A novel intramolecular G-quartet-containing fold of single-stranded d(GT)8 and d(GT)16 oligonucleotides

Biophysical Chemistry

Volumn 143, Issue 3, 2009, Pages 161-165

  Kaluzhny, Dmitry ^a   Shchyolkina, Anna ^a   Livshits, Michael ^a   Lysov, Yury ^a   Borisova, Olga ^a  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

Author keywords

CD spectra; Fluorescence of EtBr; G quadruplexes; GT repeats

Indexed keywords

DINUCLEOTIDE; ETHIDIUM BROMIDE; GUANINE; OLIGONUCLEOTIDE; SINGLE STRANDED DNA; THYMINE;

ARTICLE; CIRCULAR DICHROISM; COMPLEX FORMATION; CONTROLLED STUDY; DNA CONFORMATION; DNA DETERMINATION; HUMAN; LOW TEMPERATURE; MELTING POINT; MOLECULAR PROBE; MOUSE; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; PROTEIN FOLDING; RELAXATION TIME; THERMOSTABILITY;

CIRCULAR DICHROISM; DNA, SINGLE-STRANDED; ETHIDIUM; G-QUADRUPLEXES; HUMANS; NUCLEIC ACID CONFORMATION; POLYDEOXYRIBONUCLEOTIDES; THERMODYNAMICS; TRANSITION TEMPERATURE;

EID: 67349217685     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2009.05.006     Document Type: Article

References (24)

1. Huppert J.L. Four-stranded nucleic acids: function and targeting of G-quadruplexes. Chem. Soc. Rev. 37 (2008) 1375-1384
2. Hugnot J.P., Recan D., Jeanpierre M., Kaplan C., and Tolun A. A highly informative CACA repeat polymorphism upstream of the human dystrophin gene (DMD). Nucleic Acids Res. 19 (1991) 3159-3168
3. Cox R., and Mirkin S.M. Characteristic enrichment of DNA repeats in different genomes. Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 5237-5242
4. Denschlag D., Marculescu R., Unfried G., Hefler L.A., Exner M., Hashemi A., Riener E.K., Keck C., Tempfer C.B., and Wagner O. The size of a microsatellite polymorphism of the haem oxygenase 1 gene is associated with idiopathic recurrent miscarriage. Mol. Hum. Reprod. 10 (2004) 211-214
5. Cai Q., Gao Y.T., Wen W., Shu X.O., Jin F., Smith J.R., and Zheng W. Association of breast cancer risk with a GT dinucleotide repeat polymorphism upstream of the estrogen receptor-alpha gene. Cancer Res. 63 (2003) 5727-5730
6. Borisova O.F., Shchyolkina A.K., Timofeev E.N., and Florentiev V.L. Evidence for the tetraplex structure of the d(GT)n repetitive sequences in solution. FEBS Lett. 306 (1992) 140-142
7. Shchyolkina A.K., Borisova O.F., Livshits M.A., Klement R., and Jovin T.M. The telomeric dG(GT)4G sequence can adopt a parallel-stranded double helical conformation. J. Biomol. Struct. Dyn. 18 (2001) 493-503
8. Beschetnova I.A., Kaluzhny D.N., Livshits M.A., Shchyolkina A.K., and Borisova O.F. Ethidium probing of the parallel double- and four-stranded structures formed by the telomeric DNA sequences dG(GT)4G and d(GT)5. J. Biomol. Struct. Dyn. 20 (2003) 789-799
9. LePecq J.B., and Paoletti C. A fluorescent complex between ethidium bromide and nucleic acids. J. Mol. Biol. 27 (1967) 86-106
10. Edwards Y.J., Elgar G., Clark M.S., and Bishop M.J. The identification and characterization of microsatellites in the compact genome of the Japanese pufferfish, Fugu rubripes: perspectives in functional and comparative genomic analyses. J. Mol. Biol. 278 4 (1998) 843-854
11. Mirkin S.M. Discovery of alternative DNA structures: a heroic decade (1979-1989). Front Biosci. 13 (2008) 1064-1071
12. Wyatt J.R., Davis P.W., and Freier S.M. Kinetics of G-quartet-mediated tetramer formation. Biochemistry 35 24 (1996) 8002-8008
13. Bugaut A., and Balasubramanian S. A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes. Biochemistry 47 2 (2008) 689-697
14. + solution under molecular crowding condition. J. Am. Chem. Soc. 129 36 (2007) 11185-11191
15. Vorlícková M., Bednárová K., Kejnovská I., and Kypr J. Intramolecular and intermolecular guanine quadruplexes of DNA in aqueous salt and ethanol solutions. Biopolymers 86 1 (2007) 1-10
16. Smirnov I.V., and Shafer R.H. Electrostatics dominate quadruplex stability. Biopolymers 85 1 (2007) 91-101
17. Lane A.N., Chaires J.B., Gray R.D., and Trent J.O. Stability and kinetics of G-quadruplex structures. Nucleic Acids Res. 36 17 (2008) 5482-5515
18. Duhamel J., Kanyo J., Dinter-Gottlieb G., and Lu P. Fluorescence emission of ethidium bromide intercalated in defined DNA duplexes: evaluation of hydrodynamics components. Biochemistry 35 (1996) 16687-16697
19. Parkinson G.N., Lee M.P., and Neidle S. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417 (2002) 876-880
20. Hasel P., Huppert J., Balasubramanien S., and Neidle S. Loop-length-dependent folding of G-quadruplexes. J. Am. Chem. Soc. 26 (2004) 16405-16415
21. Freizinger E., Schimanski A., and Lippert B. Thymine-metal ion interactions: relevance for thymine quartet structures. J. Biol. Inorg. Chem. 6 (2001) 378-389
22. Ito H., Tanaka S., and Miyasaka M. Circular dichroism spectra of DNA quadruplexes [d(G(5)T(5))](4) as formed with G(4) and T(4) tetrads and [d(G(5)T(5)). d(A(5)C(5))]2 as formed with Watson-Crick-like (G-C)(2) and (T-A)(2) tetrads. Biopolymers 65 2 (2002) 61-80
23. Gros J., Rosu F., Amrane S., De Sian A., Gabelica V., Lacroix L., and Mergny J.L. Guanines are a quartets best friend: impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes. Nucleic Acids Res. 35 (2007) 3064-3075
24. Yu H.O., Miuoschi D., and Sugimoto N. Characterization of structure and stability of long telomeric DNA G-quadruplexes. J. Am. Chem. Soc. 128 (2006) 15461-15468