title: Pyrrole-imidazole hairpin polyamides with high affinity at 5'-CGCG-3' DNA sequence; influence of cytosine methylation on binding.
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.
authors.affiliation: Department of Chemistry, Faculty of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.
authors.forename: Masafumi
authors.initials: M
authors.lastname: Minoshima
authors.forename: Toshikazu
authors.initials: T
authors.lastname: Bando
authors.forename: Shunta
authors.initials: S
authors.lastname: Sasaki
authors.forename: Jun
authors.initials: J
authors.lastname: Fujimoto
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Sugiyama
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D001665:Binding Sites; D018899:CpG Islands; D003596:Cytosine / Q000378:metabolism*; D004247:DNA / Q000737:chemistry; D019175:DNA Methylation; D007093:Imidazoles / Q000138:chemical synthesis / Q000737:chemistry*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011758:Pyrroles / Q000138:chemical synthesis / Q000737:chemistry*; D020349:Surface Plasmon Resonance
chemical_list: D007093:Imidazoles; D009838:Oligodeoxyribonucleotides; D011758:Pyrroles; D003596:Cytosine; D004247:DNA