Effect of cations on purine·purine·pyrimidine triple helix formation in mixed-valence salt solutions

European Journal of Biochemistry

Volumn 260, Issue 3, 1999, Pages 801-809

  Floris, Romina ^b   Scaggiante, Bruna ^b   Manzini, Giorgio ^b   Quadrifoglio, Franco ^b   Xodo, Luigi E ^a  

^a UNIVERSITY OF UDINE   (Italy)

^b NONE

Author keywords

bcr gene; Bivalent cations; Ki ras gene; Monovalent cations; Purine purine pyrimidine triplex

Indexed keywords

CATION; PURINE; PYRIMIDINE; SODIUM CHLORIDE;

ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; CONCENTRATION RESPONSE; DNA FOOTPRINTING; ELECTROPHORETIC MOBILITY; HYDROGEN BOND; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION; TRIPLE HELIX;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CATIONS, DIVALENT; CATIONS, MONOVALENT; DNA; GENES, RAS; HUMANS; MAGNESIUM; MICE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; ONCOGENE PROTEINS; POTASSIUM; PROTEIN-TYROSINE KINASES; PROTO-ONCOGENE PROTEINS; PROTO-ONCOGENE PROTEINS C-BCR; SEQUENCE ALIGNMENT;

EID: 0000884532     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1327.1999.00219.x     Document Type: Article

References (61)

