Triple Helix Stability Applications

Triple Helix Stability Applications

I. in vitro/In vivo Applications as Gene Modulators

A. Transcription Modulation

TFOs can be used as effective transcription modulators. The binding of a TFO in the major groove of DNA can alter gene expression in several ways: interfering with transcription factor binding (5), interfering with initiation complex formation (6), or arresting transcription elongation (7). In the latter case, the TFO used can be either unmodified or conjugated to psoralen or other DNA-damaging agents. Gene expression can be both downregulated or upregulated (8).

B. Replication Inhibition

Binding of TFOs upstream or downstream of the replication initiation site can induce inhibition of DNA polymerase elongation (9). Triple helices also bind to purine-rich triple-helix DNA binding proteins that are involved in replication. For example, in S. cerevisiae, the CDP1 gene codes for a triple-helix DNA binding protein that is involved in chromosome condensation/de-condensation. Condensation is facilitated by triple-helix binding, and de-condensation by triple-helix release (10).

C. Site-Specific Mutagenesis

TFOs coupled to DNA-damaged agents can be used to induce site-specific DNA damage for site-specific mutagenesis and recombination applications. Diverse damaging agents can be coupled to the TFO, as needs require. Examples include psoralen, Fe-EDTA, orthophenantroline, metalloporphyrins.

References

(1) Duca, M., Vekhoff, P., Oussedik, K., Halby, L., Arimondo, P.B. The triple helix: 50 years later, the outcome. Nucleic Acids Res. (2008), 36: 5123-5138. (2) Vasquez, K.M., Narayanan, L., Glazer, P.M. Specific mutations induced by triplex forming oligonucleotides in mice. Science (2000), 290: 530-533. (3) Maxwell, A., Burton, N.P., O'Hagen, N. High-throughput assays for DNA gyrase and other topoisomerases. Nucleic Acids Res. (2006), 34: e104. (4) Levy, O., Ptacin, J.L., Pease, P.J., Gore, J., Eisen, M.B., Bustamante, C., Cozzarelli, N.R. Identification of oligonucleotide sequences that direct the movement of the Escherischia coli FtsK translocase. Proc. Natl. Acad. Sci. USA (2005), 102: 17618-17623. (5) Svinarchuk, F., Nagibneva, I., Cherny D., Ait-Si-Ali, S., Pritchard, L.L, Robin, P., Malvy, C., Harel-Bellan, A., Chern, D. Recruitment of transcription factors to the target site by triplex-forming oligonucleotides. Nucleic Acids Res. (1997), 25: 3459-3464. (6)Karympalis, V., Kalopita, K., Zarros, A., Carageorgiou, H. Regulation of gene expression via triple helical formations. Biochemistry (2004), 69: 855-860. (7) Giovannangeli, C, Helene, C. Triplex-forming molecules for modulation of DNA information processing. Curr. Opin. Mol. Theor. (2000), 2: 288-296. (8) Song, J., Intody, Z., Li, M., Wilson, J.H. Activation of gene expression by triplex-directed psoralen crosslinks. Gene (2004), 324: 183-190.