| Polyamides composed of pyrrole (Py) and imidazole (Im) amino acids bind as antiparallel, side-by side dimers in the minor groove of DNA to sequences containing both (A,T) and (G,C) base pairs. Initial polyamides based on the 2:1 model have demonstrated new, predictable specificities but only modest affinities. Chapter 2 describes the thermodynamic characterization of a series of covalently linked polyamides, revealing an increase in affinity (;Chapter 4 explores the generality of the 2:1 polyamide:DNA model by systematically varying the imidazole content and position within a series of eight three-ring polyamides. Of ten homodimeric and heterodimeric combinations of polyamides characterized, four bind as expected, indicating that the 2:1 model, while not completely general, is a valuable predictive tool. This work adds three new sequences to the targetable repertoire for polyamides, 5;Chapter 7 examines the simultaneous binding of an oligonucleotide in the major groove of DNA and a polyamide in the minor groove. Quantitative footprinting experiments indicate that the stability of a triple helix is not affected by simultaneous recognition in the minor groove, suggesting that oligonucleotide-polyamide conjugates could be designed for sequence-specific DNA recognition. Chapter 8 describes experiments designed to determine the DNA-binding orientation of a portion of a high mobility group protein. Although the synthetic peptides bind A,T-rich DNA, no specific cleavage was observed, precluding determination of binding orientation. |
