O'Hare, Celia Caroline; (2004) Sequence specific interactions, intracellular distribution and effects on transcription of novel DNA minor groove-binding polyamides. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

Targeting DNA with small molecules has been a useful therapeutic approach in the treatment of human cancers. Interest in selective disruption of replication and transcription by DNA-interactive ligands has intensified with the wealth of new genetic targets provided by the discovery of key genes associated with genetic diseases such as cancer. This has resulted in the development not only of novel conventional chemotherapy agents but also of molecules with potential to modulate the expression of disease related genes. Minor groove-binding polyamides offer a promising means of disrupting gene expression at predetermined sites. Investigations are presented into the sequence specificity, intracellular uptake and effects on transcription of a number of novel polyamides. A structure-binding activity relationship was determined for a polyamide series comprised of thiazole (T), imidazole (I) or pyrrole (P) heterocycles examining the effects of linker length, heterocycle permutation and N-terminal head group. Linkage with a cross-linked motif increased binding affinity for N-terminal amino or formyl polyamides, with six or seven carbons linkers producing the strongest binding. Optimal selectivity was achieved for the TIP series with either TIP-C7-formyl or TIP-C7-amino, with specificity of the leading thiazole modulated by the adjacent head group. Use of an N-terminal acetyl or hydrogen abrogated binding irrespective of linkage or heterocycle composition. Examination of the binding of formyl-III showed a hundred-fold preference for a single TG mismatch site, relative to a CG match site demonstrating the utility of an I:I pair for TG mismatch recognition. Evaluation of the uptake and distribution of TIP-C7-amino in cells suggested that it was not taken up via passive uptake mechanisms, although it was able to bind DNA when directly introduced into the nucleus. This was irrespective of the cell line examined, although a cell-type dependent anti-proliferative effect was observed at high concentrations. TIP-C7-amino failed to inhibit proliferation in S. cerevisiae and caused consistent changes in the transcription of only 0.5% of yeast genome, suggesting inefficient cell uptake. This was in contrast to distamycin, which produced a detectable effect on both the proliferation and transcription of these cells. These studies have implications for the design of linked polyamides as sequence selective agents targeting DNA in cells.

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