjip ^b   Balasubramanian, Shankar ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b University of Illinois at Urbana Champaign   (United States)

^c NATIONAL HEART AND LUNG INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; SINGLE STRANDED DNA; STEM CELL FACTOR RECEPTOR; TELOMERE BINDING PROTEIN;

ARTICLE; COMPLEX FORMATION; CONFORMATION; DNA SEQUENCE; DNA STRUCTURE; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENETIC TRANSCRIPTION; HUMAN; HYDROGEN BOND; NUCLEAR MAGNETIC RESONANCE; ONCOGENE C MYC; PROMOTER REGION; PROTEIN MOTIF; PROTO ONCOGENE; TELOMERE; THERMOSTABILITY; TRANSCRIPTION INITIATION;

BASE SEQUENCE; DNA; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; POTASSIUM; PROMOTER REGIONS (GENETICS); PROTO-ONCOGENE PROTEINS C-KIT;

EID: 34250845845     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja070497d     Document Type: Article

References (21)

1. Simonsson, T. Biol. Chem. 2001, 382, 621.
2. Sen, D.; Gilbert, W. Methods Enzymol. 1992, 211, 191.
3. Huppert, J.; Balasubramanian, S. Nucleic Acids Res. 2005, 33, 2908.
4. Blackburn, E. H. Nature 1991, 350, 569.
5. Balagurumoorthy, P.; Brahmachari, S. K. J. Mol. Biol. 1994, 269, 21858.
6. Henderson, E. C.; Hardin, C. I.; Walk, I.; Tinoco, I., Jr.; Blackburn, E. H. Cell 1987, 51, 899.
7. Paeschke, K.; Simonsson, T.; Postberg, J.; Rhodes, D.; Lipps, H. J. Nat. Struct. Mol. Biol. 2005, 12, 847.
8. Huppert, J.; Balasubramanian, S. Nucleic Acids Res. 2007, 35, 406.
9. Simonsson, T.; Pecinka, P.; Kubista, M. Nucleic Acids Res. 1998, 26, 1167.
10. Phan, A. T.; Modi, Y. S.; Patel, D. J. J. Am. Chem. Soc. 2004, 126, 8710.
11. (a) Siddiqui-Jain, A.; Grand, C. L.; Bearss, D. J.; Hurley, L. H. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11593.
12. (b) Fernando, H.; Reszka, A. P.; Huppert, J.; Ladame, S.; Rankin, S.; Venkitaraman, A. R.; Neidle, S.; Balasubramanian, S. Biochemistry 2006, 45, 7854. Additional reports are cited in the SI.
13. Ha, T. Biochemistry 2004, 43, 4055.
14. Ying, L. M.; Green, J. J.; Li, H. T.; Klenerman, D.; Balasubramanian, S. Proc. Natl Acad. Sci. U.S.A. 2003, 100, 14629.
15. Lee, J. Y.; Okumus, B.; Kim, D. S.; Ha, T. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 18938.
16. G blocks that naturally flank the c-kit quadruplex have been deliberately included to ensure the system reflects the natural sequence context. Additional explanation is given in the SI.
17. Park, G. H.; Plummer, H. K., III; Krystal, G. W. Blood 1998, 92, 4138.
18. The C-rich strand may form an i-motif structure, but CD spectroscopy of kit-1 revealed that the i-motif is formed only at pH 5.4 but not at pH 7.4.
19. Okumus, B.; Wilson, T. J.; Lilley, D. M.; Ha, T. Biophys. J. 2004, 87, 2798.
20. Huang, Z.; Ji, D.; Wang, S.; Xia, A.; Koberling, F.; Patting, M.; Erdmann, R. J. Phys. Chem. A 2006, 110, 45.
21. We cannot rule out that quadruplex formation in kit-1 is a consequence of a kinetically trapped quadruplex formed during annealing. This possibility was minimized by slow annealing at a linear rate of 0.1°C/min.