A K cation-induced conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats

Journal of Molecular Biology

Volumn 282, Issue 3, 1998, Pages 637-652

  Bouaziz, Serge ^a   Kettani, Abdelali ^a   Patel, Dinshaw J ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

DNA quadruplexes targeted to HIV integrase; G G G C repeat containing DNA quadruplexes; Monovalent cation dependent conformational transitions; Potential K cation coordination sites; Potential K cation encapsulation within a hairpin loop

Indexed keywords

INTEGRASE; MONOVALENT CATION; POTASSIUM ION; SODIUM ION;

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; DIMERIZATION; DNA STRUCTURE; PRIORITY JOURNAL; TANDEM REPEAT;

EID: 0032566709     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2031     Document Type: Article

References (37)

1. Berns, K. I. & Linden, R. M. (1995). The cryptic life cycle of adeno-associated virus. BioEssays, 17, 237-245.
2. Bishop, J. S., Guy-Caffey, J. K., Ojwang, J. O., Smith, S. R., Hogan, M. E., Cossum, P. A., Rando, R. F. & Chaudhary, M. (1996). Intramolecular G-quartet motifs confer nuclease resistance to a potent anti-HIV oligonucleotide. J. Biol. Chem. 271, 5698-5703.
3. Brünger, A. T. (1992). X-PLOR. A System for X-ray Crystallography and NMR, Yale University Press, New Haven, CT.
4. Gellert, M., Lipsett, M. N. & Davies, D. R. (1962). Helix formation by guanylic acid. Proc. Natl Acad. Sci. USA, 48, 2013-2018.
5. Guschlbauer, W., Chantof, J. F. & Thiele, D. (1990). Four-stranded nucleic acid structures 25 years later: from guanosine gels to telomeric DNA. J. Biomol. Struct. Dynam. 8, 491-511.
6. Hardin, C. C., Henderson, E., Watson, T. & Prosser, J. K. (1991). Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates. Biochemistry, 30, 4460-4472.
7. 3GCG). Biochemistry, 32, 833-841.
8. Howard, F. B. & Miles, H. T. (1982). Poly (inosinic acid) helices: essential chelation of alkali metal ions in the axial channel. Biochemistry, 21, 6736-6745.
9. 1H NMR. Biochemistry, 35, 15383-15390.
10. Jing, N., Rando, R. F., Pommier, Y. & Hogan, M. E. (1997a). Ion selective folding of loop domains in a potent anti-HIV oligonucleotide. Biochemistry, 36, 12498-12505.
11. Jing, N., Gao, X., Rando, R. F. & Hogan, M. E. (1997b). Potassium-induced loop conformational transition of a potent anti-HIV oligonucleotide. J. Biomol. Struct. Dynam. 15, 573-585.
12. Kang, C., Zhang, X., Ratliff, R., Moyzis, R. & Rich, A. (1992). Crystal structure of a four-stranded Oxytricha telomeric DNA. Nature, 356, 126-131.
13. Kettani, A., Bouaziz, S., Zhao, H. & Jones, R. A. (1998). Solution structure of a Na cation stabilized DNA quadruplex containing G·G·G·G and G·C·G·C tetrads formed by G-G-G-C repeats observed in adeno-associated viral DNA. J. Mol. Biol. 282, 619-636.
14. Laughlan, G., Murchie, A. I., Norman, D. G., Moore, M. H., Moody, P. C., Lilley, D. M. & Luisi, B. (1994). The high resolution crystal structure of a parallel-stranded guanine tetraplex. Science, 265, 520-524.
15. Lavery, R. & Sklenar, H. (1989). Defining the structure of regular nucleic acids: conventions and principles. J. Biomol. Struct. Dynam. 6, 655-667.
16. Marshall, W. S., Beaton, G., Stein, C. A., Matsukura, M. & Caruthers, M. H. (1992). Inhibition of human immunodeficiency virus activity by phosphorodithioate oligodeoxycytidine. Proc. Natl Acad. Sci. USA, 89, 6265-6269.
17. Mazumder, A., Neamati, N., Ojwang, J. O., Sunder, S., Rando, R. F. & Pommier, Y. (1996). Inhibition of the human immunodeficiency virus type I integrase by guanosine quartet structures. Biochemistry, 35, 13762-13771.
