Acta Med. 2004, 47: 151-156
https://doi.org/10.14712/18059694.2018.82
Triplex Forming Oligonucleotides – Tool for Gene Targeting
References
1. PB, Garestier T, Helene C, Sun JS. Detection of competing DNA structures by thermal gradient gel electrophoresis: from self-association to triple helix formation by (G,A)-containing oligonucleotides. Nucleic Acids Res 2001; 29(4):E15.
<https://doi.org/10.1093/nar/29.4.e15>
<PubMed>
2. DP, Bruice TC. Triple-helix formation of DNA oligomers with methylthiourea- linked nucleosides (DNmt): a kinetic and thermodynamic analysis. Proc Natl Acad Sci U S A 1999; 96(8):4384–9.
<https://doi.org/10.1073/pnas.96.8.4384>
<PubMed>
3. PJ, Macaulay VM, McLean MJ et al. Characteristics of triplex-directed photoadduct formation by psoralen-linked oligodeoxynucleotides. Nucleic Acids Res 1995; 23(21):4283–9.
<https://doi.org/10.1093/nar/23.21.4283>
<PubMed>
4. MJ. An overabundance of long oligopurine tracts occurs in the genome of simple and complex eukaryotes. Nucleic Acids Res 1995; 23(4):689–95.
<https://doi.org/10.1093/nar/23.4.689>
<PubMed>
5. E, Maurisse R, Dutreix M, Sun_JS. Stimulation of RecA-mediated D-loop formation by oligonucleotide-directed triple-helix formation: guided homologous recombination (GOREC). Biochemistry 2001; 40(6):1779–86.
<https://doi.org/10.1021/bi001605a>
6. SW, Lebowitz J, Zacharias W et al. The integral divalent cation within the intermolecular purine*purine. pyrimidine structure: a variable determinant of the potential for and characteristics of the triple helical association. Nucleic Acids Res 1999; 27(2):695–702.
<https://doi.org/10.1093/nar/27.2.695>
<PubMed>
7. DA, Corey DR. Novel antisense and peptide nucleic acid strategies for controlling gene expression. Biochemistry 2002; 41(14):4503–10.
<https://doi.org/10.1021/bi0122112>
8. M, Czernuszewicz G, Postel EH, Flint SJ, Hogan ME. Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro. Science 1988; 241(4864):456–9.
<https://doi.org/10.1126/science.3293213>
9. JM, Weeks DL. Positively charged oligonucleotides overcome potassiummediated inhibition of triplex DNA formation. Nucleic Acids Res 1996; 24(11): 2143–9.
<https://doi.org/10.1093/nar/24.11.2143>
<PubMed>
10. JM, Weeks DL. Oligonucleotide-based strategies to reduce gene expression. Differentiation 2001; 69(2–3):75–82.
<https://doi.org/10.1046/j.1432-0436.2001.690201.x>
11. HJ, Chan PP, Vasquez KM, Gupta RC, Glazer PM. Triplex-induced recombination in human cell-free extracts. Dependence on XPA and HsRad51. J Biol Chem 2001; 276(21):18018–23.
<https://doi.org/10.1074/jbc.M011646200>
12. VV, Potaman VN, Frank_Kamenetskii MD et al. Stability of peptide nucleic acids in human serum and cellular extracts. Biochem Pharmacol 1994; 48(6):1310–3.
<https://doi.org/10.1016/0006-2952(94)90171-6>
13. PB, Burli RW. Sequence-specific DNA recognition by polyamides. Curr Opin Chem Biol 1999; 3(6):688–93.
<https://doi.org/10.1016/S1367-5931(99)00027-7>
14. RH, Rao TS, Bodepudi V, Seth DM, Jayaraman K, Revankar GR. Azole substituted oligonucleotides promote antiparallel triplex formation at non-homopurine duplex targets. Nucleic Acids Res 1995; 23(4):647–53.
<https://doi.org/10.1093/nar/23.4.647>
<PubMed>
15. G, Takasugi M, Helene C, Sage E. Triple helix-directed psoralen crosslinks are recognized by Uvr(A)BC excinuclease. J Mol Biol 1998; 278(4): 815–25.
