Triplex-forming molecules: From concepts to applications

Journal of Gene Medicine

Volumn 3, Issue 4, 2001, Pages 299-310

  Faria, Marcella ^a   Giovannangeli, Carine ^b  

^a FEDERAL UNIVERSITY OF SÃO PAULO   (Brazil)

^b MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

Author keywords

Peptide nucleic acid (PNA); Recombination; Transcription; Triple helix

Indexed keywords

ANIMALIA;

DNA; PEPTIDE NUCLEIC ACID; TRIPLEX DNA;

ANIMAL; CELL CULTURE; CHEMISTRY; CONFORMATION; DNA DAMAGE; GENE EXPRESSION REGULATION; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; REVIEW; SITE DIRECTED MUTAGENESIS;

ANIMALS; CELLS, CULTURED; DNA; DNA DAMAGE; GENE EXPRESSION REGULATION; MUTAGENESIS, SITE-DIRECTED; NUCLEIC ACID CONFORMATION; PEPTIDE NUCLEIC ACIDS; RECOMBINATION, GENETIC; TRANSCRIPTION, GENETIC;

EID: 0035404317     PISSN: 1099498X     EISSN: None     Source Type: Journal    
DOI: 10.1002/jgm.192     Document Type: Article

References (97)

1. Le Doan T, Perrouault L, Praseuth D, et al. Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-a-thymidilate covalently linked to an azidoproflavine derivative. Nucleic Acids Res 1987; 15: 7749-7760.
2. Moser D, Dervan PB. Sequence-specific cleavage of double-helical DNA by triple-helix formation. Science 1987; 238: 645-650.
3. White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature 1998; 391: 468-471.
4. Helene C. DNA recognition. Reading the minor groove. Nature 1998; 391: 436-438.
5. Floreancig PE, Swalley SE, Trauger JW, Dervan PB. Recognition of the minor groove of DNA by hairpin polyamides containing a-substituted-b-amino acids. J Am Chem Soc 2000; 122: 6342-6350.
6. Dickinson LA, Gulizia RJ, Trauger JW, et al. Inhibition of RNA polymerase II transcription in human cells by synthetic DNA-binding ligands. Proc Natl Acad Sci USA 1998; 95: 12890-12895.
7. Mapp AK, Ansari AZ, Ptashne M, Dervan PB. Activation of gene expression by small molecule transcription factors. Proc Natl Acad Sci USA 2000; 97: 3930-3935.
8. Isalan M, Klug A, Choo Y. Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers. Biochemistry 1998; 37: 12026-12033.
9. Kim JS, Pabo CO. Getting a handhold on DNA: design of polyzinc finger proteins with femtomolar dissociation constants. Proc Natl Acad Sci USA 1998; 95: 2812-2817.
10. Beerli RR, Segal DJ, Dreier B, Barbas III CF. Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks. Proc Natl Acad Sd U S A 1998; 95: 14628-14633.
11. Beerli RR, Dreier B, Barbas CF. Positive and negative regulation of endogenous genes by designed transcription factors. Proc Natl Acad Sci USA 2000; 97: 1495-1500.
12. Thuong NT, Hélène C.Sequence-specific recognition modification of double-helical DNA. Angew Chem Int Engl 1993; 32: 666-690.
13. Arimondo PB, Barcelo F, Sun JS, Maurizot JC, Garestier T, Helene C. Triple helix formation by (G,A)-containing oligonucleotides: asymmetric sequence effect. Biochemistry 1998; 37: 16627-16635.
14. Debin A, Laboulais C, Ouali M, Malvy C, Le Bret M, Svinarchuk F. Stability of G,A triple helices. Nucleic Acids Res 1999; 27: 2699-2707.
15. Mills M, Arimondo PB, Lacroix L, et al. Energetics of strand-displacement reactions in triple helices: a spectroscopic study. J Mol Biol 1999; 291: 1035-1054.
16. Olivas WM, Maher III LJ. Competitive triplex/quadruplex equilibria involving guanine-rich oligonucleotides. Biochemistry 1995; 34: 278-284.
17. Svinarchuk F, Cherny D, Debin A, Delain E, Malvy C. A new approach to overcome potassium-mediated inhibition of triplex formation. Nucleic Acids Res 1996; 24: 3858-3865.
18. Noonberg SB, François JC, Garestier T, Hélène C. Effect of competing self-structure on triplex formation with purine-rich oligodeoxynucleotides containing GA repeats. Nucleic Acids Res 1995; 23: 1956-1963.
