The long-term goal of our project on DNA hybrids is to find highly specific therapeutic agents that bind DNA or RNA targets. Our approach is to search structure space with covalent hybrids of oligodeoxyribonucleotides and non-nucleic acid ligands. The oligonucleotide portion in these hybrids provides the target affinity required for our spectrometrically monitored selection experiments. It brings non-nucleic acid ligands into a specific nucleic acid context where it is easily optimized based on affinity. NMR experiments provide the structural information required to move in structure space in a directed way, a feature indispensable for selections with small combinatorial libraries (2-35 compounds). Last year, we performed experiments with three complexes. A typical session included NOESY, TOCSY, DQF-COSY, and ID temperature series with conventional and gradient-based experiments. The aminoacyl-hybrid W-TGCGCAC was studied at 500 MHz at the very beginning of January, as reported in last year's report. We are planning to perform one more series of experiments to further refine this structure. The second complex is that of the steroid-DNA hybrid (chl-TGCGCA)2- We have acquired spectra at 500 MHz, 750 MHz, and 600 MHz and assigned most of the resonances. A qualitative structure has emerged, which not only explains why our steroid-hybrids show dramatically increased affinity (18 kcal/mol AAH), selectivity (RNA/DNA and mismatch selectivity increase >6 'C ATm) and hyperchromicity (25-100% depending on sequence), but also suggests a structural picture for complexes between steroidal diamines and AT-rich DNA. Such diamines are antibiotics whose DNA-binding properties have puzzled research ers for decades. Finally, we have acquired a series of spectra of a hybrid between oxolinic acid and DNA at 600 MHz. This has led to a qualitative structure that, surprisingly, finds the quinolone in the major groove of the DNA and not stacked on the exposed terminal base pair. We expect these results to help the design of new topoisomerase inhibitors. The dramatic increase of affinity seen for our hybrids (+26 'C ATm for OA-TGCGCA) is a step towards closing the gap between oligonucleotideand small molecule-ligands. The quinolone terminus with a molecular weight of 261 Da provides as much affinity as four additional A:T base pairs.
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