Structural transition from antiparallel to parallel G-quadruplex of d(G4T4G4) induced by Ca2+

Nucleic Acids Research

Volumn 31, Issue 4, 2003, Pages 1156-1163

  Miyoshi, Daisuke ^a   Nakao, Akihiro ^a   Sugimoto, Naoki ^a  

^a KONAN UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM ION; DIVALENT CATION; GUANINE; OLIGONUCLEOTIDE;

APPARATUS; ATOMIC FORCE MICROSCOPY; CALCIUM BINDING; CIRCULAR DICHROISM; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA STRAND; GEL PERMEATION CHROMATOGRAPHY; IN VITRO STUDY; IN VIVO STUDY; ISOMERISM; KINETICS; NUCLEIC ACID STRUCTURE; NUCLEOTIDE SEQUENCE; OLIGOMERIZATION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVIEW; SCANNING ELECTRON MICROSCOPY; THERMODYNAMICS;

BASE SEQUENCE; BINDING SITES; CALCIUM; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CIRCULAR DICHROISM; DNA; GUANINE; KINETICS; MICROSCOPY, ATOMIC FORCE; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; THERMODYNAMICS;

EID: 0037440745     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg211     Document Type: Review

References (42)

1. Williamson,J.R., Raghuraman,M.K. and Cech,T.R. (1989) Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell, 59, 871-880.
2. Basu,S., Szewczak,A.A., Cocco,M. and Strobel,S.A. (2000) Direct detection of monovalent metal ion binding to a DNA G-quartet by 205T1 NMR. J. Am. Chem. Soc., 122, 3240-3245.
3. Keniry,M.A. (2001) Quadruplex structures in nucleic acids. Biopolymers, 56, 123-146.
4. Bock,L.C., Griffin,L.C., Latham,J.A., Vermaas,E.H. and Toole,J.J. (1992) Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature, 355, 564-566.
5. Williamson,J.R. (1994) G-quartet structures in telomeric DNA. Annu. Rev. Biophys. Biomol. Struct. Biol., 23, 703-730.
6. Kettani,A., Kumar,R.A. and Patel,D.J. (1995) Solution structure of a DNA quadruplex containing the fragile X syndrome triplet repeat. J. Mol. Biol., 254, 638-656.
7. Blackburn,E.H. (1994) Telomeres: no end in sight. Cell, 77, 621-623.
8. Arthanari,H. and Bolton,P.H. (2001) Functional and dysfunctional roles of quadruplex DNA in cells. Chem. Biol., 72, 1-10.
9. Macaya,R.F., Schultze,P., Smith,F.W., Roe,J.A. and Feigon,J. (1993) Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. Proc. Natl Acad. Sci. USA, 90, 3745-3749.
10. Jing,N. and Hogan,M.E. (1998) Structure-activity of tetrad-forming oligonucleotides as a potent anti-HIV therapeutic drug. J. Biol. Chem., 273, 34992-34999.
11. Forman,S.L., Fettinger,J.C., Pieraccini,S., Gottarelli,G. and Davis.J.T. (2000) Toward artificial ion channels: a lipophilic G-quadruplex J. Am. Chem. Soc., 122, 4060-4067.
12. Sugimoto,N., Toda,T. and Ohmichi,T. (1998) Reaction field for efficient porphyrin metallation catalysis produced by self-assembly of a short DNA oligonucleotide. Chem. Commun., 1533-1534.
13. 4). FEBS Lett., 496, 128-133.
14. 2+. Biophys. J., 73, 348-356.
15. 2+ facilitates intermolecular G-quadruplex formation of telomeric sequences. Biochemistry, 31, 3769-3776.
16. Venczel,E.A. and Sen,D. (1993) Parallel and antiparallel G-DNA structures from a complex telomeric sequence. Biochemistry, 32, 6220-6228.
17. Parkinson,G.N., Lee,M.,P. and Neidle,S. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature, 417, 876-880.
18. Sugimoto,N., Nakano,M. and Nakano,S. (2000) Thermodynamics-structure relationship of single mismatches in RNA-DNA duplexes. Biochemistry, 39, 11270-11281.