19. Faruqi AF, Krawczyk SH, Matteucci MD, Glazer PM. Potassium-resistant triple helix formation and improved intracellular gene targeting by oligodeoxyribonucleotides containing 7-deazaxanthine. Nucleic Acids Res 1997; 25: 633-640.
20. Escude C, Giovannangeli C, Sun JS, et al. Stable triple helices formed by oligonucleotide N3′→P5′ phosphoramidates inhibit transcription elongation. Proc Natl Acad Sci USA 1996; 93: 4365-4369.
21. Dagle JM, Weeks DL. Positively charged oligonucleotides overcome potassium-mediated inhibition of triplex DNA formation. Nucleic Acids Res 1996; 24: 2143-2149.
22. Faria M, Wood CD, Perrouault L, et al. Targeted inhibition of transcription elongation in cells mediated by triplex-forming oligonucleotides. Proc Natl Acad Sci USA 2000; 97: 3862-3867.
23. Bailey C, Weeks DL. Understanding oligonucleotide-mediated inhibition of gene expression in Xenopus laevis oocytes. Nucleic Acids Res 2000; 28: 1154-1161.
24. Skorski T, Perrotti D, Nieborowska-Skorska M, Gryaznov S, Calabretta B. Antileukemia effect of c-myc N3′-P5′ phosphoramidate antisense oligonucleotides in vivo. Proc Natl Acad Sci USA 1997; 94: 3966-3971.
25. Bentin T, Nielsen PE. Triplexes involving pNA. In Triple Helix-forming Oligonucleotides, Malvy C, Harel-Bellan A, Pritchard LL (eds). Kluwer Academic Publishers: Norwell, 1999; 245-256.
26. Faruqi AF, Egholm M, Glazer PM. Peptide nucleic acid-targeted mutagenesis of a chromosomal gene in mouse cells. Proc Natl Acad Sci USA 1998; 95: 1398-1403.
27. Wang G, Xu X, Pace B, et al. Peptide nucleic acid (PNA) binding-mediated induction of human gamma- globin gene expression. Nucleic Acids Res 1999; 27: 2806-2813.
28. Cutrona G, Carpaneto EM, Ulivi M, et al. Effects in live cells of a c-myc anti-gene PNA linked to a nuclear localization signal. Nat Biotechnol 2000; 18: 300-303.
29. Pooga M, Soomets U, Hallbrink M, et al. Cell penetrating PNA constructs regulate galanin receptor levels and modify pain transmission in vivo. Nat Biotechnol 1998; 16: 857-861.
30. Zarytova V, Levina A. Oligonucleotides as artificial DNases. In Triple Helix-forming Oligonucleotides, Malvy C, Harel-Bellan A, Pritchard LL (eds). Kluwer Academic Publishers: Norwell, 1999; 87-97.
31. Giovannangeli C, Diviacco S, Labrousse V, Gryaznov S, Charneau P, Helene C. Accessibility of nuclear DNA to triplex-forming oligonucleotides: the integrated HIV-1 provirus as a target. Proc Natl Acad Sci USA 1997; 94: 79-84.
32. Grigoriev M, Praseuth D, Guieysse AL, et al. Inhibition of gene expression by triple helix-directed DNA cross-linking at specific sites. Proc Natl Acad Sci USA 1993; 90: 3501-3505.
33. Intody Z, Perkins BD, Wilson JH, Wensel TG. Blocking transcription of the human rhodopsin gene by triplex-mediated DNA photocrosslinking. Nucleic Acids Res 2000; 28: 4283-4290.
34. Barre FX, Ait-Si-Ali S, Giovannangeli C, et al. Unambiguous demonstration of triple-helix-directed gene modification. Proc Natl Acad Sci USA 2000; 97: 3084-3088.
35. Guieysse AL, Praseuth D, Giovannangeli C, Asseline U, Helene C. Psoralen adducts induced by triplex-forming oligonucleotides are refractory to repair in HeLa cells. J Mol Biol 2000; 296: 373-383.
36. François JC, Saison-Behmoaras T, Barbier C, Chassignol M, Thuong NT, Hélène C. Sequence-specific recognition and cleavage of duplex DNA via triple helix formation by oligonucleotides covalently linked to a phenanthroline-copper chelate. Proc Natl Acad Sci USA 1989; 86: 9702-9706.
37. Zain R, Marchand C, Sun J, et al. Design of a triple-helix-specific cleaving, hem Biol 1999; 6: 771-777.
38. Escude C, Nguyen CH, Kukreti S, et al. Rational design of a triple helix-specific intercalating ligand. Proc Natl Acad Sci USA 1998; 95: 3591-3596.
