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Issue No.06 - Nov.-Dec. (2012 vol.9)
pp: 1826-1830
G. Papadakis , Dept. of Biol., Univ. of Crete, Heraklion, Greece
E. Gizeli , Dept. of Biol., Univ. of Crete, Heraklion, Greece
Triplex forming oligonucleotides (TFOs) represent a class of drug candidates for antigene therapy. Based on strict criteria, we investigated the potential of 25 known oncogenes to be regulated by TFOs in the mRNA synthesis level and we report specific target sequences found in seven of these genes.
DNA, Bioinformatics, Genomics, Encoding, Stability analysis, Cancer,triplex forming oligos, Antigene therapy, oncogenes, transcription inhibition
G. Papadakis, E. Gizeli, "In Silico Search of DNA Drugs Targeting Oncogenes", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.9, no. 6, pp. 1826-1830, Nov.-Dec. 2012, doi:10.1109/TCBB.2012.127
[1] M. Faria and C. Giovannangeli, “Triplex-Forming Molecules: From Concepts to Applications,” J. Gene Medicine, vol. 3, pp. 299-310, 2001.
[2] M. Cooney, G. Czernuszewicz, E.H. Postel, S.J. Flint, and M.E. Hogan, “Site-Specific Oligonucleotide Binding Represses Transcription of the Human C-myc Gene in Vitro,” Science, vol. 241, pp. 456-459, 1988.
[3] C. Hélène, “The Anti-Gene Strategy: Control of Gene Expression by Triplex Forming Oligonucleotides,” Anti-Cancer Drug Design, vol. 6, pp. 569-584, 1991.
[4] H.E. Moser and P.B. Dervan, “Sequence-Specific Cleavage of Double Helical DNA by Triple Helix Formation,” Science, vol. 238, pp. 645-650, 1987.
[5] G. Felsenfeld, D.R. Davies, and A. Rich, “Formation of a Three-Stranded Polynucleotide Molecule,” J. Am. Chemical Soc., vol. 79, pp. 2023-2024, 1957.
[6] K. Fox, “Targeting DNA with Triplexes,” Current Medicinal Chemistry, vol. 7, pp. 17-37, 2000.
[7] J.S. Sun, T. De Bizemont, G. Duval-Valentin, T. Montenay-Garestier, and C. Hélène, “Extension of the Range of Recognition Sequences for Triple Helix Formation by Oligonucleotides Containing Guanines and Thymines,” C.R. Academy Sciences, vol. 313, pp. 585-590, 1991.
[8] M. Duca, P. Vekhoff, K. Oussedik, L. Halby, and P.B. Arimondo, “The Triple Helix: 50 Years Later, the Outcome,” Nucleic Acids Research, vol. 36, pp. 5123-5138, 2008.
[9] D. Bednarski and S.M. Firestine, “Regulation of Transcription by Synthetic DNA-Bending Agents,” ChemBioChem, vol. 7, pp. 1715-1721, 2006.
[10] D.A. Liberles and P.B. Dervan, “Design of Artificial Sequence-Specific DNA Bending Ligands,” Proc. Nat'l Academy of Sciences USA, vol. 93, pp. 9510-9514, 1996.
[11] G. Papadakis, A. Tsortos, and E. Gizeli, “Triple-Helix DNA Structural Studies Using a Love Wave Acoustic Biosensor,” Biosensors Bioelectronics, vol. 25, pp. 702-707, 2009.
[12] E.H. Postel, S.J. Flint, D.J. Kessler, and M.E. Hogan, “Evidence that a Triplex-Forming Oligodeoxyribonucleotide Binds to the C-Myc Promoter in HeLa Cells, Thereby Reducing C-Myc mRNA Levels,” Proc. Nat'l Academy Sciences USA, vol. 88, pp. 8227-8231, 1991.
