Concentration-dependent structural transitions of human telomeric DNA sequences

Biochemistry

Volumn 51, Issue 37, 2012, Pages 7357-7366

  Abu Ghazalah, Rashid M ^a   Rutledge, Steve ^a   Lau, Lewis W Y ^a   Dubins, David N ^a   MacGregor, Robert B ^a   Helmy, Amr S ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CATION SPECIES; CD SPECTRA; CONCENTRATION DEPENDENCE; CONCENTRATION-DEPENDENT; G-QUADRUPLEX STRUCTURE; G-QUADRUPLEXES; HIGH-RESOLUTION SPECTROSCOPY; HUMAN TELOMERIC DNA; HYBRID SEQUENCES; ROOM TEMPERATURE; SAMPLE PREPARATION TECHNIQUES; STRUCTURAL TRANSITIONS; TELOMERIC SEQUENCES; VIBRATIONAL MODES;

DNA SEQUENCES; OLIGONUCLEOTIDES;

AGGREGATES;

GUANINE QUADRUPLEX; MONOMER; OLIGODEOXYRIBONUCLEOTIDE;

ARTICLE; CHEMICAL REACTION KINETICS; CIRCULAR DICHROISM; CONCENTRATION (PARAMETERS); DILUTION; DISSOCIATION; DNA SEQUENCE; DNA STRUCTURE; HUMAN; HYBRID; MEASUREMENT; PRIORITY JOURNAL; RAMAN SPECTROMETRY; ROOM TEMPERATURE; TELOMERE; VIBRATION;

BASE SEQUENCE; CHROMOSOMES, HUMAN; HUMANS; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; TELOMERE;

EID: 84866433142     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi300689t     Document Type: Article

References (51)

