Journal
NUCLEIC ACIDS RESEARCH
Volume 36, Issue 9, Pages 2889-2894Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkn116
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To investigate the binding of 5CpG3 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'CGCG3', were synthesized. The binding affinities of the 5'CGCG3' sequence to the PyIm 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) 10(6)M and 1.7 (+/- 0.4) 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'CpGpCpG3' were replaced with 5-methylcytosines (Cs-m), the K-d value of polyamide 2 increased to 5.8 (+/- 0.7) 10(9)(M), which indicated about 3-fold higher binding than the unmethylated 5'CGCG3' sequence. These results suggest that polyamide 2 would be suitable to target CpG-rich sequences in the genome.
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