[13] M. Faria, C.D. Wood, L. Perrouault, J.S. Nelson, A. Winter, M.R.H. White, C. Hélène, and C. Giovannangeli, “Targeted Inhibition of Transcription Elongation in Cells Mediated by Triplex-Forming Oligonucleotides,” Proc. Nat'l Academy of Sciences USA, vol. 97, pp. 3862-3867, 2000.
[14] L.A. Christensen, R.A. Finch, A.J. Booker, and K.M. Vasquez, “Targeting Oncogenes to Improve Breast Cancer Chemotherapy,” Cancer Research, vol. 66, pp. 4089-4094, 2006.
[15] J.R. Goñi, X. de la Cruz, and M. Orozco, “Triplex-Forming Oligonucleotide Target Sequences in the Human Genome,” Nucleic Acids Research, vol. 32, pp. 354-360, 2004.
[16] J.R. Goñi, J.M. Vaquerizas, J. Dopazo, and M. Orozco, “Exploring the Reasons for the Large Density of Triplex-Forming Oligonucleotide Target Sequences in the Human Regulatory Regions,” BMC Genomics, vol. 7, pp. 63-72, 2006.
[17] Q. Wu, S.S. Gaddis, M.C. MacLeod, E.F. Walborg, H.D. Thames, J. DiGiovanni, and K.M. Vasquez, “High-Affinity Triplex-Forming Oligonucleotide Target Sequences in Mammalian Genomes,” Molecular Carcinogen, vol. 46, pp. 15-23, 2007.
[18] S.S. Gaddis, Q. Wu, H.D. Thames, J. DiGiovanni, E.F. Walborg, M.C. MacLeod, and K.M. Vasquez, “A Web-Based Search Engine for Triplex-Forming Oligonucleotide Target Sequences,” Oligonucleotides, vol. 16, pp. 196-201, 2006.
[19] S.W. Ebbinghaus, H. Fortinberry, and H.B. GamperJr., “Inhibition of Transcription Elongation in the HER-2/neu Coding Sequence by Triplex-Directed Covalent Modification of the Template Strand,” Biochemistry, vol. 38, pp. 619-628, 1999.
[20] J.M. Kalish, M.M. Seidman, D.L. Weeks, and P.M. Glazer, “Triplex-Induced Recombination and Repair in the Pyrimidine Motif,” Nucleic Acids Research, vol. 33, pp. 3492-3502, 2005.
[21] E.M. McGuffie and C.V. Catapano, “Design of a Novel Triple Helix-Forming Oligodeoxyribonucleotide Directed to the Major Promoter of the C-Myc Gene,” Nucleic Acids Research, vol. 30, pp. 2701-2709, 2002.
[22] S. Reither and A. Jeltsch, “Specificity of DNA Triple Helix Formation Analyzed by a FRET Assay,” BMC Biochemistry, vol. 3, pp. 27-36, 2002.
[23] Z. Wang and T.M. Rana, “DNA Damage-Dependent Transcriptional Arrest and Termination of RNA Polymerase II Elongation Complexes in DNA Template Containing HIV-1 Promoter,” Proc. Nat'l Academy Sciences USA, vol. 94, pp. 6688-6693, 1997.
[24] R.W. Roberts and D.M. Crothers, “Specificity and Stringency in DNA Triplex Formation,” Proc. Nat'l Academy Sciences USA, vol. 88, pp. 9397-9401, 1991.
[25] L.J. MaherIII, “Inhibition of T7 RNA Polymerase Initiation by Triple-Helical DNA Complexes: A Model for Artificial Gene Repression,” Biochemistry, vol. 31, pp. 7587-7594, 1992.
[26] R. Besch, C. Giovannangeli, and K. Degitz, “Trplex-Forming Oligonucleotides - Sequence-Specific DNA Ligands as Tools for Gene Inhibition and for Modulation of DNA-Associated Functions,” Current Drug Targets, vol. 5, pp. 691-703, 2004.