1. Behe, M.J. (1995) An overabundance of long oligopurine tracts in the genome of simple and complex eukaryotes. Nucleic Acids Res. 23, 689-691.
2. Beal, P.A. & Dervan, P.B. (1991) Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation. Science 251, 1360-1363.
3. Durland, R.H., Kessler, D.J., Gunnell, S., Duvic, M., Pettitt, B.M. & Hogan, M.E. (1991) Binding of triple helix forming oliginucleotides to sites in gene promoters. Biochemistry 30, 9246-9255.
4. Pilch, D.S. & Shafer, R.H. (1991) Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix. Biochemistry 30, 6081-6087.
5. Xodo, L. (1995) Characterization of the DNA formed by d(TGGGTGGGTGGT-TGGGTGGG) and a critical R·Y sequence located in the promoter of the murine Ki-ras proto-oncogene. FEBS Lett. 370, 153-157.
6. Xodo, L., Pirulli, D. & Quadrifoglio, F. (1997) A kinetic study of triple-helix formation ar a critical R·Y sequence of the murine c-Ki-ras promoter by AG and GT oligonucleotides. Eur. J. Biochem. 248, 424-432.
7. Alunni-Fabbroni, M., Pirulli, D., Manzini, G. & Xodo, L. (1996) AG oligonucleotides form extraordinary stable triple helices with a critical R·Y sequence of the murine Ki-ras promoter and inhibit transcription in transfected NIH 3T3 cells. Biochemistry 35, 16261-16369.
8. Alunni-Fabbroni, M., Manzini, G., Quadrifoglio, F. & Xodo, L. (1996) Guanine-rich oligonucleotides targeted to a critical R·Y sites in the Ki-ras promoter. Effect of competing self-structures on triplex formation. Eur. J. Biochem. 238, 141-151.
9. Svinarchuk, F., Paoletti, J. & Malvy, C. (1995) An unusually stable purine-purine-pyrimidine short triplex. The third strand stabilises double-stranded DNA. J. Biol. Chem. 270, 14068-14071.
10. Svinarchuk, F., Debin, A., Bertrand, J.R. & Malvy, C. (1996) Investigation of the intracellular stability and formation of a triplex formed with a short purine oligonucleotide targeted to the murine c-pim-1 oncogene promoter. Nucleic Acids Res. 24, 295-302.
11. Doronina, S.O. & Behr, J.P. (1997) Towards a general triple helix mediated DNA recognition scheme. Chem. Soc. Rev. 26, 63-71.
12. Vasquez, K. & Wilson, J. (1996) Triplex-directed modification of genes and gene activity. Trends Biol. Sci. 23, 4-9.
13. Giovannangeli, C. & Hélène, C. (1997) Progress in developments of triplex-base strategies. Antisense Nucleic Acid Drug Dev. 7, 413-421.
14. Cooney, M., Czernuszewicz, G., Postel, E.H., Flint, S.J. & Hogan, M. (1988) Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro. Science 241, 456-459.
15. Orson, F.M., Thomas, D.W., McShan, M.W., Kessler, D.J. & Hogan, M.E. (1991) Oligonucleotide inhibition of IL2R alpha mRNA transcription by promoter region collinear triplex formation in lymphocytes. Nucleic Acids Res. 19, 3435-3441.
16. Postel, E.H., Flint, S.J., Kessler, D.J. & Hogan, M.E. (1991) Evidence that a triplex-forming oligodeoxyribonucleotide binds to the c-myc promoter in HeLa cells, thereby reducing c-myc mRNA levels. Proc. Natl Acad. Sci. USA 88, 8227-8231.
17. McShan, M.W., Rossen, R.D., Laughter, A.H., Trial, J., Kessler, D.J., Zendegui, J.G., Hogan, M.E. & Orson, F.M. (1992) Inhibition of transcription of HIV-1 in infected human cells by oligodeoxynucleotides designed to form DNA triple helices. J. Biol. Chem. 267, 5712-5721.
18. Grigoriev, M., Praseuth, D., Robin, P., Hemar, A., Saison-Behmoaras, T., Dautry-Varsat, A., Thuong, N.T. & Hélène, C. (1992) A triple helix-forming oligonucleotide-intercalator conjugate acts as a transcriptional repressor via inhibition of NF kappa B binding to interleukin-2 receptor alpha-regulatory sequence. J. Biol. Chem. 267, 3389-3395.
19. Scaggiante, B., Morassutti, C., Tolazzi, G., Michelutti, A., Baccarani, M. & Quadrifoglio, F. (1994) Effect of unmodified triple helix-forming oligodeoxyribonucleotide targeted to human multidrug-resistance gene mdrl in MDR cancer cells. FEBS Lett. 352, 380-384.
20. Kovacs, A., Kandala, J.C., Weber, K.T. Guntaka, R.V. (1996) Triple helix-forming oligonucleotide corresponding to the polypyrimidine sequence in the rat alpha 1 (I) collagen promoter specifically inhibits factor binding and transcription. J. Biol. Chem. 271, 1805-1812.
21. Kim, H.G. & Miller, D.M. (1995) Inhibition of in vitro transcription by a triplex-forming oligonucleotide targeted to human c-myc P2 promoter. Biochemistry 25, 8165-8171.
22. Xodo, L., Manzini, G. & Quadrifoglio, F. (1998) Formation of stable DNA triple helices within the human bcr promoter ar a critical oligopurine site interrupted in the middle by two adjacent pyrimidines. Antisense Nucleic Acids Drug Dev. 8, 477-488.
23. Weerasinghe, S., Smith, P.E. & Pettitt, B.M. (1995) Structure and stability of a model pyrimidine-purine-purine DNA triplex with a G·C·T mismatched by simulation. Biochemistry 34, 16270-16278.
24. Dittrich, K., Gu, J., Tinder, R., Hogan, M. & Gao, X. (1994) T·C·G triplet in an antiparallel DNA triplex. Conformational studies by NMR. Biochemistry 33, 4111-4120.
25. Kukreti, S., Sun, J.-S., Garestier, T. & Hélène, C. (1997) Extension of the range of DNA sequence available for triplex formation: stabilization of mismatched triplexes by acridine-containing oligonucleotides. Nucleic Acids Res. 25, 4264-4270.
26. Gowers, D.M. & Fox, K.R. (1997) DNA triple helix formation at oligopurine sites containing multiple contiguous pyrimidines. Nucleic Acids Res. 25, 3787-3794.
27. Beal, P.A. & Dervan, P.B. (1992) The influence of single base triplet changes on the stability of a pur.pur.pyr triple helix determined by affinity cleaving. Nucleic Acids Res. 20, 2773-2776.
28. Durland, R.H., Rao, T.S., Revankar, G.R., Tinsley, J.H., Myrick, M.A., Seth, D.M., Rayford, J., Singh, P. & Jayaraman, K. (1994) Binding of T and T analogs to CG base pairs in antiparallel triplexes. Nucleic Acid Res. 22, 3233-3240.
