DNA complexes containing novel aromatic residues

Abstract

The investigation of DNA complexes containing novel aromatic residues was performed. In the first part of this work, a series of novel nucleosides possessing a C1’-carboxamide linkage between the aryl moiety and the sugar group were successfully introduced into a single strand DNA oligonucleotide. The results of the thermal denaturation studies indicate that the incorporation of the modified nucleosides into DNA complexes destabilizes the DNA duplexes. However, the “bulged” complexes are only slightly destabilized and they are the most stable complexes among all the DNA complexes containing novel aromatic residues. This suggests that the carboxamide motif may be a general method for the insertion of non-natural residues into DNA for applications such as spectroscopic probes. The second part of this study involves a seven step synthesis of novel aryl C-nucleosides. The aromatic residues are directly linked to the deoxyribose moieties through a carbon-carbon connection instead of the original carbon-nitrogen glycoside bond. Three novel C-nucleosides containing 4-substituted phenyl residues were successfully synthesized by following this synthesis scheme. The isomer problem involved in the multi-step synthesis of aryl C-nucleoside was resolved and as a result, the β-aryl C-2′-deoxynucleoside can be successfully separated from the α-aryl C-2′-deoxynucleoside. The synthesized aryl C-nucleoside can be introduced into a DNA oligonucleotide as a non-natural nucleobase. The third part of this research was focused on the determination of the structure of DNA oligonucleotide duplexes containing aryl C-nucleoside using 2D NMR techniques and computational methods. 2D NMR experiments including COSY and NOESY were performed, followed by resonance assignment and structure calculation to construct the preliminary 3D structure of DNA oligonucleotide duplex containing aryl C-nucleoside. Due to the limitation of the obtained restrains from NMR experiment, the study of molecular modeling has been performed to compensate the ambiguous of the preliminary structure. Conflicts between the calculated duplex structure and the data from the NMR experiment were observed, so an alternate possible structure of hairpin was proposed. The results of thermal denaturation study and molecular modeling may indicate that the hairpin structure is more preferred than the duplex structure for the non-natural DNA oligonucleotide containing aryl C-nucleoside.