Inhibition of DNA Major Groove Binding Proteins by Hairpin Polyamides

Small molecules that bind to any predetermined DNA sequence in the human genome are potentially useful tools for molecular biology and human medicine. Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) are cell permeable small molecules that bind DNA according to a set of "pairing rules" with affinities and specificites similar to many naturally occurring DNA binding proteins. Im/Py polyamides offer a general approach to the chemical regulation of gene expression, provided inhibition of DNA binding for a variety of transcription factor families can be achieved. Polyamides bound in the minor groove have been shown to co-occupy the DNA helix with proteins in the major groove. We demonstrate here that polyamides containing a positively charged moiety directed to the DNA backbone can effectively inhibit DNA binding by an exclusively major groove protein, potentially by competing with the positively charged protein side chains for contacts to the negatively charged phosphate backbone. The requisite positive patch can be achieved with a naturally derived C-terminal Arg-Pro-Arg tripeptide (Chapter 2) or a simple synthetic diaminoalkyl chain delivered from the N-1 of a single pyrrole residue (Chapter 3). The functional repertoire of poly amides as synthetic ligands for the control of transcription factor binding has been expanded to include proteins which bind exclusively in the major groove of DNA. The broad targetable sequence repertoire of polyamides, coupled with the ubiquity of backbone contacts in protein recognition of DNA, make phosphate neutralization by a positive patch a promising approach for inhibition of major groove transcription factors. Other investigations into polyamide:DNA recognition have afforded N=aminoalkylpyrrole- containing polyamides that offer enhanced affinity without compromising specificity (Chapter 3), desmethylpyrrole-containing polyamides that increase water solubility while retaining subnanomolar affinity (Chapter 4 ), and structural insight into the lower affinities observed with Hp-containing polyamides (Chapter 5).