29. Cheng, A.-J. & Van Dyke, W. (1993) Monovalent cation effects on the intermolecular purine-purine-pyrimidine triplex helix formation. Nucleic Acids Res. 21, 5630-5635.
30. Balaskaya, S.V., Belotserkovskii, B.P. & Johnston, B.H. (1996) Alternate-strand triplex formation, modulation of binding to matched and mismatched duplexes by sequence choice in the Pu-Pu-Py block. Biochemistry 35, 13328-13337.
31. Pascolo, E. & Toulmé. J.J. (1996) Double hairpin complexes allow accomodation of all four base pairs in triple helices containing both DNA and RNA strands. J. Biol. Chem. 271, 24187-24192.
32. Musso, M., Thomas, T., Shirahata, A., Sigal, L.H., Van Dyke, M.W. & Thomas, T.J. (1997) Effects of chain length modification and bis (ethyl) substitution of spermine analogs on purine-purine-pyrimidine triplex DNA stabilization, aggregation and conformational transitions. Biochemistry 36, 1441-1449.
33. Sambrook, J., Fritsch, E.F. & Maniatis, T. (1989) Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring, Harbor, NY, USA.
34. Manning, G.S. (1978) The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 11, 179-246.
35. Record, M.T. Jr, Anderson, C.F. & Lohman, T.M. (1978) Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening and effects on water activity. Q. Rev. Biophys. 11, 103-178.
36. Latimer, L.J.P., Hampel, K. & Lee, J.S. (1989) Synthetic repeating sequence DNAs containing phosphorothioates: nuclease sensitivity and triplex formation. Nucleic Acids Res. 17, 1549-1561.
37. Plum, G.E., Park, Y.W., Singleton, S.F., Dervan, P.B. & Breslauer, K.J. (1990) Thermodynamic characterization of the stability and the melting behaviour of a DNA triplex: a spectroscopic and calorimetric study. Proc. Natl Acad. Sci. USA 87, 9436-9440.
38. 12 sequences bridged by two hexethylene glycol chains. Biochemistry 31, 9197-9204.
39. Rougée, M., Faucon, B., Mergny, J.L., Barcelo, F., Giovannangeli. C., Garestier, T. & Hélène, C. (1992) Kinetics and thermodynamics of triple-helix formation: effects of ionic strength and mismatches. Biochemistry 31, 9269-9278.
40. Xodo, L. (1995) Kinetic analysis of triple-helix formation by pyrimidine oligonucleotides and duplex DNA. Eur. J. Biochem. 228, 918-926.
41. Singleton, S.F. & Dervan, P.B. (1993) Equilibrium association constants for oligonucleotide-directed triple helix formation at single DNA sites: linkage to cation valence concentration. Biochemistry 32, 13171-13179.
42. Hoffman, E.K., Trusko, S.P., Murphy, M. & George, D.L. (1990) An S1 nuclease-sensitive homopurine-homopyrimidine domain in the c-Ki-ras promoter interacts with a nuclear factor. Proc. Natl Acad. USA 87, 2705-2709.
43. Blume, S.W., Guarcello, V., Zacharias, W. & Miller, D.M. (1997) Divalent transition metal cations counteract potassium-induced quadruplex assembly of oligo (dG) sequences. Nucleic Acids Res. 25, 617-625.
44. Olivas, W.M. & Maher, L.J. (1995) Competitive triplex/quadruplex equilibria involving guanine-rich oligonucleotides. Biochemistry 34, 278-284.
45. Hampel, K.J., Crosson, P. & Lee, J.S. (1991) Polyamines favor DNA triplex formation ar neutral pH. Biochemistry 30, 4455-4459.
46. Musso, M. & van Dyke, M.W. (1995) Polyamine effects on purine-purine-pyrimidine triple helix formation by phosphodiester and phosphorothioate oligodeoxyribonucleotides. Nucleic Acids Res. 23, 2320-2327.
47. Guschlbauer, W., Chantot, J.-F. & Thiele, D. (1990) Four-stranded nucleic acid structures 25 years later: from guanosine gels to telomer DNA. J. Biomol. Struct. Dyn. 8, 491-501.
48. Rhodes, D. & Giraldo, R. (1994) Telomere structure and function. Curr. Opin. Struct. Biol. 5, 311-322.
49. 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.
50. Milligan, I.F., Krawczyk, S.H., Wadwa, N.I., & Matteucci, M.D. (1993) An anti-parallel triple helix motif with oligodeoxynucleotides containing 2′-deoxyguanosine and 7-deaza-2′-deoxyxanthosine. Nucleic Acids Res. 21, 367-375.
51. Olivas, W.M. & Maher, L.J. (1995) Overcoming potassium-mediated triplex inhibition. Nucleic Acids Res. 23, 1936-1941.
52. Noonberg, S.B., Francois, J.C., Garestier, T. & Hélène, C. (1995) Effect of competing self-structure on triplex formation with purine-rich oligonucleotides containing GA repeats. Nucleic Acids Res. 23, 1956-1963.
53. Lee, J.S. (1990) The stability of polypurine tetraplexes in the presence of mono- and divalent cations. Nucleic Acids Res. 18, 6057-6060.
54. Williamson, J.R. (1994) G-quartet structures in telomeric DNA. Annu. Rev. Biophys. Biomol. Struct. 23, 703-730.
55. Balagurumoorthy, P. & Brahmachari, S.K. (1994) Structure and stability of human telomere sequence. J. Biol. Chem. 34, 21858-21869.
56. + in DNA quadruplex is dominated by relative free of hydration: a thermodynamic analysis by 1H NMR. Biochemistry 35, 15383-15390.
57. Kohwi, Y. & Kohwi-Shigematsu, T. (1988) Magnesium ion-dependent triple-helix structure formed by homopurine-homopyrimidine sequences in supercoiled plasmid DNA. Proc. Natl Acad. Sci. USA 85, 3781-3785.
58. 2- with DNA: assessment of metal binding sites and DNA conformations by spectroscopic and thermal denaturation studies. Inorganica Chim. Acta 153, 79-86.
59. Potaman, V.N. & Soyfer, V.N. (1994) Divalent metal cations upon coordination to the N7 of purines differentially stabilize the PyPuPu DNA triplex due to unequal Hoogsteen-type hydrogen bond enhancement. J. Biomol. Struct. Dyn. 11, 1035-1040.
60. Sponar, J., Sabat, M., Burda, J.V., Doody, A.M., Leszczynski, J. & Hobza, P. (1998) Stabilization of purine-purine-pyrimidine DNA triplets by divalent metal cations. J. Biomol. Struct. Dynamics 16, 139-143.48.
61. Malkov, V.A., Voloshin, O.N., Soyfer, V.N. & Frank-Kamenetskii, D. (1993) Cation and sequence effects on stability of intermolecular pyrimidine-purine-purine triplex. Nucleic Acids Res. 21, 585-591.