<https://doi.org/10.1006/jmbi.1998.1728>
16. G, Thuong NT, Helene C. Specific inhibition of transcription by triple helix-forming oligonucleotides. Proc Natl Acad Sci U S A 1992; 89(2): 504–8.
<https://doi.org/10.1073/pnas.89.2.504>
<PubMed>
17. SW, Gee JE, Rodu B, Mayfield CA, Sanders G, Miller DM. Triplex formation inhibits HER-2/neu transcription in vitro. J Clin Invest 1993; 92(5): 2433–9.
<https://doi.org/10.1172/JCI116850>
<PubMed>
18. M, Buchardt O, Christensen L et al. PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 1993; 365(6446):566–8.
<https://doi.org/10.1038/365566a0>
19. C, Giovannangeli C, Sun JS et al. Stable triple helices formed by oligonucleotide N3’—>P5’ phosphoramidates inhibit transcription elongation. Proc Natl Acad Sci U S A 1996; 93(9):4365–9.
<https://doi.org/10.1073/pnas.93.9.4365>
<PubMed>
20. 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(3):990–1000.
<https://doi.org/10.1128/MCB.20.3.990-1000.2000>
21. AF, Seidman MM, Segal DJ, Carroll D, Glazer PM. Recombination induced by triple-helix-targeted DNA damage in mammalian cells. Mol Cell Biol 1996; 16(12):6820–8.
<https://doi.org/10.1128/MCB.16.12.6820>
22. G. DDR aRA. Formation of a three-stranded poly-nucleotide molecule. J Am Chem Soc 1957: 79:2023–4.
<https://doi.org/10.1021/ja01565a074>
23. JC, Saison_Behmoaras T, Helene C. Sequence-specific recognition of the major groove of DNA by oligodeoxynucleotides via triple helix formation. Footprinting studies. Nucleic Acids Res 1988; 16(24):11431–40.
<https://doi.org/10.1093/nar/16.24.11431>
<PubMed>
24. R. Peptide-nucleic acids (PNAs): a tool for the development of gene expression modifiers. Curr Pharm Des 2001; 7(17):1839–62.
<https://doi.org/10.2174/1381612013397087>
25. JE, Blume S, Snyder RC, Ray R, Miller DM. Triplex formation prevents Sp1 binding to the dihydrofolate reductase promoter. J Biol Chem 1992; 267(16): 11163–7.
26. PA, Glazer PM. Targeted mutagenesis of simian virus 40 DNA mediated by a triple helix-forming oligonucleotide. J Virol 1993; 67(12):7324–31.
27. PA, Gunther EJ, Gasparro FP, Glazer PM. Targeted mutagenesis of DNA using triple helix-forming oligonucleotides linked to psoralen. Proc Natl Acad Sci U S A 1993; 90(16):7879–83.
<https://doi.org/10.1073/pnas.90.16.7879>
<PubMed>
28. C. The anti-gene strategy: control of gene expression by triplex-formingoligonucleotides. Anticancer Drug Des 1991; 6(6):569–84.
29. . The structure of crystals containing a hydrogen-bonded complex of 1- methylthymine and 9-methyladenine. Acta Crystallograf 1959; 12:822.
<https://doi.org/10.1107/S0365110X59002389>
30. CY, Bi G, Miller PS. Triplex formation by oligonucleotides containing novel deoxycytidine derivatives. Nucleic Acids Res 1996; 24(13):2606–13.
<https://doi.org/10.1093/nar/24.13.2606>
<PubMed>
31. 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(17):11541–8.
<https://doi.org/10.1074/jbc.274.17.11541>
32. J, Parks ME, Dervan PB. Cyclic polyamides for recognition in the minor groove of DNA. Proc Natl Acad Sci U S A 1995; 92(22):10389–92.
