Kinetic stability of intermolecular DNA quadruplexes

Biophysical Journal

Volumn 89, Issue 1, 2005, Pages 365-373

  Merkina, Elena E ^a   Fox, Keith R ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BUFFER; DNA; FLUORESCENT DYE; GUANINE; OLIGODEOXYRIBONUCLEOTIDE; POTASSIUM;

ARTICLE; CHEMICAL REACTION KINETICS; COMPLEX FORMATION; DISSOCIATION; FLUORESCENCE; HALF LIFE TIME; HEATING; INTERMOLECULAR DNA QUADRUPLEX; MELTING POINT; MOLECULAR STABILITY; PHOTOCHEMICAL QUENCHING; THERMODYNAMICS;

EID: 23244467145     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.061259     Document Type: Article

References (38)

1. Simonsson, T. 2001. G-quadruplex DNA structures-variations on a theme. Biol. Chem. 382:621-628.
2. Williamson, J. R. 1994. G-quartet structures on telomeric DNA. Annu. Rev. Biophys. Biomol. Struct. 23:703-730.
3. Keniry, M. A. 2000. Quadruplex structures in nucleic acids. Biopolymers. 56:123-146.
4. Sen, D., and W. Gilbert. 1988. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature. 334:364-366.
5. Williamson, J. R., M. K. Raghuraman, and T. R. Cech. 1989. Monovalent cation induced structure of telomeric DNA-the G-quartet model. Cell. 59:871-880.
6. Sen, D., and W. Gilbert. 1990. A sodium-potassium switch in the formation of 4-stranded G4-DNA. Nature. 344:410-414.
7. Laughlan, G., A. I. H. Murchie, D. G. Norman, M. H. Moore, P. C. Moody, D. M. J. Lilley, and B. Luisi. 1994. The high-resolution crystal structure of a parallel stranded guanine tetraplex. Science. 265:520-524.
8. Phillips, K., Z. Dauter, A. I. Murchie, D. M. J. Lilley, and B. Luisi. 1997. The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Angstrom resolution. J. Mol. Biol. 273:171-182.
9. Sundquist, W. I., and A. Klug. 1989. Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature. 342:825-829.
10. 2. Eur. J. Biochem. 233:631-643.
11. Henderson, E., C. C. Hardin, S. K. Walk, I. Tinoco, and E. H. Blackburn. 1987. Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs. Cell. 51:899-908.
12. Macaya, R. F., P. Schultze, F. W. Smith, J. A. Roe, and J. Feigon. 1993. Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. Proc. Natl. Acad. Sci. USA. 90:3745-3749.
13. 3] G-tetraplex. Structure. 1:76-94.
14. Parkinson, G. N., M. P. H. Lee, and S. Neidle. 2002. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature. 417:876-880.
15. 3] G-tetraplex. J. Mol. Biol. 251:263-282.
16. Simonsson, T., P. Pecinka, and M. Kubista. 1998. DNA tetraplex formation in the control regions of c-myc. Nucleic Acids Res. 26:1167-1172.
17. Siddiqui-Jain, A., C. L. Grand, D. J. Bearss, and L. H. Hurley. 2002. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl. Acad. Sci. USA. 99:11593-11598.
18. Murchie, A. I., and D. M. J. Lilley. 1992. Retinoblastoma susceptibility genes contain 5′ sequences with a high propensity to form guanine-tetrad structures. Nucleic Acids Res. 20:49-53.
19. n nucleotide repeats form a stable tetrahelical structure. Proc. Natl. Acad. Sci. USA. 91:4950-4954.
20. Howell, R. M., K. J. Woodford, M. N. Weitzmann, and K. Usdin. 1996. The chicken beta-globin gene promoter forms a novel "cinched" tetrahelical structure. J. Biol. Chem. 271:5208-5214.
21. Lew, A., W. J. Rutter, and G. C. Kennedy. 2000. Unusual DNA structure of the diabetes susceptibility locus IDDM2 and its effect on transcription by the insulin promoter factor Pur-1/MAZ. Proc. Natl. Acad. Sci. USA. 97:12508-12512.
22. Jing, N., R. F. Rando, Y. Pommier, and M. E. Hogan. 1997. Ion selective folding of loop domains in a potent anti-HIV oligonucleotide. Biochemistry. 36:12498-12505.
23. 4T). Nature. 360:280-282.
24. Wang, Y., and D. J. Patel. 1993b. Solution structure of a parallel-stranded G-quadruplex DNA. J. Mol. Biol. 234:1171-1183.
25. Hardin, C. C., M. J. Corregan, D. V. Lieberman, and B. A. Brown. 1997. Allosteric interactions between DNA strands and monovalent cations in DNA quadruplex assembly, thermodynamic evidence for three linked association pathways. Biochemistry. 36:15428-15450.
26. Wyatt, J. R., P. W. Davis, and S. M. Freier. 1996. Kinetics of G-quartet-mediated tetramer formation. Biochemistry. 35:8002-8008.
27. Mergny, J.-L., A. De Cian, A. Ghelab, B. Saccà, and L. Lacroix. 2005. Kinetics of tetramolecular quadruplexes. Nucleic Acids Res. 33:81-94.
28. Cheong, C., and P. B. Moore. 1992. Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures. Biochemistry. 31:8406-8414.
29. Darby, R. A. J., M. Sollogoub, C. McKeen, L. Brown, A. Risitano, N. Brown, C. Barton, T. Brown, and K. R. Fox. 2002. High throughput measurement of duplex, triplex and quadruplex melting curves using molecular beacons and a LightCycler. Nucleic Acids Res. 30:e39.
30. Risitano, A., and K. R. Fox. 2003. Stability of intramolecular DNA quadruplexes: comparison with DNA duplexes. Biochemistry. 42:6507-6513.
31. Risitano, A., and K. R. Fox. 2004. Influence of loop size on the stability of intramolecular DNA quadruplexes. Nucleic Acids Res. 32:2598-2606.
32. +-GC and T-AT triplets. Nucleic Acids Res. 31:5598-5606.
33. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
34. Mergny, J.-L., A.-T. Phan, and L. Lacroix. 1998. Following G-quartet formation by UV-spectroscopy. FEBS Lett. 435:74-78.
35. 4 quadruplex. Int. J. Biol. Macromol. 31:131-137.
36. Moreira, B. G., Y. You, M. A. Behlke, and R. Owczarzy. 2005. Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability. Biochem. Biophys. Res. Commun. 327:473-484.
37. 4T. Biochemistry. 31:2455-2459.
38. Guo, Q., M. Lu, and N. R. Kallenbach. 1993. Effect of thymine tract length on the structure and stability of model telomeric sequences. Biochemistry. 32:3596-3603.