Observation of water molecules within the bimolecular d(G 3CT4G3C)2 G-Quadruplex

Biochemistry

Volumn 50, Issue 19, 2011, Pages 4155-4161

  Zavasnik, Jaka ^a   Podbevsek, Peter ^a   Plavec, Janez ^a,b,c  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^b UNIVERSITY OF LJUBLJANA   (Slovenia)

^c EN FIST CENTRE OF EXCELLENCE   (Slovenia)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIUM ION BINDING; AMMONIUM IONS; BASE PAIRS; CARBONYL GROUPS; CATION BINDING; ELECTROSTATIC INTERACTIONS; FAST MOVEMENT; G-QUADRUPLEX STRUCTURE; G-QUADRUPLEXES; G-QUARTET; SOLUTION STATE NUCLEAR MAGNETIC RESONANCE; STRUCTURAL ELEMENTS; WATER MOLECULE; WATSON-CRICK BASE PAIRS;

AMMONIUM COMPOUNDS; BINDING SITES; DNA SEQUENCES; HIGH ENERGY PHYSICS; HYDROGEN BONDS; MAGNETIC RESONANCE; OLIGONUCLEOTIDES; POSITIVE IONS; RATE CONSTANTS;

MOLECULES;

AMMONIA; CARBONYL DERIVATIVE; CYSTEINE; GLYCINE; GUANINE QUADRUPLEX; OLIGONUCLEOTIDE; POTASSIUM ION; SODIUM ION; WATER;

AQUEOUS SOLUTION; ARTICLE; BASE PAIRING; BINDING SITE; HYDROGEN BOND; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL;

AMMONIA; BASE PAIRING; CATIONS, MONOVALENT; CYTOSINE; G-QUADRUPLEXES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; OLIGONUCLEOTIDES; THYMINE; WATER;

EID: 79955836118     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi200201n     Document Type: Article

References (40)

