Pyrrole-imidazole hairpin polyamides with high affinity at 5CGCG3 DNA sequence; influence of cytosine methylation on binding
Pyrrole-imidazole hairpin polyamides with high affinity at 5CGCG3 DNA sequence; influence of cytosine methylation on binding
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DOI：
10.1093/nar/gkn116
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发表时间：
2008-05-01
影响因子：
14.9
通讯作者：
Sugiyama, Hiroshi
中科院分区：
文献类型：
--
作者：
Minoshima, Masafumi;Bando, Toshikazu;Sugiyama, Hiroshi
为了研究小分子与 5CpG3 序列的结合，合成了两种吡咯 (Py) 咪唑 (Im) 发夹聚酰胺：PyImPyIm-gamma-PyImPyIm-beta-Dp (1) 和 PyIm-beta-Im-gamma-PyIm-beta-Im-beta-Dp (2)，它们可识别序列 5'CGCG3'。通过表面等离子共振(SPR)分析测量5'CGCG3'序列与PyIm发夹聚酰胺的结合亲和力。 SPR数据显示聚酰胺1和2的解离平衡常数(K-d)分别为1.1(+/-0.3)10(6)M和1.7(+/-0.4)10(8)M。聚酰胺2对该序列具有很强的结合亲和力，比聚酰胺1高65倍。此外，当5'CpGpCpG3'中的所有胞嘧啶被5-甲基胞嘧啶（Cs-m）取代时，聚酰胺2的K-d值增加到5.8（+/- 0.7）10（9）（M），这表明结合力比未甲基化的5'CGCG3'高约3倍序列。这些结果表明聚酰胺 2 适合靶向基因组中富含 CpG 的序列。
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.