Duplex formation at the 5′ end affects the quadruplex conformation of the human telomeric repeat overhang in sodium but not in potassium

Biochemistry

Volumn 48, Issue 47, 2009, Pages 11169-11177

  Gaynutdinov, Timur I ^a   Brown, Patrick ^b   Neumann, Ronald D ^a   Panyutin, Igor G ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTICANCER DRUG; CD SPECTROSCOPY; DNA MOLECULES; DUPLEX FORMATION; INTERFACE POSITION; QUADRUPLEX STRUCTURES; QUADRUPLEXES; REALISTIC MODEL; REPEATED SEQUENCES; SINGLE-STRANDED OVERHANGS; TELOMERE FUNCTION; TELOMERES; TELOMERIC DNA; TELOMERIC SEQUENCES;

DNA; GENES; ISOMERS; NUCLEIC ACIDS; OLIGONUCLEOTIDES; POTASSIUM; SODIUM; SODIUM CHLORIDE;

CONFORMATIONS;

DNA; OLIGONUCLEOTIDE; POTASSIUM; POTASSIUM CHLORIDE; SODIUM; SODIUM CHLORIDE;

ARTICLE; CIRCULAR DICHROISM; DNA CONFORMATION; DNA DETERMINATION; HUMAN; ISOTOPE LABELING; PRIORITY JOURNAL; STRUCTURE ANALYSIS; TELOMERE;

CIRCULAR DICHROISM; DNA, SINGLE-STRANDED; G-QUADRUPLEXES; HUMANS; IODINE RADIOISOTOPES; MOLECULAR SEQUENCE DATA; POTASSIUM; REPETITIVE SEQUENCES, NUCLEIC ACID; SODIUM; TELOMERE;

EID: 72749122010     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi901063g     Document Type: Article

References (31)

1. n, present at the telomeres of human chromosomes. Proc. Natl. Acad. Sci. U.S.A. 85, 6622-6626.
2. Sfeir, A. J., Chai, W., Shay, J. W., and Wright, W. E. (2005) Telomere-end processing the terminal nucleotides of human chromosomes. Mol. Cell 18, 131-138. (Pubitemid 40444654)
3. 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.
4. Sen, D., and Gilbert, W. (1988) Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334, 364-366. (Pubitemid 18177667)
5. Williamson, J. R., Raghuraman, M. K., and Cech, T. R. (1989) Monovalent cation-induced structure of telomeric DNA: TheG-quartet model. Cell 59, 871-880.
6. Panyutin, I. G., Kovalsky, O. I., Budowsky, E. I., Dickerson, R. E., Rikhirev, M. E., and Lipanov, A. A. (1990) G-DNA: A twice-folded DNA structure adopted by single-stranded oligo(dG) and its implications for telomeres. Proc. Natl. Acad. Sci. U.S.A. 87, 867-870.
7. Wang, Y., and Patel, D. J. (1993) Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure 1, 263-282. (Pubitemid 2031126)
8. Parkinson, G. N., Lee, M. P., and Neidle, S. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417, 876-880.
9. 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. (Pubitemid 43985634)
10. + solution: An intramolecular (3+1) G-quadruplex scaffold. J. Am. Chem. Soc. 128, 9963-9970.
11. 125I-radioprobing. Nucleic Acids Res. 32, 5359-5367.
12. Wlodarczyk, A., Grzybowski, P., Patkowski, A., and Dobek, A. (2005) Effect of ions on the polymorphism, effective charge, and stability of human telomeric DNA. Photon correlation spectroscopy and circular dichroism studies. J. Phys. Chem. B 109, 3594-3605.
13. + solutions. Nucleic Acids Res. 31, 1605-1613.
14. 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. (Pubitemid 47073725)
15. Gaynutdinov, T. I., Neumann, R. D., and Panyutin, I. G. (2008) Structural polymorphism of intramolecular quadruplex of human telomeric DNA: Effect of cations, quadruplex-binding drugs and flanking sequences. Nucleic Acids Res. 36, 4079-4087.
16. + solution: A stable basket-type G-quadruplex with only two G-tetrad layers. J. Am. Chem. Soc. 131, 4301-4309.
17. Neidle, S., and Parkinson, G. N. (2008) Quadruplex DNA crystal structures and drug design. Biochimie 90, 1184-1196.
18. Rezler, E. M., Bearss, D. J., and Hurley, L. H. (2003) Telomere inhibition and telomere disruption as processes for drug targeting. Annu. Rev. Pharmacol. Toxicol. 43, 359-379.
19. 125I incorporated into a triplex-forming oligonucleotide correlates with geometry of the triplex. Nucleic Acids Res. 25, 883-887.
20. + solution: Insights into structure polymorphism of the human telomeric sequence. Nucleic Acids Res. 35, 4927-4940.
21. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) UCSF Chimera: A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612.
22. Rezler, E. M., Seenisamy, J., Bashyam, S., Kim, M. Y., White, E., Wilson, W. D., and Hurley, L. H. (2005) Telomestatin and diseleno sapphyrin bind selectively to two different forms of the human telomeric G-quadruplex structure. J. Am. Chem. Soc. 127, 9439-9447.
23. Giraldo, R., Suzuki, M., Chapman, L., and Rhodes, D. (1994) Promotion of parallelDNAquadruplexes by a yeast telomere binding protein: A circular dichroism study. Proc. Natl. Acad. Sci. U.S.A. 91, 7658-7662.
24. Hardin, C. C., Watson, T., Corregan, M., and Bailey, C. (1992) Cation-dependent transition between the quadruplex and Watson-Crick hairpin forms of d(CGCG3GCG). Biochemistry 31, 833-841.
25. Rujan, I. N., Meleney, J. C., and Bolton, P. H. (2005) Vertebrate telomere repeat DNAs favor external loop propeller quadruplex structures in the presence of high concentrations of potassium. Nucleic Acids Res. 33, 2022-2031.
26. Gray,R. D., Li, J., and Chaires, J. B. (2009) Energetics and Kinetics of a Conformational Switch in G-Quadruplex DNA. J. Phys. Chem. B 113, 2676-2683.
27. Vorlickova, M., Chladkova, J., Kejnovska, I., Fialova, M., and Kypr, J. (2005) Guanine tetraplex topology of human telomereDNAis governed by the number of (TTAGGG) repeats. Nucleic Acids Res. 33, 5851-5860. (Pubitemid 41742604)
28. Kypr, J., Kejnovska, I., Renciuk, D., and Vorlickova, M. (2009) Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res. 37, 1713-1725.
29. Dapic, V., Abdomerovic, V., Marrington, R., Peberdy, J., Rodger, A., Trent, J. O., and Bates, P. J. (2003) Biophysical and biological properties of quadruplex oligodeoxyribonucleotides. Nucleic Acids Res. 31, 2097-2107. (Pubitemid 37442077)
30. + solution. Nucleic Acids Res. 34, 5715-5719.
31. + solution under molecular crowding condition. J. Am. Chem. Soc. 129, 11185-11191.