39. Matteucci M, Lin HY, Huang T, et al. Sequence-specific targeting of duplex DNA using a camptothecin-triple helix forming oligonucleotide conjugate and topoisomerase I. J Am Chem Soc 1997; 119: 6939-6940.
40. Arimondo PB, Bailly C, Boutonne A, Sun JS, Garestier T, Helene C. Targeting topoisomerase I cleavage to specific sequences of DNA by triple helix-forming oligonucleotide conjugates. A comparison between a rebeccamycin derivative and camptothecin. C R Acad Sci III 1999; 322: 785-790.
41. Guieysse AL, Praseuth D. Triplex-binding proteins. In Triple Helix-forming Oligonucleotides, Malvy C, Harel-Bellan A, Pritchard LL (eds). Kluwer Academic Publishers: Norwell, 1999; 223-231.
42. Nelson LD, Musso M, Van Dyke MW. The yeast STM1 gene encodes a purine motif triple helical DNA-binding protein. J Biol Chem 2000; 275: 5573-5581.
43. Musso M, Bianchi-Scarra G, Van Dyke MW. The yeast CDP1 gene encodes a triple-helical DNA-binding protein. Nucleic Acids Res 2000; 28: 4090-4096.
44. Svinarchuk F, Debin A, Bertrand JR, Malvy C. Investigation of the intracellular stability and formation of a triple helix formed with a short purine oligonucleotide targeted to the murine c-pim-1 proto-oncogene promotor. Nucleic Acids Res 1996; 24: 295-302.
45. Belousov ES, Afonina IA, Kutyavin IV, et al. Triplex targeting of a native gene in permeabilized intact cells: covalent modification of the gene for the chemokine receptor CCR5. Nucleic Acids Res 1998; 26: 1324-1328.
46. Oh DH, Hanawalt PC. Triple helix-forming oligonucleotides target psoralen adducts to specific chromosomal sequences in human cells. Nucleic Acids Res 1999; 27: 4734-4742.
47. Sedelnikova OA, Panyutin IG, Luu AN, Neumann RD. The stability of DNA triplexes inside cells as studied by iodine-125 radioprinting. Nucleic Acids Res 1999; 27: 3844-3850.
48. Postel EH, Flint SJ, Kessler DJ, Hogan ME. 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 1991; 88: 8227-8231.
49. Grigoriev M, Praseuth D, Guieysse AL, et al. Inhibition of interleukin-2 receptor alpha-subunit gene expression by oligonucleotide-directed triple helix formation. C R Acad Sci III 1993; 316: 492-495.
50. Tu GC, Cao QN, Israel Y. Inhibition of gene expression by triple helix formation in hepatoma cells. J Biol Chem 1995; 270: 28402-28407.
51. Kovacs A, Kandala JC, Weber KT, Guntaka RV. 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 1996; 271: 1805-1812.
52. Joseph J, Kandala JC, Veerapanane D, Weber KT, Guntaka RV. Antiparallel polypurine phosphorothioate oligonucleotides form stable triplexes with the rat alpha 1(I) collagen gene promoter and inhibit transcription in cultured rat fibroblasts. Nucleic Acids Res 1997; 25: 2182-2188.
53. Kochetkova M, Shannon MF. DNA triplex formation selectively inhibits granulocyte-macrophage colony-stimulating factor gene expression in human T cells. J Biol Chem 1996; 271: 14438-14444.
54. Ing NH, Beekman JM, Kessler DJ, et al. In vivo transcription of a progesterone-responsive gene is specifically inhibited by a triplex-forming oligonucleotide. Nucleic Acids Res 1993; 21: 2789-2796.
55. Aggarwal BB, Schwarz L, Hogan ME, Rando RF. Triple helix-forming oligodeoxyribonucleotides targeted to the human tumor necrosis factor (TNF) gene inhibit TNF production and block the TNF-dependent growth of human glioblastoma tumor cells. Cancer Res 1996; 56: 5156-5164.
56. Porumb H, Gousset H, Letellier R, et al. Temporary ex vivo inhibition of the expression of the human oncogene HER2 (NEU) by a triple helix-forming oligonucleotide. Cancer Res 1996; 56: 515-522.
57. Ritchie S, Boyd FM, Wong J, Bonham K. Transcription of the human c-Src promoter is dependent on Sp1, a novel pyrimidine binding factor SPy, and can be inhibited by triplex-forming oligonucleotides. J Biol Chem 2000; 275: 847-854.