1. Neidle, S. and Balasubramanian, S. (2006) Quadruplex nucleic acids, Royal Society of Chemistry, Cambridge, U.K.
2. Davis, J. T. (2004) G-Quartets 40 Years Later: From 5′-GMP to Molecular Biology and Supramolecular Chemistry Angew. Chem., Int. Ed. 43, 668-698 (Pubitemid 38197045)
3. Phan, A. T., Kuryavyi, V., and Patel, D. J. (2006) DNA architecture: From G to Z Curr. Opin. Struct. Biol. 16, 288-298 (Pubitemid 43831655)
4. Burge, S., Parkinson, G. N., Hazel, P., Todd, A. K., and Neidle, S. (2006) Quadruplex DNA: Sequence, topology and structure Nucleic Acids Res. 34, 5402-5415 (Pubitemid 44742430)
5. Huppert, J. L. (2008) Four-stranded nucleic acids: Structure, function and targeting of G-quadruplexes Chem. Soc. Rev. 37, 1375-1384
6. Leonard, G. A., Zhang, S., Peterson, M. R., Harrop, S. J., Helliwell, J. R., Cruse, W. B., Langlois d'Estaintot, B., Kennard, O., Brown, T., and Hunter, W. N. (1995) Self-association of a DNA loop creates a quadruplex: Crystal structure of d(GCATGCT) at 1.8 Å resolution Structure 3, 335-340
7. Kettani, A., Kumar, A. R., and Patel, D. J. (1995) Solution Structure of a DNA Quadruplex Containing the Fragile X Syndrome Triplet Repeat J. Mol. Biol. 254, 638-656 (Pubitemid 26001797)
8. Salisbury, S. A., Wilson, S. E., Powell, H. R., Kennard, O., Lubini, P., Sheldrick, G. M., Escaja, N., Alazzouzi, E., Grandas, A., and Pedroso, E. (1997) The bi-loop, a new general four-stranded DNA-motif Proc. Natl. Acad. Sci. U.S.A. 94, 5515-5518 (Pubitemid 27241800)
9. Webba da Silva, M. (2003) Association of DNA Quadruplexes through G:C:G:C Tetrads. Solution Structure of d(GCGGTGGAT) Biochemistry 42, 14356-14365
10. Oostra, B. and Chiurazzi, P. (2001) The fragile X gene and its function Clin. Genet. 60, 399-408 (Pubitemid 34083255)
11. O'Donnell, W. T. and Warren, S. T. (2002) A decade of molecular studies of fragile X syndrome Annu. Rev. Neurosci. 25, 315-338 (Pubitemid 34748020)
12. Hagerman, P. J. and Hagerman, R. J. (2004) The Fragile-X Premutation: A Maturing Perspective Am. J. Hum. Genet. 74, 805-816 (Pubitemid 38568956)
13. Garber, K. B., Visootsak, J., and Warren, S. T. (2008) Fragile X syndrome Eur. J. Hum. Genet. 16, 666-672 (Pubitemid 351753362)
14. Hud, N. V. and Plavec, J. (2006) The Role of Cations in Determining Quadruplex Structure and Stability. In Quadruplex nucleic acids, pp 100-130, Royal Society of Chemistry, Cambridge, U.K.
15. Hud, N. V. and Plavec, J. (2003) A unified model for the origin of DNA sequence-directed curvature Biopolymers 69, 144-158
16. Kettani, A., Bouaziz, S., Gorin, A., Zhao, H., Jones, R. A., and Patel, D. J. (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 (Pubitemid 28428857)
17. Bouaziz, S., Kettani, A., and Patel, D. J. (1998) A K cation-induced conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats J. Mol. Biol. 282, 637-652 (Pubitemid 28428858)
18. Hud, N. V., Schultze, P., and Feigon, J. (1998) Ammonium Ion as an NMR Probe for Monovalent Cation Coordination Sites of DNA Quadruplexes J. Am. Chem. Soc. 120, 6403-6404 (Pubitemid 28346417)
19. Hud, N. V., Schultze, P., Sklenar, V., and Feigon, J. (1999) Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex J. Mol. Biol. 285, 233-243 (Pubitemid 29034040)
20. Drew, H. R. and Dickerson, R. E. (1981) Structure of a B-DNA dodecamer: III. Geometry of hydration J. Mol. Biol. 151, 535-556 (Pubitemid 12252694)
21. Otwinowski, Z., Schevitz, R. W., Zhang, R.-G., Lawson, C. L., Joachimiak, A., Marmorstein, R. Q., Luisi, B. F., and Sigler, P. B. (1988) Crystal structure of trp represser/operator complex at atomic resolution Nature 335, 321-329
22. Shakked, Z., Guzikevich-Guerstein, G., Frolow, F., Rabinovich, D., Joachimiak, A., and Sigler, P. B. (1994) Determinants of repressor/operator recognition from the structure of the trp operator binding site Nature 368, 469-473 (Pubitemid 24115356)
23. Kubinec, M. G. and Wemmer, D. E. (1992) NMR evidence for DNA bound water in solution J. Am. Chem. Soc. 114, 8739-8740
24. Qian, Y. Q., Otting, G., and Wüthrich, K. (1993) NMR detection of hydration water in the intermolecular interface of a protein-DNA complex J. Am. Chem. Soc. 115, 1189-1190
25. Liepinsh, E., Otting, G., and Wüthrich, K. (1992) NMR observation of individual molecules of hydration water bound to DNA duplexes: Direct evidence for a spine of hydration water present in aqueous solution Nucleic Acids Res. 20, 6549-6553 (Pubitemid 23052674)
26. 2 segments Nucleic Acids Res. 22, 2249-2254 (Pubitemid 24209532)
27. Sunnerhagen, M., Denisov, V. P., Venu, K., Bonvin, A. M. J. J., Carey, J., Halle, B., and Otting, G. (1998) Water molecules in DNA recognition I: hydration lifetimes of trp operator DNA in solution measured by NMR spectroscopy J. Mol. Biol. 282, 847-858 (Pubitemid 28442351)
28. Johannesson, H. and Halle, B. (1998) Minor Groove Hydration of DNA in Solution: Dependence on Base Composition and Sequence J. Am. Chem. Soc. 120, 6859-6870 (Pubitemid 28378343)
29. Denisov, V. P., Carlström, G., Venu, K., and Halle, B. (1997) Kinetics of DNA hydration J. Mol. Biol. 268, 118-136 (Pubitemid 27192683)
30. Maltseva, T. V., Agback, P., and Chattopadhyaya, J. (1993) How Much hydration is necessary for the stabilisation of DNA-duplex? Nucleic Acids Res. 21, 4246-4252 (Pubitemid 23279013)
31. Phan, A. T., Leroy, J.-L., and Gueron, M. (1999) Determination of the residence time of water molecules hydrating B′-DNA and B-DNA, by one-dimensional zero-enhancement nuclear overhauser effect spectroscopy J. Mol. Biol. 286, 505-519 (Pubitemid 29090166)
32. Miyoshi, D., Karimata, H., and Sugimoto, N. (2006) Hydration Regulates Thermodynamics of G-Quadruplex Formation under Molecular Crowding Conditions J. Am. Chem. Soc. 128, 7957-7963 (Pubitemid 43945737)
33. 3) J. Am. Chem. Soc. 132, 17105-17107
34. Montelione, G. T. and Wagner, G. (1989) 2D chemical exchange NMR spectroscopy by proton-detected heteronuclear correlation J. Am. Chem. Soc. 111, 3096-3098
35. Podbevsek, P., Hud, N. V., and Plavec, J. (2007) NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution Nucleic Acids Res. 35, 2554-2563 (Pubitemid 47073669)
36. 2 G-Quadruplex J. Am. Chem. Soc. 130, 14287-14293
37. + ions Org. Biomol. Chem. 2, 1970-1973
38. Sket, P. and Plavec, J. (2010) Tetramolecular DNA Quadruplexes in Solution: Insights into Structural Diversity and Cation Movement J. Am. Chem. Soc. 132, 12724-12732
39. Trajkovski, M., Sket, P., and Plavec, J. (2009) Cation localization and movement within DNA thrombin binding aptamer in solution Org. Biomol. Chem. 7, 4677-4684
40. 4 Fragment Biopolymers 89, 797-806