Targeting the ICB2 Site of the Topoisomerase II Alpha Promoter with a Formamido-pyrrole-imidazole-pyrrole H-pin Polyamide

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The synthesis, DNA binding characteristics and biological activity of an N-formamido pyrrole-and imidazole-containing H-pin polyamide (f-PIP H-pin, 2) designed to selectively target the ICB2 site on the topoII alpha promoter, is reported herein. Thermal denaturation, circular dichroism, isothermal titration calorimetry, surface plasmon resonance and DNase I footprinting studies demonstrated that 2 maintained the selectivity of the unlinked parent monomer f-PIP (1) and with a slight enhancement in binding affinity (K-eq = 5 x 10(5) M-1) to the cognate site (5 '-TACGAT-3 '). H-pin 2 also exhibited comparable ability to inhibit NF-Y binding to 1, as demonstrated by gel shift studies. However, in stark contrast to monomer 1, the H-pin did not affect the up-regulation of topoisomerase II alpha (topoII alpha) in cells (Western blot), suggesting that the H-pin does not enter the nucleus. This study is the first to the authors' knowledge that reports such a markedly different cellular response between two compounds of almost identical binding characteristics.