Inhibition of transcription factor binding to the HER2 promoter by triplex-forming oligodeoxyribonucleotides

We have identified a 28-bp homopurine/homopyrimidine sequence capable of triple helix (triplex) formation with G+T-rich oligodeoxyribonucleotides (oligos) within the critical proximal promoter of the HER2/neu/c-erbB2 (HER2) proto-oncogene. To investigate the possible therapeutic potential of triplex-forming oligos in HER2 overexpressing breast cancers, we have studied the ability of triplex formation to compete with and to inhibit the binding of a transcription factor to its consensus sequence at an adjacent site. Competition binding assays demonstrate that a triplex-forming oligo can inhibit transcription factor binding in a sequence-specific manner. Moreover, we find that the addition of both nucleotide and non-nucleotide 'tails' to triplex-forming oligos do not confer any enhancement of binding affinity, but provide additional inhibition of transcription factor binding, potentially by steric hindrance.