Transcription inhibition induced by modified triple helix-forming oligonucleotides: a quantitative assay for evaluation in cells11Edited by M. Yaniv

Drosophila melanogaster kl-3 and kl-5 Y-loops harbor triple-stranded nucleic acids

“…This association is also supported by a large number of studies on various systems indicating that triplex formation inside the promoter region usually downregulates gene expression (reviewed by Faria and Giovannangeli, 2001). However, it is unlikely that this is the function of the triplexes associated to the lampbrush-like loops of primary spermatocytes, because both the kl-5 and D. hydei Y-loops are transcriptionally active (Bonaccorsi et al, 1990;Hackstein and Hochstenbach, 1995).…”

“…Although triplexes are well characterized in vitro, their biological significance in living organisms is still under discussion (Zain and Sun, 2003). It has been demonstrated that, upon formation, these structures can frequently downregulate (Cooney et al, 1988; Birg et al, 1990; Faria et al, 2000;Faria et al, 2001) and sometimes upregulate (reviewed in Faria and Giovannangeli, 2001) gene expression, a fact which demonstrates their potential in gene control and suggests their use in gene therapy (Wang et al, 1995;Vasquez et al, 2000) (for a review, see Rogers et al, 2005). The structures are also able to impair DNA polymerization (Dayn et al, 1992), and can influence DNA recombination and repair (Faruqi et al, 1996;Wang et al, 1996;Faruqi et al, 2000;Vasquez et al, 2002;Kalish et al, 2005;Raghavan et al, 2005) (for reviews, see Seidman and Glazer, 2003; Chin et al, 2007).…”

Specific Inhibition of ICAM-1 Expression Mediated by Gene Targeting with Triplex-forming Oligonucleotides

“…An oligonucleotide was designed to form a triple helix at this site: TFOgt contains guanosine and thymidine nucleosides, allowing formation of T⅐AxT and C⅐GxG base triplets (with (⅐) standing for Watson-Crick interactions and (x) standing for reverse Hoogsteen interactions) after binding in an antiparallel orientation with respect to the purine strand of the double helical target sequence. We chose to use psoralen-conjugated oligonucleotides because: (i) they can be photo-induced to become irreversibly bound to their target DNA sequence and (ii) in the absence of photoactivation of the psoralen moiety, such conjugates have also been described to have increased antigene activity in cells as compared with the corresponding unconjugated oligonucleotides (17). For the demonstration of sequencespecific binding activity of the TFOgt oligonucleotide, two control oligodeoxynucleotides were designed, COgt1 and COgt2 (Fig.…”

“…Triplex-mediated inhibition of transcription may be achieved by interfering with transcription initiation (competition of TFOs with transcription factors at the promoter) or by interfering with transcription elongation (RNA synthesis arrest at triplex structures). The arrest of RNA synthesis in cells has been only recently described, and a limited number of studies are presently available for plasmid-harbored genes (17,18) or integrated foreign sequences (19). In addition to the inhibition of transcription, the possibility of forming specific and stable complexes at selected genomic sites might induce drastic cellular responses such as modifications of cell cycle checkpoints, especially in malignant cells (20).…”

Chemical Tools for Targeted Mutagenesis of DNA Based on Triple Helix Formation

“…13,14) The binding characteristics and sequence specificity of TFOs give these oligonucleotides vast potential in gene modification, such as inhibition of gene expression, inhibition of replication, and induction of site-specific mutagenesis. [15][16][17][18][19][20][21][22][23][24][25] However, there are a number of obstacles to TFO activity under physiologic conditions. [26][27][28][29] Recent developments in nucleoside and oligonucleotide analogue chemistry show great promise for solving the problems of TFO bioactivity and target options.…”