Design, Synthesis, And Dna Binding Characteristics Of A Group Of Orthogonally Positioned Diamino, N-formamido, Pyrrole- And Imidazole-containing Polyamides

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Orthogonally positioned diamino/dicationic polyamides (PAs) have good water solubility and enhanced binding affinity, whilst retaining DNA minor groove and sequence specificity compared to their monoamino/monocationic counterparts. The synthesis and DNA binding properties of the following diamino PAs: f-I (P) under barI (3a), f-I (P) under barP (4), f-(P) under bar IP (5), and f-P (P) under barP (6) are described. (P) under bar denotes the site where a 1-propylamino group is attached to the NI-position of the heterocycle. Binding of the diamino PAs to DNA was assessed by DNase I footprinting, thermal denaturation, circular dichroism titration, biosensor surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC) studies. According to SPR studies, f-I (P) under barI (3a) bound more strongly (K-eq = 2.4 x 10(8) M-1) and with comparable sequence selectivity to its cognate sequence 5'-ACGCGT-3' when compared to its monoamino analog f-IPI (1). The binding of f-I (P) under barI (3a) to 5'-ACGCGT-3' via the stacked dimer motif was balanced between enthalpy and entropy, and that was quite different from the enthalpy-driven binding of its monoamino parent f-IPI (1). f-I (P) under barP (4) also bound more strongly to its cognate sequence 5'-ATGCAT-3' (K-eq = 7.4 x 10(6) M-1) via the side-by-side stacked motif than its monoamino analog f-IPP (2a). Although f-P (P) under barP (6) bound via a 1:1 motif, it bound strongly to its cognate sequence 5'-AAATTT-3' (K-eq = 4.8 x 10(7) M-1), 15-times higher than the binding of its monoamino analog f-PPP (2c), albeit f-PPP bound via the stacked motif. Finally, f-(P) under bar IP (5) bound to its target sequence 5'-ATCGAT-3' as a stacked dimer and it has the lowest affinity among the diamino PAs tested (K-eq10(5) M-1). This was about two times lower in affinity than the binding of its monoamino analog f-PIP (2b). The results further demonstrated that the 'core rules' of DNA recognition by monoamino PAs also apply to their diamino analogs. Specifically, PAs that contain a stacked IP core structure bind most strongly (highest binding constants) to their cognate GC doublet, followed by the binding of PAs with a stacked PP structure to two degenerate AT base pairs, and finally the binding of PAs with a PI core to their cognate CG doublet. (C) 2013 Elsevier Ltd. All rights reserved.