<https://doi.org/10.1073/pnas.92.22.10389>
<PubMed>
33. H, Demidov VV, Nielsen PE, Frank_Kamenetskii MD. An experimental study of mechanism and specificity of peptide nucleic acid (PNA) binding to duplex DNA. J Mol Biol 1999; 286(5):1337–45.
<https://doi.org/10.1006/jmbi.1998.2578>
34. 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 U S A 2000; 97(16):9003–8.
<https://doi.org/10.1073/pnas.160004997>
<PubMed>
35. A, Puri N, Cuenoud B et al. Cell cycle modulation of gene targeting by a triple helix-forming oligonucleotide. J Biol Chem 2003; 278(13):11072–7.
<https://doi.org/10.1074/jbc.M211837200>
36. C, Ebbinghaus S, Gee J et al. Triplex formation by the human Ha-ras promoter inhibits Sp1 binding and in vitro transcription. J Biol Chem 1994; 269(27):18232–8.
37. JL, Sun JS, Rougee M et al. Sequence specificity in triple-helix formation: experimental and theoretical studies of the effect of mismatches on triplex stability. Biochemistry 1991; 30(40):9791–8.
<https://doi.org/10.1021/bi00104a031>
38. PS, Bi G, Kipp SA, Fok V, DeLong RK. Triplex formation by a psoralenconjugated oligodeoxyribonucleotide containing the base analog 8-oxo-adenine. Nucleic Acids Res 1996; 24(4):730–6.
<https://doi.org/10.1093/nar/24.4.730>
<PubMed>
39. M, Arimondo PB, Lacroix L, Garestier T, Klump H, Mergny JL. Chemical modification of the third strand: differential effects on purine and pyrimidine triple helix formation. Biochemistry 2002; 41(1):357–66.
<https://doi.org/10.1021/bi011122m>
40. PE. Peptide nucleic acids as therapeutic agents. Curr Opin Struct Biol 1999; 9(3):353–7.
<https://doi.org/10.1016/S0959-440X(99)80047-5>
41. PE. Targeting double stranded DNA with peptide nucleic acid (PNA). Curr Med Chem 2001; 8(5):545–50.
<https://doi.org/10.2174/0929867003373373>
42. IG, Neumann RD. Sequence-specific DNA double-strand breaks induced by triplex forming 125I labeled oligonucleotides. Nucleic Acids Res 1994; 22(23):4979–82.
<https://doi.org/10.1093/nar/22.23.4979>
<PubMed>
43. J, Salmon JM, Vigo J, Viallet P. Mag-indo1 affinity for Ca(2+), compartmentalization and binding to proteins: the challenge of measuring Mg(2+) concentrations in living cells. Anal Biochem 2001; 290(2):221–31.
<https://doi.org/10.1006/abio.2000.4983>
44. G. Thermodynamics of oligonucleotide triple helices. Nucleic Acids Sciences 1997; 44:241–256.
45. EH. Modulation of c-myc transcription by triple helix formation. Ann N Y Acad Sci 1992; 660:57–63.
<https://doi.org/10.1111/j.1749-6632.1992.tb21057.x>
46. 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 U S A 1991; 88(18):8227–31.
<https://doi.org/10.1073/pnas.88.18.8227>
<PubMed>
47. V, Cogoi S, Spessotto P et al. Antigene effect in K562 cells of a PEGconjugated triplex-forming oligonucleotide targeted to the bcr/abl oncogene. Biochemistry 2002; 41(2):502–10.
<https://doi.org/10.1021/bi011314h>
48. RW, Crothers DM. Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition. Science 1992; 258(5087):1463–6.
<https://doi.org/10.1126/science.1279808>
49. SF, Dervan PB. Influence of pH on the equilibrium association constants for oligodeoxyribonucleotide-directed triple helix formation at single DNA sites. Biochemistry 1992; 31(45):10995–1003.
<https://doi.org/10.1021/bi00160a008>
50. SV, Simmons CG, Norton JC, Wise TW, Corey DR. Enhancement of strand invasion by oligonucleotides through manipulation of backbone charge. Nat Biotechnol 1996; 14(13):1700–4.