58. Catapano CV, McGuffie EM, Pacheco D, Carbone GM. Inhibition of gene expression and cell proliferation by triple helix-forming oligonucleotides directed to the c-myc gene. Biochemistry 2000; 39: 5126-5138.
59. Musso M, Wang JC, Van Dyke MW. In vivo persistence of DNA triple helices containing psoralen-conjugated oligodeoxyribonucleotides. Nucleic Acids Res 1996; 24: 4924-4932.
60. Michelotti EF, Tomonaga T, Krutzsch H, Levens D. Cellular nucleic acid binding protein regulates the CT element of the human c-myc protooncogene. J Biol Chem 1995; 271: 9494-9499.
61. Neurath MF, Max EE, Strober W. Pax (BSAP) regulates the murine immunoglobulin 3′ a enhancer by suppressing binding of NF-aP, a protein that controls heavy chain transcription. Proc Natl Acad Sci USA 1995; 92: 5336-5340.
62. Kuznetsova S, Ait-Si-Ali S, Nagibneva I, et al. Gene activation by triplex-forming oligonucleotide coupled to the activating domain of protein VP16. Nucleic Acids Res 1999; 27: 3995-4000.
63. Mollegaard NE, Buchardt O, Egholm M, Nielsen PE. Peptide nucleic acid. DNA strand displacement loops as artificial transcription promoters. Proc Natl Acad Sci USA 1994; 91: 3892-3895.
64. Westin L, Blomquist P, Milligan JF, Wrange O. Triple helix DNA alters nucleosomal histone-DNA interactions and acts as a nucleosome barrier. Nucleic Acids Res 1995; 23: 2184-2191.
65. Brown PM, Madden CA, Fox KR. Triple-helix formation at different positions on nucleosomal DNA. Biochemistry 1998; 37: 16139-16151.
66. Shevelev A, Burfeind P, Schulze E, et al. Potential triple helix-mediated inhibition of IGF-I gene expression significantly reduces tumorigenicity of glioblastoma in an animal model. Cancer Gene Ther 1997; 4: 105-112.
67. Rininsland F, Johnson TR, Chernicky CL, et al. Suppression of insulin-like growth factor type I receptor by a triple-helix strategy inhibits IGF-I transcription and tumorigenic potential of rat C6 glioblastoma cells. Proc Natl Acad Sci USA 1997; 94: 5854-5859.
68. Vasquez KM, Narayanan L, Glazer PM. Specific mutations induced by triplex-forming oligonucleotides in mice. Science 2000; 290: 530-533.
69. Zendegui JG, Vasquez KM, Tinsley JH, Kessler DJ, Hogan ME. In vivo stability and kinetics of absorption and disposition of 3′ phosphopropyl amine oligonucleotides. Nucleic Acids Res 1992; 20: 307-314.
70. Wang G, Seidman MM, Glazer PM. Mutagenesis in mammalian cells induced by triple helix formation and transcription-coupled repair. Science 1996; 271: 802-805.
71. Vasquez KM, Wang G, Havre PA, Glazer PM. Chromosomal mutations induced by triplex-forming oligonucleotides in mammalian cells. Nucleic Acids Res 1999; 27: 1176-1181.
72. Majumdar A, Khorlin A, Dyatkina N, et al. Targeted gene knockout mediated by triple helix forming oligonucleotides. Nat Genet 1998; 20: 212-214.
73. Wang G, Levy DD, Seidman MM, Glazer PM. Targeted mutagenesis in mammalian cells mediated by intracellular triple helix formation. Mol Cell Biol 1995; 15: 1759-1768.
74. Barre FX, Giovannangeli C, Helene C, Harel-Bellan A. Covalent crosslinks introduced via a triple helix-forming oligonucleotide coupled to psoralen are inefficiently repaired. Nucleic Acids Res 1999; 27: 743-749.
75. Barre FX, Asseline U, Harel-Bellan A. Asymmetric recognition of psoralen interstrand crosslinks by the nucleotide excision repair and the error-prone repair pathways. J Mol Biol 1999; 286: 1379-1387.
76. Faruqi AF, Datta HJ, Carroll D, Seidman MM, Glazer PM. Triple-helix formation induces recombination in mammalian cells via a nucleotide excision repair-dependent pathway. Mol Cell Biol 2000; 20: 990-1000.