[27] Z. Intody, B.D. Perkins, J.H. Wilson, and T.G. Wensel, “Blocking Transcription of the Human Rhodopsin Gene by Triplex-Mediated DNA Photocrosslinking,” Nucleic Acids Research, vol. 28, pp. 4283-4290, 2000.
[28] D.L. Weeks and C. Bailey, “Understanding Oligonucleotide-Mediated Inhibition of Gene Expression in Xenopus Laevis Oocytes,” Nucleic Acids Research, vol. 28, pp. 1154-1161, 2000.
[29] E.E. Merkina and K.R. Fox, “Kinetic Stability of Intermolecular DNA Quadruplexes,” Biophysics J., vol. 89, pp. 365-373, 2005.
[30] F. Sha, R. Mu, D. Henderson, and F.-M. Chen, “Self-Aggregation of DNA Oligomers with XGG Trinucleotide Repeats: Kinetic and Atomic Force Microscopy Measurements,” Biophysics J., vol. 77, pp. 410-423, 1999.
[31] R. Floris, B. Scaggiante, G. Manzini, F. Quadrifoglio, and L.E. Xodo, “Effect of Cations on Purine.Purine.Pyrimidine Triple Helix Formation in Mixed-Valence Salt Solutions,” European J. Biochemistry, vol. 260, pp. 801-809, 1999.
[32] W.M. Olivas and L.J. MaherIII, “Competitive Tripled/Quadruplex Equilibria Involving Guanine-Rich Oligonucleotides,” Biochemistry, vol. 34, pp. 278-284, 1995.
[33] J.R. Williamson, “Guanine Quartets,” Current Opinion Structural Biology, vol. 3, pp. 357-362, 1993.
[34] A.-J. Cheng, J.C. Wang, and M.W. Van Dyke, “Self-Association of G-Rich Oligodeoxyribonucleotides under Conditions Promoting Purine-Motif Triplex Formation,” Antisense Nucleic Acid, vol. 8, pp. 215-225, 1998.
[35] J.-L. Mergny, A. De Cian, A. Ghelab, B. Sacca, and L. Lacroix, “Kinetics of Tetramolecular Quadruplexes,” Nucleic Acids Research, vol. 33, pp. 81-94, 2005.
[36] J. Liu, R-H. Xu, Y-X. Jin, and D-B. Wang, “Triplex Targeting of Human PDGF-B (C-Sis, Proto-Oncogene) Promoter Specifically Inhibits Factors Binding and PDGF-B Transcription,” Nucleic Acids Research, vol. 29, pp. 783-791, 2001.
[37] S. Koilan, D. Hamilton, N. Baburyan, M.K. Padala, K.T. Weber, and R.V. Guntaka, “Prevention of Liver Fibrosis by Triple Helix-Forming Oligodeoxyribonucleotides Targeted to the Promoter Region of Type I Collagen Gene,” Oligonucleotides, vol. 20, pp. 231-237, 2010.
[38] P. Vekhoff, A. Ceccaldi, D. Polverari, J. Pylouster, C. Pisano, and P.B. Arimondo, “Triplex Formation on DNA Targets: How to Choose the Oligonucleotide,” Biochemistry, vol. 47, p. 12277, 2008.
[39] M.M. Seidman and P.M. Glazer, “The Potential for Gene Repair via Triple Helix Formation,” J. Clinical Investigation, vol. 112, pp. 487-494, 2003.
[40] J.S. Lee, M.L. Woodsworth, L.J. Latimer, and A.R. Morgan, “Poly(Pyrimidine). Poly(Purine) Synthetic DNAs Containing 5-Methylcytosine form Stable Triplexes at Neutral pH,” Nucleic Acids Research, vol. 12, pp. 6603-6614, 1984.
[41] N. Sugimoto, P. Wu, H. Hara, and Y. Kawamoto, “pH and Cation Effects on the Properties of Parallel Pyrimidine Motif DNA Triplexes,” Biochemistry, vol. 40, pp. 9396-9405, 2001.
