Abstract
To investigate the binding of 5'-CpG-3' sequences by small molecules, two pyrrole (Py)-imidazole (Im) hairpin polyamides, PyImPyIm-gamma-PyImPyIm-beta-Dp (1) and PyIm-beta-Im-gamma-PyIm-beta-Im-beta-Dp (2), which recognize the sequence 5'-CGCG-3', were synthesized. The binding affinities of the 5'-CGCG-3' sequence to the Py-Im hairpin polyamides were measured by surface plasmon resonance (SPR) analysis. SPR data revealed that dissociation equilibrium constants (K(d)) of polyamides 1 and 2 were 1.1 (+/- 0.3) x 10(-6) M and 1.7 (+/- 0.4) x 10(-8) M, respectively. Polyamide 2 possesses great binding affinity for this sequence, 65-fold higher than polyamide 1. Moreover, when all cytosines in 5'-CpGpCpG-3' were replaced with 5-methylcytosines ((m)Cs), the K(d) value of polyamide 2 increased to 5.8 (+/- 0.7) x 10(-9) (M), which indicated about 3-fold higher binding than the unmethylated 5'-CGCG-3' sequence. These results suggest that polyamide 2 would be suitable to target CpG-rich sequences in the genome.