Recognition of Specific DNA Sequences by Stacked Pyrrole- and Imidazole- Containing Polyamides: An Efficient Screening Method Based on Competitive Dialysis

A competitive dialysis method has been developed to screen compounds for their DNA binding properties, and it is based on directly comparing the binding of polyamide molecules to a series of distinctively varied, short, synthetic deoxyribonucleotides. Relative binding ratios for each polyamideoligonucleotide pairing were calculated from the concentrations of free polyamide and total polyamide in order to quantitatively compare binding to different DNA sequences. This approach works well as a preliminary screen to determine the viability of novel small molecules, prior to investing significant resources in further characterization and development of possible sequence specific DNA targeted therapeutic agents. The trends in binding affinities of the four triamide molecules (f-ImPyIm, distamycin A, f-PyPyPy and f-ImImPy; where Im is imidazole and Py is pyrrole) correlated well with data obtained from surface plasmon resonance (SPR) studies. Results from circular dichroism studies confirmed the minor groove side-by-side stacked binding motif of the triamides, and thermal stability experiments corroborated the improved DNA stability of promising polyamide-DNA complexes. The affinity of distamycin A for its cognate DNA sequence (A3T3) was unambiguously selected over the other DNA sequences tested. Alternatively, as expected from SPR, circular dichroism and thermal melting experiments, f-ImImPy showed very poor affinity for DNA sequences tested, including its cognate DNA, TCGA. Thus, the very good (distamycin A) and very poor (f-ImImPy) DNA binders were effectively screened.