<https://doi.org/10.1038/nbt1296-1700>
51. N, Wu P, Hara H, Kawamoto Y. pH and cation effects on the properties of parallel pyrimidine motif DNA triplexes. Biochemistry 2001; 40(31): 9396–405.
<https://doi.org/10.1021/bi010666l>
52. RM, Thomas T, Wada M, Sigal LH, Shirahata A, Thomas TJ. Facilitation of the cellular uptake of a triplex-forming oligonucleotide by novel polyamine analogues: structure-activity relationships. Biochemistry 1999; 38(40): 13328–37.
<https://doi.org/10.1021/bi991004n>
53. H. Thermodynamic and kinetic effects of N3’—>P5’ phosphoramidate modification on pyrimidine motif triplex DNA formation. Biochemistry 2001; 40(4):1063–9.
<https://doi.org/10.1021/bi001895v>
54. H, Hari Y, Sekiguchi M, Obika S, Imanishi T. 2’-O,4’-C-methylene bridged nucleic acid modification promotes pyrimidine motif triplex DNA formation at physiological pH: thermodynamic and kinetic studies. J Biol Chem 2001; 276(4):2354–60.
<https://doi.org/10.1074/jbc.M007783200>
55. KM, Dagle JM, Weeks DL, Glazer PM. Chromosome targeting at short polypurine sites by cationic triplex-forming oligonucleotides. J Biol Chem 2001; 276(42):38536–41.
<https://doi.org/10.1074/jbc.M101797200>
56. KM, Narayanan L, Glazer PM. Specific mutations induced by triplexforming oligonucleotides in mice. Science 2000; 290(5491):530–3.
<https://doi.org/10.1126/science.290.5491.530>
57. KM, Wang G, Havre PA, Glazer PM. Chromosomal mutations induced by triplex-forming oligonucleotides in mammalian cells. Nucleic Acids Res 1999; 27(4):1176–81.
<https://doi.org/10.1093/nar/27.4.1176>
<PubMed>
58. KM, Wensel TG, Hogan ME, Wilson JH. High-efficiency triple-helix-mediated photo-cross-linking at a targeted site within a selectable mammalian gene. Biochemistry 1996; 35(33):10712–9.
<https://doi.org/10.1021/bi960881f>
59. KM, Wilson JH. Triplex-directed modification of genes and gene activity. Trends Biochem Sci 1998; 23(1):4–9.
<https://doi.org/10.1016/S0968-0004(97)01158-4>
60. J, Klump HH. Electrostatic effects in DNA triple helices. Biochemistry 1994; 33(45):13502–8.
<https://doi.org/10.1021/bi00249a039>
61. E, Malek S, Feigon J. Structure of a G.T.A triplet in an intramolecular DNA triplex. Biochemistry 1992; 31(20):4838–46.
<https://doi.org/10.1021/bi00135a015>
62. G, Seidman MM, Glazer PM. Mutagenesis in mammalian cells induced by triple helix formation and transcription-coupled repair. Science 1996; 271(5250): 802–5.
<https://doi.org/10.1126/science.271.5250.802>
63. DE, Dervan PB. Targeting the minor groove of DNA. Curr Opin Struct Biol 1997; 7(3):355–61.
<https://doi.org/10.1016/S0959-440X(97)80051-6>
64. 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(6666):468–71.
<https://doi.org/10.1038/35106>
65. LE, Manzini G, Quadrifoglio F. Formation of stable DNA triple helices within the human bcr promoter at a critical oligopurine target interrupted in the middle by two adjacent pyrimidines. Antisense Nucleic Acid Drug Dev 1998; 8(6):477–88.
<https://doi.org/10.1089/oli.1.1998.8.477>
66. LE, Manzini G, Quadrifoglio F, van der Marel GA, van Boom JH. Effect of 5-methylcytosine on the stability of triple-stranded DNA—a thermodynamic study. Nucleic Acids Res 1991; 19(20):5625–31.
<https://doi.org/10.1093/nar/19.20.5625>
<PubMed>