18. Miura, T., Benevides, J. M. & 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.
19. Nicholls, A., Sharp, K. & Honig, B. H. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11, 281-296.
20. Nilges, M. (1995). Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE cross-peaks and disulfide connectivities. J. Mol. Biol. 245, 645-660.
21. Padmanabhan, K., Padmanabhan, K. P., Ferrara, J. D., Sadler, J. E. & Tulinski, A. (1993). The structure of α-thrombin inhibited by a 15-mer single-stranded DNA aptamer. J. Biol. Chem. 268, 17651-17654.
22. Patel, D. J., Kozlowski, S. A., Nordheim, A. & Rich, A. (1982). Right-handed and left-handed DNA studies of B-DNA and Z-DNA by using proton nuclear Overhauser effect and phosphorus NMR. Proc. Natl Acad. Sci. USA, 79, 1413-1417.
23. Patel, D. J., Bouaziz, S., Kettani, A. & Wang, Y. (1999). Structures of guanine-rich and cytosine-rich quadruplexes formed in vitro by telomeric, centromeric and triplet repeat disease DNA sequences. In Oxford Handbook of Nucleic Acid Structure (Neidle, S., ed.), Oxford University Press, Oxford, in the press.
24. Phillips, K., Dauter, Z., Murchie, A. I. H., Lilley, D. M. J. & Luisi, B. (1997). The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Å resolution. J. Mol. Biol. 273, 171-182.
25. Pilch, D. S., Plum, G. E. & Breslauer, K. J. (1995). The thermodynamics of DNA structures which contain lesions or guanine tetrads. Curr. Opin. Struct. Biol. 5, 334-342.
26. Pinnavaia, T. J., Marshall, C. L., Mettler, C. M., Fisk, C. L., Miles, H. T. & Becker, E. D. (1978). Alkali metal ion specificity in the solution ordering of a nucleotide, 5′-guanosine monophosphate. J. Am. Chem. Soc. 100, 3625-3627.
27. Rando, R. F., Ojwang, J., Elbaggari, A., Reyes, G. R., Tinder, R., McGarth, M. S. & Hogan, M. E. (1995). Suppression of human immunodeficiency virus type 1 activity in vitro by oligonucleotides which form intramolecular tetrads. J. Biol. Chem. 270, 1754-1760.
28. Rhodes, D. & Giraldo, R. (1995). Telomere structures and function. Curr. Opin. Struct. Biol. 5, 311-322.
29. Saenger, W. (1984). Principles of Nucleic Acid Structure, Springer-Verlag Inc., New York.
30. Schultze, P., Smith, F. W. & Feigon, J. (1994). Refined solution structure of the dimeric quadruplex formed from the Oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG). Structure, 2, 221-233.
31. Sen, D. & Gilbert, W. (1988). Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications in meiosis. Nature, 334, 364-366.
32. Smith, F. W. & Feigon, J. (1992). Quadruplex structure of Oxytricha telomeric DNA oligonucleotides. Nature, 356, 164-168.
33. Sundquist, W. I. & Klug, A. (1989). Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature, 342, 825-829.
34. Williamson, J. R. (1993). Guanine quartets. Curr. Opin. Struct. Biol. 3, 357-362.
35. Williamson, J. R., Raghuraman, M. K. & Cech, T. R. (1989). Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell, 59, 871-880.
36. Wyatt, J. R., Vickers, T. A., Roberson, J. L., Buckheit, R. W., Jr, Klimkait, T., DeBaets, E., Davis, P. W., Rayner, B., Imbach, J. L. & Ecker, D. J. (1994). Combinatorially selected guanosine-quartet is a potent inhibitor of human immunodeficiency virus envelope-mediated cell fusion. Proc. Natl Acad. Sci. USA, 91, 1356-1360.
37. Xu, Q., Deng, H. & Braunlin, W. H. (1993). Selective localization and rotational immobilization of univalent cations on quadruplex DNA. Biochemistry, 32, 13130-13137.