[42] J. Volker and H.H. Klump, “Electrostatic Effects in DNA Triple Helices,” Biochemistry, vol. 33, pp. 13502-13508, 1994.
[43] D. Praseuth, A.L. Guieysse, and C. Hélène, “Triple Helix Formation and the Antigene Strategy for Sequence-Specific Control of Gene Expression,” Biochimica Biophysica Acta, vol. 1489, pp. 181-206, 1999.
[44] N. Puri, A. Majumdar, B. Cuenoud, F. Natt, P. Martin, A. Boyd, P.S. Miller, and M.M. Seidman, “Targeted Gene Knockout by 2'-O-Aminoethyl Modified Triplex Forming Oligonucleotides,” J. Biological Chemistry, vol. 276, pp. 28991-28998, 2001.
[45] K.A. Shahid, A. Majumdar, R. Alam, S.-T. Liu, J.Y. Kuan, X. Sui, B. Cuenoud, P.M. Glazer, P.S. Miller, and M.M. Seidman, “Targeted Cross-Linking of the Human $\beta$ -Globin Gene in Living Cells Mediated by a Triple Helix Forming Oligonucleotide,” Biochemistry, vol. 45, pp. 1970-1978, 2006.
[46] M.M. Seidman, N. Puri, A. Majumdar, B. Cuenoud, P.S. Miller, R. Alam, “The Development of Bioactive Triple Helix-Forming Oligonucleotides,” Annals NewYork Academy of Sciences, vol. 1058, pp. 119-127, 2005.
[47] R. Alam, A. Majumdar, A.K. Thazhathveetil, S.-T. Liu, J.-L. Liu, N. Puri, B. Cuenoud, S. Sasaki, P.S. Miller, and M.M. Seidman, “Extensive Sugar Modification Improves Triple Helix Forming Oligonucleotide Activity in Vitro but Reduces Activity in Vivo,” Biochemistry, vol. 46, pp. 10222-10233, 2007.
[48] G. Cooper, Oncogenes, second ed. Jones and Bartlett Publishers, 1995.
[49] B. Vogelstein and K.W. Kinzler, The Genetic Basis of Human Cancer, second ed. McGraw-Hill, 1998.
[50] K.M. Vasquez and P.M. Glazer, “Triplex-Forming Oligonucleotides: Principles and Applications,” Q. Rev. Biophysics, vol. 35, pp. 89-107, 2002.
[51] G.M. Carbone, E.M. McGuffie, A. Collier, and C.V. Catapano, “Selective Inhibition of Transcription of the Ets2 Gene in Prostate Cancer Cells by a Triplex-Forming Oligonucleotide,” Nucleic Acids Research, vol. 31, pp. 833-843, 2003.
[52] F.A. Rogers, M. Manoharan, P. Rabinovitch, D.C. Ward, and P.M. Glazer, “Peptide Conjugates for Chromosomal gene Targeting by Triplex-Forming Oligonucleotides,” Nucleic Acids Research, vol. 32, pp. 6595-6604, 2004.
[53] P.A. Futreal, L. Coin, M. Marshall, T. Down, T. Hubbard, R. Wooster, N. Rahman, and M.R. Stratton, “A Census of Human Cancer Genes,” Nature Rev. Cancer, vol. 4, pp. 177-183, 2004.
[54] K.M. Vasquez, L. Narayanan, and P.M. Glazer, “Specific Mutations Induced by Triplex-Forming Oligonucleotides in Mice,” Science, vol. 290, pp. 530-533, 2000.
[55] K.M. Vasquez and J.H. Wilson, “Triplex Directed Modification of Genes and Gene Activity,” Trends Biochemical Sciences, vol. 23, pp. 4-9, 1998.
[56] P. Simon, F. Cannata, J-P. Concordet, and C. Giovannangeli, “Targeting DNA with Triplex-Forming Oligonucleotides to Modify Gene Sequence,” Biochimie, vol. 90, pp. 1109-1116, 2008.
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