77. Luo Z, Macris MA, Faruqi AF, Glazer PM. High-frequency intrachromosomal gene conversion induced by triplex-forming oligonucleotides microinjected into mouse cells. Proc Natl Acad Sci USA 2000; 97: 9003-9008.
78. Chan PP, Lin M, Faruqi AF, Powell J, Seidman MM, Glazer PM. Targeted correction of an episomal gene in mammalian cells by a short DNA fragment tethered to a triplex-forming oligonucleotide. J Biol Chem 1999; 274: 11541-11548.
79. Culver KW, Hsieh WT, Huyen Y, et al. Correction of chromosomal point mutations in human cells with bifunctional oligonucleotides. Nat Biotechnol 1999; 17: 989-993.
80. Diesbach P, Berens C, N'Kuli F, et al. Identification, purification and partial characterisation of an oligonucleotide receptor in membranes of HepG2 cells. Nucleic Acids Res 2000; 28: 868-874.
81. Lorenz P, Misteli T, Baker BF, Bennett CF, Spector DL. Nucleocytoplasmic shuttling: a novel in vivo property of antisense phosphorothioate oligodeoxynucleotides. Nucleic Acids Res 2000; 28: 582-592.
82. Laktionov PP, Dazard JE, Vives E, et al. Characterisation of membrane oligonucleotide-binding proteins and oligonucleotide uptake in keratinocytes. Nucleic Acids Res 1999; 27: 2315-2324.
83. Dheur S, Dias N, van Aerschot A, et al. Polyethylenimine but not cationic lipid improves antisense activity of 3′-capped phosphodiester oligonucleotides. Antisense Nucleic Acid Drug Dev 1999; 9: 515-525.
84. Wang Z, Rana TM. DNA damage-dependent transcriptional arrest and termination of RNA polymerase II elongation complexes in DNA template containing HIV-1 promoter. Proc Natl Acad Sci USA 1997; 94: 6688-6693.
85. Firman K, Szczelkun MD. Measuring motion on DNA by the type I restriction endonuclease EcoR124I using triplex displacement. EMBO J 2000; 19: 2094-2102.
86. Liberles DA, Dervan PB. Design of artificial sequence-specific DNA bending ligands. Proc Natl Acad Sci USA 1996; 93: 9510-9514.
87. Zelphati O, Liang X, Nguyen C, et al. PNA-dependent gene chemistry: stable coupling of peptides and oligonucleotides to plasmid DNA. Biotechniques 2000; 28: 304-310, 312-314, 316.
88. Wils P, Escriou V, Warnery A, et al. Efficient purification of plasmid DNA for gene transfer using triple-helix affinity chromatography. Gene Ther 1997; 4: 323-330.
89. Escriou V, Lagneaux D, Crouzet J, Wils P, Scherman D. Triple helix formation on plasmid DNA determined by a size-exclusion Chromatographic method. Anal Biochem 1997; 248: 102-110.
90. Zelphati O, Liang X, Hobart P, Felgner PL. Gene chemistry: functionally and conformationally intact fluorescent plasmid DNA. Hum Gene Ther 1999; 10: 15-24.
91. Neves C, Byk G, Escriou V, Bussone F, Scherman D, Wils P. Novel method for covalent fluorescent labeling of plasmid DNA that maintains structural integrity of the plasmid. Bioconjug Chem 2000; 11: 51-55.
92. Branden LJ, Mohamed AJ, Smith CI. A peptide nucleic acid-nuclear localization signal fusion that mediates nuclear transport of DNA. Nat Biotechnol 1999; 17: 784-787.
93. Neves C, Byk G, Scherman D, Wils P. Coupling of a targeting peptide to plasmid DNA by covalent triple helix formation. FEBS Lett 1999; 453: 41-45.
94. Zanta MA, Belguise-Valladier P, Behr JP. Gene delivery: a single nuclear localization signal peptide is sufficient to carry DNA to the cell nucleus. Proc Natl Acad Sci USA 1999; 96: 91-96.
95. Escude C, Garestier T, Helene C. Padlock oligonucleotides for duplex DNA based on sequence-specific triple helix formation. Proc Natl Acad Sci USA 1999; 96: 10603-10607.
96. Giovannangeli C, Helene C. Triplex technology takes off. Nat Biotechnol 2000; 18: 1245-1246.
97. de Bizemont T, Duval-Valentin G, Sun JS, Bisagni E, Garestier T, Helene C. Alternate strand recognition of double-helical DNA by (T,G)-containing oligonucleotides in the presence of a triple helix-specific ligand. Nucleic Acids Res 1996; 24: 1136-1143.