1. Gellert, M., Lipsett, M. N., and Davies, D. R. (1962) Helix formation by guanylic acid Proc. Natl. Acad. Sci. U.S.A. 48, 2013-2018
2. Hazel, P., Huppert, J., Balasubramanian, S., and Neidle, S. (2004) Loop-length-dependent folding of G-quadruplexes J. Am. Chem. Soc. 126, 16405-16415
3. Bugaut, A. and Balasubramanian, S. (2008) A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes Biochemistry 47, 689-697
4. Risitano, A. and Fox, K. R. (2004) Influence of loop size on the stability of intramolecular DNA quadruplexes Nucleic Acids Res. 32, 2598-2606
5. Guo, Q., Lu, M., and Kallenbach, N. R. (1993) Effect of thymine tract length on the structure and stability of model telomeric sequences Biochemistry 32, 3596-3603
6. Guedin, A., Alberti, P., and Mergny, J. L. (2009) Stability of intramolecular quadruplexes: Sequence effects in the central loop Nucleic Acids Res. 37, 5559-5567
7. Guedin, A., Gros, J., Alberti, P., and Mergny, J. L. (2010) How long is too long? Effects of loop size on G-quadruplex stability Nucleic Acids Res. 38, 7858-7868
8. Crnugelj, M., Sket, P., and Plavec, J. (2003) Small change in a G-rich sequence, a dramatic change in topology: New dimeric G-quadruplex folding motif with unique loop orientations J. Am. Chem. Soc. 125, 7866-7871
9. Tang, C. F. and Shafer, R. H. (2006) Engineering the quadruplex fold: Nucleoside conformation determines both folding topology and molecularity in guanine quadruplexes J. Am. Chem. Soc. 128, 5966-5973
10. Rachwal, P. A., Brown, T., and Fox, K. R. (2007) Effect of G-tract length on the topology and stability of intramolecular DNA quadruplexes Biochemistry 46, 3036-3044
11. Sen, D. and Gilbert, W. (1990) A Sodium-Potassium Switch in the Formation of 4-Stranded G4-Dna Nature 344, 410-414
12. Miura, T., Benevides, J. M., and Thomas, G. J., Jr. (1995) A phase diagram for sodium and potassium ion control of polymorphism in telomeric DNA J. Mol. Biol. 248, 233-238
13. Nielsen, M. C. and Ulven, T. (2010) Macrocyclic G-quadruplex ligands Curr. Med. Chem. 17, 3438-3448
14. 3) J. Am. Chem. Soc. 132, 17105-17107
15. Fan, H. Y., Shek, Y. L., Amiri, A., Dubins, D. N., Heerklotz, H., Macgregor, R. B., Jr., and Chalikian, T. V. (2011) Volumetric characterization of sodium-induced G-quadruplex formation J. Am. Chem. Soc. 133, 4518-4526
16. Lane, A. N., Chaires, J. B., Gray, R. D., and Trent, J. O. (2008) Stability and kinetics of G-quadruplex structures Nucleic Acids Res. 36, 5482-5515
17. Viglasky, V., Bauer, L., and Tluckova, K. (2010) Structural features of intra- and intermolecular G-quadruplexes derived from telomeric repeats Biochemistry 49, 2110-2120
18. Krishnan-Ghosh, Y., Liu, D., and Balasubramanian, S. (2004) Formation of an interlocked quadruplex dimer by d(GGGT) J. Am. Chem. Soc. 126, 11009-11016
19. Marsh, T. C. and Henderson, E. (1994) G-Wires: Self-Assembly of a Telomeric Oligonucleotide, d(GGGGTTGGGG), into Large Superstructures Biochemistry 33, 10718-10724
20. Poon, K. and Macgregor, R. B., Jr. (2000) Formation and structural determinants of multi-stranded guanine-rich DNA complexes Biophys. Chem. 84, 205-216
21. 3] G-tetraplex Structure 1, 263-282
22. Parkinson, G. N., Lee, M. P., and Neidle, S. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA Nature 417, 876-880
23. + solutions Nucleic Acids Res. 31, 1605-1613
24. 125I-radioprobing Nucleic Acids Res. 32, 5359-5367
25. Ourliac-Garnier, I., Elizondo-Riojas, M. A., Redon, S., Farrell, N. P., and Bombard, S. (2005) Cross-links of quadruplex structures from human telomeric DNA by dinuclear platinum complexes show the flexibility of both structures Biochemistry 44, 10620-10634
26. Li, J., Correia, J. J., Wang, L., Trent, J. O., and Chaires, J. B. (2005) Not so crystal clear: The structure of the human telomere G-quadruplex in solution differs from that present in a crystal Nucleic Acids Res. 33, 4649-4659
27. Ying, L., Green, J. J., Li, H., Klenerman, D., and Balasubramanian, S. (2003) Studies on the structure and dynamics of the human telomeric G quadruplex by single-molecule fluorescence resonance energy transfer Proc. Natl. Acad. Sci. U.S.A. 100, 14629-14634
28. Dai, J., Carver, M., and Yang, D. (2008) Polymorphism of human telomeric quadruplex structures Biochimie 90, 1172-1183
29. Ambrus, A., Chen, D., Dai, J., Bialis, T., Jones, R. A., and Yang, D. (2006) Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution Nucleic Acids Res. 34, 2723-2735
30. + solution: Insights into structure polymorphism of the human telomeric sequence Nucleic Acids Res. 35, 4927-4940
31. + solution: An intramolecular (3 + 1) G-quadruplex scaffold J. Am. Chem. Soc. 128, 9963-9970
32. + solution Nucleic Acids Res. 34, 5715-5719
33. + solution Bioorg. Med. Chem. 14, 5584-5591
34. Dai, J., Punchihewa, C., Ambrus, A., Chen, D., Jones, R. A., and Yang, D. (2007) Structure of the intramolecular human telomeric G-quadruplex in potassium solution: A novel adenine triple formation Nucleic Acids Res. 35, 2440-2450
35. + solution: A stable basket-type G-quadruplex with only two G-tetrad layers J. Am. Chem. Soc. 131, 4301-4309
36. + solutions Nucleic Acids Res. 37, 6625-6634
37. Abu-Ghazalah, R. M., Irizar, J., Helmy, A. S., and Macgregor, R. B., Jr. (2010) A study of the interactions that stabilize DNA frayed wires Biophys. Chem. 147, 123-129
38. Cantor, C. R., Warshaw, M. M., and Shapiro, H. (1970) Oligonucleotide Interactions. 3. Circular Dichroism Studies of Conformation of Deoxyoligonucleotides Biopolymers 9, 1059-1077
39. Irizar, J., Dinglasan, J., Goh, B., Khetani, A., Anis, H., Anderson, D., Goh, C., and Helmy, A. S. (2008) Raman Spectroscopy of Nanoparticles Using Hollow-Core Photonic Crystal Fibers IEEE J. Sel. Top. Quantum Electron. 14, 1214-1222
40. Cregan, R. F., Mangan, B. J., Knight, J. C., Birks, T. A., Russell, P. S., Roberts, P. J., and Allan, D. C. (1999) Single-mode photonic band gap guidance of light in air Science 285, 1537-1539
41. Laughlan, G., Murchie, A. I., Norman, D. G., Moore, M. H., Moody, P. C., Lilley, D. M., and Luisi, B. (1994) The high-resolution crystal structure of a parallel-stranded guanine tetraplex Science 265, 520-524
42. Phillips, K., Dauter, Z., Murchie, A. I., Lilley, D. M., and Luisi, B. (1997) The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Å resolution J. Mol. Biol. 273, 171-182
43. Paramasivan, S., Rujan, I., and Bolton, P. H. (2007) Circular dichroism of quadruplex DNAs: Applications to structure, cation effects and ligand binding Methods 43, 324-331
44. Balagurumoorthy, P. and Brahmachari, S. K. (1994) Structure and stability of human telomeric sequence J. Biol. Chem. 269, 21858-21869
45. Miura, T. and Thomas, G. J., Jr. (1994) Structural polymorphism of telomere DNA: Interquadruplex and duplex-quadruplex conversions probed by Raman spectroscopy Biochemistry 33, 7848-7856
46. Krafft, C., Benevides, J. M., and Thomas, G. J. (2002) Secondary structure polymorphism in Oxytricha nova telomeric DNA Nucleic Acids Res. 30, 3981-3991
47. Masiero, S., Trotta, R., Pieraccini, S., De, T. S., Perone, R., Randazzo, A., and Spada, G. P. (2010) A non-empirical chromophoric interpretation of CD spectra of DNA G-quadruplex structures Org. Biomol. Chem. 8, 2683-2692
48. Gray, D. M., Wen, J. D., Gray, C. W., Repges, R., Repges, C., Raabe, G., and Fleischhauer, J. (2008) Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities Chirality 20, 431-440
49. Bishop, G. R. and Chaires, J. B. (2003) Characterization of DNA structures by circular dichroism. Current Protocols in Nucleic Acid Chemistry, Chapter 7, Unit 7.11, Wiley, New York.
50. Neidle, S. and Balasubramanian, S. (2006) Quadruplex nucleic acids, Royal Society of Chemistry, Cambridge, U.K.
51. Petraccone, L., Spink, C., Trent, J. O., Garbett, N. C., Mekmaysy, C. S., Giancola, C., and Chaires, J. B. (2011) Structure and stability of higher-order human telomeric quadruplexes J. Am. Chem. Soc. 133, 20951-20961