19. Ohmichi,T., Nakano,S., Miyoshi,D. and Sugimoto,N. (2002) Long RNA dangling end has large energetic contribution to duplex stability. J. Am. Chem. Soc., 124, 10367-10372.
20. Richard,E.G. (1975) Handbook of Biochemistry and Molecular Biology: Nucleic Acids, 3rd Edn. CRC Press, Cleveland, UK, Vol. 1, p. 597.
21. Balagurumoorthy,P., Brahmachari,S.K., Mohanty,D., Bansal,M. and Sasisekharan,V. (1992) Hairpin and parallel quartet structures for telomeric sequences. Nucleic Acids Res., 20, 4061-4067.
22. 3T). Proc. Natl Acad. Sci. USA, 89, 8832-8836.
23. Schultze,P., Smith,F.W. and Feigon,J. (1994) Refined solution structure of the dimeric quadruplex formed from the Oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG). Structure, 2, 221-233.
24. + in DNA quadruplexes is dominated by relative free energies of hydration: a thermodynamic analysis by 1H NMR. Biochemistry, 35, 15383-15390.
25. 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.
26. Sclavi,B., Sullivan,M., Chance,M.R., Brenowitz,M. and Woodson,S. (1998) RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science, 279, 1940-1943.
27. Russell,R., Millett,I.S., Doniach,S. and Herschlag,D. (2000) Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nature Struct. Biol., 7, 367-370.
28. 2+ concentrations. Biochemistry, 27, 6384-6392.
29. 2+ binding interactions. Nucleic Acids Res., 17, 355-371.
30. Russell,R. and Herschlag,D. (1999) New pathways in folding of the Tetrahymena group I RNA enzyme. J. Mol. Biol., 291, 1155-1167.
31. Li,Y., Bevilacqua,P.C., Mathews,D. and Turner,D.H. (1995) Thermodynamic and activation parameters for binding of a pyrenelabeled substrate by the Tetrahymena ribozyme: docking is not diffusion-controlled and is driven by a favorable entropy change. Biochemistry, 34, 14394-14399.
32. Walter,N.G., Hampel,K.J., Brown,K.M. and Burke,J.M. (1998) Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer. EMBO J., 17, 2378-2391.
33. 2+-dependent folding of a large ribozyme without kinetic traps. Nature Struct. Biol., 6, 1091-1095.
34. Emerick,V.L., Pan,J. and Woodson,S.A. (1996) Analysis of rate-determining conformational changes during self-splicing of the Tetrahymena intron. Biochemistry, 35, 13469-13477.
35. Bhuyan,A.K. and Udgaonkar,J.B. (1999) Observation of multistate kinetics during the slow folding and unfolding of barstar. Biochemistry, 38, 9158-9168.
36. Wyatt,J.R., Davis,P.W. and Freier,S.M. (1996) Kinetics of G-quartet-mediated tetramer formation. Biochemistry, 35, 8002-8008.
37. Hardin,C.C., Perry,A.G. and White,K. (2001) Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids. Biopolymers, 56, 147-194.
38. March,T.C. and Henderson,E. (1994) G-wires: self-assembly of a telomeric oligonucleotide, d(GGGGTTGGGG), into large superstructures. Biochemistry, 33, 10718-10724.
39. Marsh,T.C., Vesenka,J. and Henderson,E. (1995) A new DNA nanostructure, the G-wire, imaged by scanning probe microscopy. Nucleic Acids Res., 23, 696-700.
40. Protozanova,E. and Macgregor,R.B.,Jr (1998) Circular dichroism of DNA frayed wires. Biophys. J., 75, 982-989.
41. 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.
42. Miyoshi,D., Nakao,A. and Sugimoto,N. (2002) Molecular crowding regulates the structural switch of the DNA G-quadruplex. Biochemistry, 42, 15017-15024.